Starting phenix.real_space_refine on Thu Mar 21 19:23:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb3_0401/03_2024/6nb3_0401.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.061 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 155 5.16 5 C 19492 2.51 5 N 4892 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 911": "OD1" <-> "OD2" Residue "B TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 509": "OD1" <-> "OD2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 633": "OD1" <-> "OD2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 805": "OD1" <-> "OD2" Residue "C TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 875": "OE1" <-> "OE2" Residue "C PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30960 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7402 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 45, 'TRANS': 912} Chain breaks: 5 Chain: "C" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" 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: "v" 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: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 16.01, per 1000 atoms: 0.52 Number of scatterers: 30960 At special positions: 0 Unit cell: (153.44, 147.96, 194.54, 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 155 16.00 O 6421 8.00 N 4892 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.07 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.05 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.06 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.23 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.04 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.08 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.02 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.16 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.04 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.11 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.13 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.08 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.06 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.08 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 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 ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN P 4 " - " MAN P 5 " " MAN Z 4 " - " MAN Z 5 " " MAN b 4 " - " MAN b 5 " " MAN c 4 " - " MAN c 5 " " MAN n 4 " - " MAN n 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 6 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A1445 " - " ASN A 592 " " NAG B1442 " - " ASN B 774 " " NAG C1423 " - " ASN C 236 " " NAG C1428 " - " ASN C 487 " " NAG C1429 " - " ASN C 592 " " NAG F 1 " - " ASN A 66 " " NAG G 1 " - " ASN A 104 " " NAG I 1 " - " ASN A 125 " " NAG J 1 " - " ASN A 155 " " NAG K 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 222 " " NAG N 1 " - " ASN A 236 " " NAG O 1 " - " ASN A 244 " " NAG P 1 " - " ASN A 410 " " NAG Q 1 " - " ASN A 487 " " NAG R 1 " - " ASN A 619 " " NAG S 1 " - " ASN A 719 " " NAG T 1 " - " ASN A 774 " " NAG U 1 " - " ASN A 785 " " NAG V 1 " - " ASN A 870 " " NAG W 1 " - " ASN A1213 " " NAG X 1 " - " ASN B 66 " " NAG Y 1 " - " ASN B 104 " " NAG Z 1 " - " ASN B 125 " " NAG a 1 " - " ASN B 155 " " NAG b 1 " - " ASN B 166 " " NAG c 1 " - " ASN B 222 " " NAG d 1 " - " ASN B 236 " " NAG e 1 " - " ASN B 244 " " NAG f 1 " - " ASN B 592 " " NAG g 1 " - " ASN B 619 " " NAG h 1 " - " ASN B 719 " " NAG i 1 " - " ASN B 785 " " NAG j 1 " - " ASN B 870 " " NAG k 1 " - " ASN B1213 " " NAG l 1 " - " ASN C 66 " " NAG m 1 " - " ASN C 104 " " NAG n 1 " - " ASN C 125 " " NAG o 1 " - " ASN C 155 " " NAG p 1 " - " ASN C 166 " " NAG q 1 " - " ASN C 222 " " NAG r 1 " - " ASN C 244 " " NAG s 1 " - " ASN C 410 " " NAG t 1 " - " ASN C 619 " " NAG u 1 " - " ASN C 719 " " NAG v 1 " - " ASN C 774 " " NAG w 1 " - " ASN C 785 " " NAG x 1 " - " ASN C 870 " " NAG y 1 " - " ASN C1213 " Time building additional restraints: 14.27 Conformation dependent library (CDL) restraints added in 5.4 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6928 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 22.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.925A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.760A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.583A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.525A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.697A pdb=" N ALA A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.295A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.842A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.137A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 954 through 959 removed outