Starting phenix.real_space_refine on Sat Aug 10 16:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1b_38830/08_2024/8y1b_38830.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 18729 2.51 5 N 4734 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "B TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 845": "OE1" <-> "OE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C ARG 932": "NH1" <-> "NH2" Residue "C GLU 1112": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 17.72, per 1000 atoms: 0.60 Number of scatterers: 29541 At special positions: 0 Unit cell: (167.398, 154.354, 204.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.02 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 12.27 Conformation dependent library (CDL) restraints added in 5.7 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 66 sheets defined 24.2% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.589A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.170A pdb=" N ILE A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.970A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.082A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.588A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.617A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.585A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.968A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.651A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.909A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.846A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 3.769A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.585A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.602A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.506A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.503A pdb=" N ARG B 397 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.788A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.849A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.935A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 863 Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.209A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.753A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.503A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.677A pdb=" N ALA B 974 " --> pdb=" O TRP B 971 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 971 through 975' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.648A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.850A pdb=" N ALA B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.548A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1070 through 1113 removed outlier: 3.682A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.748A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.760A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 344 removed outlier: 3.961A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 344' Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.704A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.605A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.956A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.511A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.535A pdb=" N VAL C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.868A pdb=" N THR C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.743A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.693A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.927A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.022A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.646A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1048 No H-bonds generated for 'chain 'C' and resid 1046 through 1048' Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.632A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.831A pdb=" N ASP A 38 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.952A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 67 removed outlier: 4.163A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.569A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 227 removed outlier: 6.897A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.276A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 307 removed outlier: 7.632A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.267A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.415A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.415A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB4, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.633A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB7, first strand: chain 'A' and resid 619 through 624 removed outlier: 4.021A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.752A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.358A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.194A pdb=" N SER A1152 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 794 " --> pdb=" O PRO A1150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 796 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR A1148 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 798 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A1146 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A 800 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1144 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 802 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A1142 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 804 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A1140 " --> pdb=" O GLN A 804 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.194A pdb=" N SER A1152 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 794 " --> pdb=" O PRO A1150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 796 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR A1148 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 798 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A1146 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A 800 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A1144 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 802 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A1142 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 804 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A1140 " --> pdb=" O GLN A 804 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.389A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC7, first strand: chain 'B' and resid 59 through 67 removed outlier: 7.760A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AC9, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.763A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.744A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AD4, first strand: chain 'B' and resid 316 through 319 removed outlier: 6.531A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.609A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 422 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 370 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.609A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AD9, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.253A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE2, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.835A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.683A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.244A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.889A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.889A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.420A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AE9, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AF1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF2, first strand: chain 'C' and resid 38 through 39 removed outlier: 8.138A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 59 through 67 removed outlier: 7.929A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.432A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AF6, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.569A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AF8, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.566A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.473A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 422 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N CYS C 370 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN C 424 " --> pdb=" O PHE C 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 368 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS C 364 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 352 through 354 removed outlier: 3.652A pdb=" N CYS C 603 " --> pdb=" O CYS C 352 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.162A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AG6, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.508A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.656A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.793A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.793A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.325A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH3, first strand: chain 'C' and resid 1202 through 1205 1069 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.68 Time building geometry restraints manager: 13.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9106 1.34 - 1.46: 7837 1.46 - 1.59: 13084 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" CA TYR A 28 " pdb=" CB TYR A 28 " ideal model delta sigma weight residual 1.524 1.576 -0.053 1.62e-02 3.81e+03 1.05e+01 bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG A2014 " pdb=" O5 NAG A2014 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C1 MAN N 6 " pdb=" O5 MAN N 6 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CA ASP C 250 " pdb=" C ASP C 250 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.34e-02 5.57e+03 7.98e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.77: 809 106.77 - 113.63: 16893 113.63 - 120.49: 11325 120.49 - 127.35: 11912 127.35 - 134.21: 218 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N PRO C 969 " pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 110.70 118.55 -7.85 1.22e+00 6.72e-01 4.14e+01 angle pdb=" N PRO B 969 " pdb=" CA PRO B 969 " pdb=" C PRO B 969 " ideal model delta sigma weight residual 110.70 118.43 -7.73 1.22e+00 6.72e-01 4.02e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 118.12 -7.42 1.22e+00 6.72e-01 3.70e+01 angle pdb=" N ASN B 132 " pdb=" CA ASN B 132 " pdb=" C ASN B 132 " ideal model delta sigma weight residual 113.37 120.91 -7.54 1.38e+00 5.25e-01 2.99e+01 angle pdb=" N GLU B 37 " pdb=" CA GLU B 37 " pdb=" C GLU B 37 " ideal model delta sigma weight residual 112.54 104.52 8.02 1.51e+00 4.39e-01 2.82e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 17916 24.61 - 49.23: 1035 49.23 - 73.84: 242 73.84 - 98.46: 27 98.46 - 123.07: 7 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PRO C 92 " pdb=" C PRO C 92 " pdb=" N PRO C 93 " pdb=" CA PRO C 93 " ideal model delta harmonic sigma weight residual 180.00 130.80 49.20 0 5.00e+00 4.00e-02 9.68e+01 dihedral pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " pdb=" CA PRO C 970 " ideal model delta harmonic sigma weight residual 180.00 144.59 35.41 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA PHE B 968 " pdb=" C PHE B 968 " pdb=" N PRO B 969 " pdb=" CA PRO B 969 " ideal model delta harmonic sigma weight residual -180.00 -144.71 -35.29 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 4899 0.331 - 0.662: 5 0.662 - 0.993: 1 0.993 - 1.323: 2 1.323 - 1.654: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 19 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 132 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.17e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 188 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.73e+01 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 19 " -0.085 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN B 19 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 19 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 19 " 0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 132 " -0.068 2.00e-02 2.50e+03 8.88e-02 9.85e+01 pdb=" CG ASN B 132 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 132 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 132 " 0.152 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 188 " -0.038 2.00e-02 2.50e+03 5.30e-02 3.51e+01 pdb=" CG ASN B 188 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 188 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 188 " 0.093 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.060 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7711 2.80 - 3.32: 23407 3.32 - 3.85: 47986 3.85 - 4.37: 55957 4.37 - 4.90: 97987 Nonbonded interactions: 233048 Sorted by model distance: nonbonded pdb=" O TRP B 89 " pdb=" OH TYR B 236 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 625 " pdb=" OD1 ASP C 660 " model vdw 2.292 3.040 nonbonded pdb=" O VAL A 636 " pdb=" OG1 THR A 666 " model vdw 2.296 3.040 ... (remaining 233043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 84.230 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 103.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 30225 Z= 0.440 Angle : 0.854 9.581 41157 Z= 0.467 Chirality : 0.068 1.654 4908 Planarity : 0.008 0.115 5172 Dihedral : 15.653 123.072 12183 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 9.92 % Allowed : 8.81 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.12), residues: 3618 helix: -2.07 (0.14), residues: 790 sheet: -1.00 (0.17), residues: 853 loop : -2.63 (0.11), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 174 HIS 0.009 0.002 HIS C1129 PHE 0.025 0.002 PHE A 968 TYR 0.030 0.002 TYR A 622 ARG 0.005 0.001 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 250 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 120 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5884 (tt0) REVERT: A 124 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 186 LYS cc_start: 0.8463 (ttmp) cc_final: 0.8030 (ttpt) REVERT: A 187 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6934 (tptp) REVERT: A 351 ASN cc_start: 0.5357 (m-40) cc_final: 0.5150 (m-40) REVERT: A 560 LEU cc_start: -0.0685 (OUTLIER) cc_final: -0.1095 (pp) REVERT: A 606 ASP cc_start: 0.1726 (OUTLIER) cc_final: 0.1239 (t0) REVERT: A 643 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7292 (m110) REVERT: A 659 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7858 (ttpm) REVERT: A 831 GLU cc_start: 0.7993 (pt0) cc_final: 0.7781 (pp20) REVERT: A 845 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 885 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8000 (tptp) REVERT: A 902 LEU cc_start: 0.7716 (tp) cc_final: 0.7485 (tt) REVERT: A 906 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 981 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 1038 GLN cc_start: 0.7231 (mm110) cc_final: 0.7014 (mm-40) REVERT: A 1091 GLN cc_start: 0.7353 (tt0) cc_final: 0.7001 (tt0) REVERT: B 97 ASP cc_start: 0.6869 (m-30) cc_final: 0.6579 (t0) REVERT: B 234 HIS cc_start: 0.6649 (m90) cc_final: 0.6199 (m90) REVERT: B 289 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7423 (tt0) REVERT: B 544 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 655 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 711 PHE cc_start: 0.6900 (m-80) cc_final: 0.6638 (m-10) REVERT: B 837 ASP cc_start: 0.7686 (m-30) cc_final: 0.7396 (m-30) REVERT: B 848 ASP cc_start: 0.7706 (m-30) cc_final: 0.7455 (m-30) REVERT: B 930 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5580 (mp0) REVERT: B 1149 LYS cc_start: 0.7818 (tttt) cc_final: 0.7458 (tttm) REVERT: C 187 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7229 (ttmm) REVERT: C 213 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.6924 (p90) REVERT: C 373 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 464 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: C 511 TYR cc_start: 0.1864 (OUTLIER) cc_final: 0.0176 (m-10) REVERT: C 652 ASN cc_start: 0.8659 (m-40) cc_final: 0.8257 (m-40) REVERT: C 698 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7681 (p) REVERT: C 780 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: C 827 ASP cc_start: 0.8085 (m-30) cc_final: 0.7740 (m-30) REVERT: C 1026 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 1124 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6716 (m) REVERT: C 1205 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (ptp) outliers start: 322 outliers final: 122 residues processed: 537 average time/residue: 0.9290 time to fit residues: 625.9966 Evaluate side-chains 308 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 162 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1213 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 151 optimal weight: 0.0010 chunk 93 optimal weight: 0.0270 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 278 ASN A 353 ASN A 410 GLN A 559 GLN A 595 ASN A 611 ASN A 621 ASN A 630 GLN A 876 HIS A 881 ASN A 984 GLN A1001 GLN A1091 GLN B 22 ASN B 26 ASN B 204 GLN B 630 GLN B 876 HIS B 894 GLN B1001 GLN B1086 ASN B1091 GLN B1122 ASN C 73 ASN C 204 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN C 630 GLN C 799 HIS C 872 ASN C 894 GLN C1001 GLN C1023 ASN C1045 GLN C1079 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 30225 Z= 0.163 Angle : 0.587 10.955 41157 Z= 0.309 Chirality : 0.049 0.840 4908 Planarity : 0.006 0.102 5172 Dihedral : 11.298 105.240 6089 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.55 % Allowed : 13.12 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3618 helix: 0.15 (0.19), residues: 762 sheet: -0.52 (0.17), residues: 855 loop : -2.22 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 174 HIS 0.004 0.001 HIS A 201 PHE 0.020 0.001 PHE C 391 TYR 0.014 0.001 TYR A 191 ARG 0.006 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 197 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6776 (tp) REVERT: A 187 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6690 (tptp) REVERT: A 263 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7741 (tpt-90) REVERT: A 659 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7839 (tttm) REVERT: A 885 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7999 (tptp) REVERT: A 902 LEU cc_start: 0.7704 (tp) cc_final: 0.7501 (tt) REVERT: A 906 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 981 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 1003 LEU cc_start: 0.8077 (mm) cc_final: 0.7524 (tp) REVERT: A 1038 GLN cc_start: 0.7126 (mm110) cc_final: 0.6879 (mm-40) REVERT: A 1089 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 1091 GLN cc_start: 0.7288 (tt0) cc_final: 0.6981 (tt0) REVERT: B 85 LEU cc_start: 0.3656 (OUTLIER) cc_final: 0.3390 (tm) REVERT: B 234 HIS cc_start: 0.6436 (m90) cc_final: 0.5976 (m90) REVERT: B 236 TYR cc_start: 0.6929 (t80) cc_final: 0.6536 (t80) REVERT: B 289 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7166 (tt0) REVERT: B 655 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8523 (mt) REVERT: B 711 PHE cc_start: 0.6833 (m-80) cc_final: 0.6584 (m-10) REVERT: B 848 ASP cc_start: 0.7605 (m-30) cc_final: 0.7323 (m-30) REVERT: B 930 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5427 (mp0) REVERT: B 1147 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8052 (m) REVERT: B 1149 LYS cc_start: 0.7846 (tttt) cc_final: 0.7523 (tttm) REVERT: C 187 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7386 (ttmm) REVERT: C 213 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7147 (p90) REVERT: C 464 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: C 511 TYR cc_start: 0.1694 (OUTLIER) cc_final: 0.0117 (m-10) REVERT: C 652 ASN cc_start: 0.8513 (m-40) cc_final: 0.8148 (m-40) REVERT: C 698 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.8034 (p) REVERT: C 827 ASP cc_start: 0.7961 (m-30) cc_final: 0.7598 (m-30) REVERT: C 894 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.6026 (pp30) REVERT: C 912 LYS cc_start: 0.8536 (tppt) cc_final: 0.8008 (tptt) REVERT: C 1066 ASP cc_start: 0.7716 (p0) cc_final: 0.7299 (p0) REVERT: C 1069 GLU cc_start: 0.7677 (tt0) cc_final: 0.7464 (pt0) REVERT: C 1071 GLN cc_start: 0.7673 (mt0) cc_final: 0.7183 (mp-120) REVERT: C 1205 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8545 (ptp) outliers start: 180 outliers final: 97 residues processed: 356 average time/residue: 0.9449 time to fit residues: 424.6104 Evaluate side-chains 275 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 160 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1185 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 930 GLU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1147 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 894 GLN Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 327 optimal weight: 0.4980 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 353 ASN B 583 ASN B 826 HIS B1059 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 ASN C 876 HIS C 894 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30225 Z= 0.264 Angle : 0.615 9.270 41157 Z= 0.322 Chirality : 0.051 0.883 4908 Planarity : 0.006 0.108 5172 Dihedral : 10.402 108.637 5996 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.58 % Allowed : 14.39 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3618 helix: 0.77 (0.20), residues: 759 sheet: -0.47 (0.17), residues: 856 loop : -2.02 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 174 HIS 0.007 0.001 HIS C1129 PHE 0.021 0.002 PHE C 968 TYR 0.026 0.002 TYR A 191 ARG 0.004 0.000 ARG B 756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 166 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6827 (tp) REVERT: A 187 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6821 (tptp) REVERT: A 659 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7860 (tttm) REVERT: A 885 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7910 (tptp) REVERT: A 902 LEU cc_start: 0.7729 (tp) cc_final: 0.7481 (tt) REVERT: A 906 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7700 (mp) REVERT: A 1003 LEU cc_start: 0.8152 (mm) cc_final: 0.7596 (tp) REVERT: A 1038 GLN cc_start: 0.7019 (mm110) cc_final: 0.6785 (mt0) REVERT: A 1091 GLN cc_start: 0.7364 (tt0) cc_final: 0.7078 (tt0) REVERT: B 85 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.3381 (tm) REVERT: B 149 THR cc_start: 0.5286 (OUTLIER) cc_final: 0.5082 (p) REVERT: B 234 HIS cc_start: 0.6394 (m90) cc_final: 0.5979 (m90) REVERT: B 236 TYR cc_start: 0.6958 (t80) cc_final: 0.6576 (t80) REVERT: B 289 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7125 (tt0) REVERT: B 655 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 711 PHE cc_start: 0.6857 (m-80) cc_final: 0.6604 (m-10) REVERT: B 848 ASP cc_start: 0.7638 (m-30) cc_final: 0.7400 (m-30) REVERT: B 1149 LYS cc_start: 0.7871 (tttt) cc_final: 0.7518 (tttm) REVERT: C 187 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7479 (ttmm) REVERT: C 213 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7046 (p90) REVERT: C 250 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6457 (t70) REVERT: C 511 TYR cc_start: 0.1692 (OUTLIER) cc_final: 0.0114 (m-10) REVERT: C 652 ASN cc_start: 0.8539 (m-40) cc_final: 0.8143 (m-40) REVERT: C 800 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: C 827 ASP cc_start: 0.7958 (m-30) cc_final: 0.7611 (m-30) REVERT: C 912 LYS cc_start: 0.8522 (tppt) cc_final: 0.7996 (tptt) REVERT: C 994 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7045 (mmm) REVERT: C 1066 ASP cc_start: 0.7722 (p0) cc_final: 0.7127 (p0) REVERT: C 1071 GLN cc_start: 0.7741 (mt0) cc_final: 0.7207 (mp-120) REVERT: C 1205 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (ptp) outliers start: 181 outliers final: 108 residues processed: 320 average time/residue: 1.0763 time to fit residues: 437.2568 Evaluate side-chains 283 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 161 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 994 MET Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 0.5980 chunk 347 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30225 Z= 0.151 Angle : 0.553 9.229 41157 Z= 0.289 Chirality : 0.049 0.728 4908 Planarity : 0.005 0.102 5172 Dihedral : 9.506 106.280 5971 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.41 % Allowed : 15.65 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3618 helix: 1.30 (0.20), residues: 758 sheet: -0.33 (0.17), residues: 855 loop : -1.85 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 971 HIS 0.004 0.001 HIS C1129 PHE 0.022 0.001 PHE C 391 TYR 0.022 0.001 TYR A 191 ARG 0.008 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 177 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6781 (tp) REVERT: A 659 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7815 (tttm) REVERT: A 885 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7957 (tptp) REVERT: A 902 LEU cc_start: 0.7682 (tp) cc_final: 0.7456 (tt) REVERT: A 1003 LEU cc_start: 0.8152 (mm) cc_final: 0.7594 (tp) REVERT: A 1038 GLN cc_start: 0.6972 (mm110) cc_final: 0.6753 (mt0) REVERT: A 1091 GLN cc_start: 0.7224 (tt0) cc_final: 0.6934 (tt0) REVERT: B 51 VAL cc_start: 0.6669 (OUTLIER) cc_final: 0.6450 (t) REVERT: B 85 LEU cc_start: 0.3793 (OUTLIER) cc_final: 0.3545 (tm) REVERT: B 234 HIS cc_start: 0.6356 (m90) cc_final: 0.5956 (m90) REVERT: B 236 TYR cc_start: 0.6884 (t80) cc_final: 0.6463 (t80) REVERT: B 289 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7056 (tt0) REVERT: B 583 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.7064 (t0) REVERT: B 655 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8573 (mt) REVERT: B 711 PHE cc_start: 0.6833 (m-80) cc_final: 0.6586 (m-10) REVERT: B 848 ASP cc_start: 0.7699 (m-30) cc_final: 0.7441 (m-30) REVERT: B 1149 LYS cc_start: 0.7879 (tttt) cc_final: 0.7510 (tttm) REVERT: C 187 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7495 (ttmm) REVERT: C 213 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7081 (p90) REVERT: C 511 TYR cc_start: 0.1706 (OUTLIER) cc_final: 0.0104 (m-10) REVERT: C 827 ASP cc_start: 0.7975 (m-30) cc_final: 0.7622 (m-30) REVERT: C 1071 GLN cc_start: 0.7669 (mt0) cc_final: 0.7191 (mp-120) REVERT: C 1205 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8631 (ptp) outliers start: 143 outliers final: 86 residues processed: 300 average time/residue: 0.9364 time to fit residues: 354.8396 Evaluate side-chains 255 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 159 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30225 Z= 0.335 Angle : 0.634 9.414 41157 Z= 0.330 Chirality : 0.051 0.698 4908 Planarity : 0.006 0.108 5172 Dihedral : 9.431 107.510 5938 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.33 % Allowed : 15.50 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3618 helix: 1.11 (0.20), residues: 760 sheet: -0.40 (0.17), residues: 852 loop : -1.86 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 174 HIS 0.009 0.001 HIS C1129 PHE 0.019 0.002 PHE B 968 TYR 0.023 0.002 TYR A 191 ARG 0.006 0.001 ARG B 932 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 158 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.6940 (tp) REVERT: A 233 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 659 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7862 (ttpm) REVERT: A 885 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7952 (tptp) REVERT: A 1003 LEU cc_start: 0.8129 (mm) cc_final: 0.7561 (tp) REVERT: A 1038 GLN cc_start: 0.7080 (mm110) cc_final: 0.6834 (mt0) REVERT: A 1091 GLN cc_start: 0.7375 (tt0) cc_final: 0.7087 (tt0) REVERT: B 83 LYS cc_start: 0.4507 (OUTLIER) cc_final: 0.4111 (pptt) REVERT: B 85 LEU cc_start: 0.3819 (OUTLIER) cc_final: 0.3574 (tm) REVERT: B 289 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7136 (tt0) REVERT: B 515 TRP cc_start: 0.6741 (p-90) cc_final: 0.6492 (p-90) REVERT: B 635 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (tp30) REVERT: B 655 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8557 (mt) REVERT: B 711 PHE cc_start: 0.6869 (m-80) cc_final: 0.6614 (m-10) REVERT: B 848 ASP cc_start: 0.7664 (m-30) cc_final: 0.7417 (m-30) REVERT: B 1112 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: B 1149 LYS cc_start: 0.7871 (tttt) cc_final: 0.7500 (tttm) REVERT: C 187 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7505 (ttmm) REVERT: C 213 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7031 (p90) REVERT: C 511 TYR cc_start: 0.1717 (OUTLIER) cc_final: 0.0114 (m-10) REVERT: C 780 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: C 800 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: C 827 ASP cc_start: 0.8028 (m-30) cc_final: 0.7712 (m-30) REVERT: C 845 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: C 1071 GLN cc_start: 0.7761 (mt0) cc_final: 0.7209 (mp-120) REVERT: C 1205 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8650 (ptp) outliers start: 173 outliers final: 116 residues processed: 308 average time/residue: 0.9567 time to fit residues: 373.1299 Evaluate side-chains 281 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 150 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 289 optimal weight: 50.0000 chunk 161 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30225 Z= 0.217 Angle : 0.578 10.499 41157 Z= 0.301 Chirality : 0.050 0.740 4908 Planarity : 0.005 0.100 5172 Dihedral : 9.120 106.020 5938 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.44 % Allowed : 17.04 % Favored : 78.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3618 helix: 1.36 (0.20), residues: 758 sheet: -0.34 (0.17), residues: 852 loop : -1.77 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 971 HIS 0.006 0.001 HIS B1129 PHE 0.023 0.001 PHE C 391 TYR 0.023 0.001 TYR A 191 ARG 0.007 0.000 ARG B 932 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 162 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6812 (tp) REVERT: A 659 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7846 (tttm) REVERT: A 885 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7942 (tptp) REVERT: A 1003 LEU cc_start: 0.8072 (mm) cc_final: 0.7507 (tp) REVERT: A 1038 GLN cc_start: 0.7069 (mm110) cc_final: 0.6816 (mt0) REVERT: A 1091 GLN cc_start: 0.7301 (tt0) cc_final: 0.7034 (tt0) REVERT: B 85 LEU cc_start: 0.3691 (OUTLIER) cc_final: 0.3423 (tm) REVERT: B 111 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4872 (mt) REVERT: B 149 THR cc_start: 0.5195 (OUTLIER) cc_final: 0.4950 (p) REVERT: B 289 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7100 (tt0) REVERT: B 515 TRP cc_start: 0.6704 (p-90) cc_final: 0.6433 (p-90) REVERT: B 655 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 711 PHE cc_start: 0.6859 (m-80) cc_final: 0.6595 (m-10) REVERT: B 848 ASP cc_start: 0.7613 (m-30) cc_final: 0.7364 (m-30) REVERT: B 1149 LYS cc_start: 0.7889 (tttt) cc_final: 0.7527 (tttm) REVERT: C 187 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7536 (ttmm) REVERT: C 213 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7086 (p90) REVERT: C 511 TYR cc_start: 0.1847 (OUTLIER) cc_final: 0.0286 (m-10) REVERT: C 652 ASN cc_start: 0.8487 (m-40) cc_final: 0.8120 (m-40) REVERT: C 827 ASP cc_start: 0.8003 (m-30) cc_final: 0.7663 (m-30) REVERT: C 1071 GLN cc_start: 0.7736 (mt0) cc_final: 0.7207 (mp-120) REVERT: C 1205 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8651 (ptp) outliers start: 144 outliers final: 105 residues processed: 287 average time/residue: 0.9509 time to fit residues: 345.4722 Evaluate side-chains 269 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 154 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 194 optimal weight: 0.0030 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30225 Z= 0.281 Angle : 0.605 9.574 41157 Z= 0.315 Chirality : 0.050 0.666 4908 Planarity : 0.006 0.108 5172 Dihedral : 9.049 106.557 5935 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.02 % Allowed : 16.61 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3618 helix: 1.22 (0.20), residues: 767 sheet: -0.34 (0.17), residues: 854 loop : -1.77 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.008 0.001 HIS C1129 PHE 0.017 0.002 PHE B 968 TYR 0.021 0.002 TYR A 191 ARG 0.012 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 152 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6923 (tp) REVERT: A 233 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (t) REVERT: A 560 LEU cc_start: -0.1205 (OUTLIER) cc_final: -0.1702 (pp) REVERT: A 659 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7784 (ttpm) REVERT: A 885 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7927 (tptp) REVERT: A 1003 LEU cc_start: 0.8135 (mm) cc_final: 0.7578 (tp) REVERT: A 1038 GLN cc_start: 0.7077 (mm110) cc_final: 0.6825 (mt0) REVERT: A 1091 GLN cc_start: 0.7322 (tt0) cc_final: 0.7004 (tt0) REVERT: B 85 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.3344 (tm) REVERT: B 289 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7121 (tt0) REVERT: B 515 TRP cc_start: 0.6707 (p-90) cc_final: 0.6455 (p-90) REVERT: B 655 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 711 PHE cc_start: 0.6866 (m-80) cc_final: 0.6597 (m-10) REVERT: B 848 ASP cc_start: 0.7631 (m-30) cc_final: 0.7399 (m-30) REVERT: B 1112 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: B 1149 LYS cc_start: 0.7866 (tttt) cc_final: 0.7497 (tttm) REVERT: C 187 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7506 (ttmm) REVERT: C 213 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6997 (p90) REVERT: C 511 TYR cc_start: 0.1844 (OUTLIER) cc_final: 0.0288 (m-10) REVERT: C 652 ASN cc_start: 0.8524 (m-40) cc_final: 0.8167 (m-40) REVERT: C 780 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: C 800 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: C 827 ASP cc_start: 0.8013 (m-30) cc_final: 0.7682 (m-30) REVERT: C 845 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: C 1071 GLN cc_start: 0.7759 (mt0) cc_final: 0.7226 (mp-120) REVERT: C 1205 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8650 (ptp) outliers start: 163 outliers final: 121 residues processed: 291 average time/residue: 0.9464 time to fit residues: 349.4988 Evaluate side-chains 285 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 150 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30225 Z= 0.176 Angle : 0.547 9.953 41157 Z= 0.286 Chirality : 0.048 0.705 4908 Planarity : 0.005 0.098 5172 Dihedral : 8.522 104.723 5933 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.47 % Allowed : 17.19 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3618 helix: 1.60 (0.20), residues: 761 sheet: -0.25 (0.17), residues: 860 loop : -1.67 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 971 HIS 0.005 0.001 HIS C1129 PHE 0.024 0.001 PHE C 391 TYR 0.022 0.001 TYR A 191 ARG 0.008 0.000 ARG B 932 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 158 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6768 (tp) REVERT: A 560 LEU cc_start: -0.1161 (OUTLIER) cc_final: -0.1655 (pp) REVERT: A 659 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7772 (tttm) REVERT: A 885 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7913 (tptp) REVERT: A 1003 LEU cc_start: 0.8076 (mm) cc_final: 0.7526 (tp) REVERT: A 1038 GLN cc_start: 0.6981 (mm110) cc_final: 0.6724 (mt0) REVERT: A 1091 GLN cc_start: 0.7219 (tt0) cc_final: 0.6979 (tt0) REVERT: A 1157 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8220 (mm) REVERT: B 85 LEU cc_start: 0.3538 (OUTLIER) cc_final: 0.3279 (tm) REVERT: B 147 GLU cc_start: 0.6189 (tp30) cc_final: 0.5987 (tp30) REVERT: B 149 THR cc_start: 0.5166 (OUTLIER) cc_final: 0.4924 (p) REVERT: B 240 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5404 (mt) REVERT: B 289 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7075 (tt0) REVERT: B 515 TRP cc_start: 0.6714 (p-90) cc_final: 0.6482 (p-90) REVERT: B 635 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: B 655 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8547 (mt) REVERT: B 711 PHE cc_start: 0.6849 (m-80) cc_final: 0.6588 (m-10) REVERT: B 848 ASP cc_start: 0.7613 (m-30) cc_final: 0.7352 (m-30) REVERT: B 890 CYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5251 (t) REVERT: B 953 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7257 (m) REVERT: B 1149 LYS cc_start: 0.7922 (tttt) cc_final: 0.7570 (tttm) REVERT: C 187 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7564 (ttmm) REVERT: C 213 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7069 (p90) REVERT: C 511 TYR cc_start: 0.1811 (OUTLIER) cc_final: 0.0267 (m-10) REVERT: C 652 ASN cc_start: 0.8483 (m-40) cc_final: 0.8117 (m-40) REVERT: C 845 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: C 1071 GLN cc_start: 0.7663 (mt0) cc_final: 0.7154 (mp-120) outliers start: 145 outliers final: 104 residues processed: 282 average time/residue: 0.9063 time to fit residues: 328.3146 Evaluate side-chains 271 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 152 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 chunk 140 optimal weight: 0.1980 chunk 253 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 chunk 322 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 838 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30225 Z= 0.139 Angle : 0.527 10.223 41157 Z= 0.275 Chirality : 0.047 0.747 4908 Planarity : 0.005 0.108 5172 Dihedral : 8.078 103.596 5926 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.36 % Allowed : 18.27 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3618 helix: 1.89 (0.21), residues: 754 sheet: -0.16 (0.17), residues: 857 loop : -1.57 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 971 HIS 0.004 0.001 HIS C1129 PHE 0.015 0.001 PHE B 968 TYR 0.027 0.001 TYR A 191 ARG 0.007 0.000 ARG B 932 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 158 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6777 (tp) REVERT: A 560 LEU cc_start: -0.1337 (OUTLIER) cc_final: -0.1823 (pp) REVERT: A 659 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7804 (tttm) REVERT: A 885 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7931 (tptp) REVERT: A 1003 LEU cc_start: 0.8062 (mm) cc_final: 0.7508 (tp) REVERT: A 1038 GLN cc_start: 0.7019 (mm110) cc_final: 0.6791 (mt0) REVERT: A 1091 GLN cc_start: 0.7163 (tt0) cc_final: 0.6902 (tt0) REVERT: A 1157 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8239 (mm) REVERT: B 34 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5595 (ptm160) REVERT: B 147 GLU cc_start: 0.6115 (tp30) cc_final: 0.5697 (tp30) REVERT: B 149 THR cc_start: 0.5272 (OUTLIER) cc_final: 0.4955 (p) REVERT: B 240 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5327 (mt) REVERT: B 289 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7107 (tt0) REVERT: B 515 TRP cc_start: 0.6656 (p-90) cc_final: 0.6382 (p-90) REVERT: B 655 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 711 PHE cc_start: 0.6840 (m-80) cc_final: 0.6583 (m-10) REVERT: B 848 ASP cc_start: 0.7714 (m-30) cc_final: 0.7437 (m-30) REVERT: B 890 CYS cc_start: 0.5549 (OUTLIER) cc_final: 0.5254 (t) REVERT: B 1149 LYS cc_start: 0.7932 (tttt) cc_final: 0.7579 (tttm) REVERT: C 187 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: C 205 GLU cc_start: 0.7800 (tt0) cc_final: 0.7539 (tt0) REVERT: C 213 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7161 (p90) REVERT: C 511 TYR cc_start: 0.1888 (OUTLIER) cc_final: 0.0288 (m-10) REVERT: C 863 GLN cc_start: 0.7332 (tt0) cc_final: 0.6844 (pt0) REVERT: C 1071 GLN cc_start: 0.7594 (mt0) cc_final: 0.7111 (mp-120) outliers start: 109 outliers final: 82 residues processed: 258 average time/residue: 0.9631 time to fit residues: 321.1031 Evaluate side-chains 246 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 152 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 0.5980 chunk 330 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 583 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30225 Z= 0.370 Angle : 0.641 10.402 41157 Z= 0.333 Chirality : 0.051 0.742 4908 Planarity : 0.006 0.107 5172 Dihedral : 8.480 104.098 5915 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.70 % Allowed : 18.18 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3618 helix: 1.33 (0.20), residues: 763 sheet: -0.20 (0.17), residues: 870 loop : -1.67 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 174 HIS 0.009 0.001 HIS C1129 PHE 0.022 0.002 PHE C 391 TYR 0.025 0.002 TYR A 191 ARG 0.006 0.001 ARG B 932 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 147 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6929 (tp) REVERT: A 233 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8311 (t) REVERT: A 659 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7862 (ttpm) REVERT: A 771 ASN cc_start: 0.5916 (OUTLIER) cc_final: 0.5642 (OUTLIER) REVERT: A 885 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7922 (tptp) REVERT: A 994 MET cc_start: 0.8418 (mmt) cc_final: 0.8116 (mmt) REVERT: A 1003 LEU cc_start: 0.8097 (mm) cc_final: 0.7548 (tp) REVERT: A 1038 GLN cc_start: 0.7040 (mm110) cc_final: 0.6774 (mt0) REVERT: A 1091 GLN cc_start: 0.7382 (tt0) cc_final: 0.7089 (tt0) REVERT: B 149 THR cc_start: 0.5373 (OUTLIER) cc_final: 0.5138 (p) REVERT: B 289 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7154 (tt0) REVERT: B 635 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: B 655 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 711 PHE cc_start: 0.6882 (m-80) cc_final: 0.6616 (m-10) REVERT: B 848 ASP cc_start: 0.7669 (m-30) cc_final: 0.7439 (m-30) REVERT: B 862 MET cc_start: 0.8275 (mmm) cc_final: 0.8016 (mmp) REVERT: B 890 CYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5203 (t) REVERT: B 1149 LYS cc_start: 0.7826 (tttt) cc_final: 0.7432 (tttm) REVERT: C 187 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7496 (ttmm) REVERT: C 213 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7152 (p90) REVERT: C 511 TYR cc_start: 0.1749 (OUTLIER) cc_final: 0.0145 (m-10) REVERT: C 652 ASN cc_start: 0.8542 (m-40) cc_final: 0.8186 (m-40) REVERT: C 780 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: C 845 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: C 1071 GLN cc_start: 0.7696 (mt0) cc_final: 0.7178 (mp-120) outliers start: 120 outliers final: 99 residues processed: 255 average time/residue: 0.9200 time to fit residues: 298.4299 Evaluate side-chains 253 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 142 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 890 CYS Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1090 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1207 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 789 GLN Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 263 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 286 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 0.0010 overall best weight: 0.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 583 ASN B 998 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.165206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112574 restraints weight = 44061.837| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.77 r_work: 0.3243 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30225 Z= 0.133 Angle : 0.528 10.775 41157 Z= 0.275 Chirality : 0.047 0.808 4908 Planarity : 0.005 0.101 5172 Dihedral : 7.748 102.099 5914 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.80 % Allowed : 19.13 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3618 helix: 1.89 (0.21), residues: 761 sheet: -0.11 (0.17), residues: 846 loop : -1.51 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 971 HIS 0.003 0.001 HIS C 201 PHE 0.014 0.001 PHE C 968 TYR 0.028 0.001 TYR A 191 ARG 0.009 0.000 ARG B 932 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8844.10 seconds wall clock time: 157 minutes 48.07 seconds (9468.07 seconds total)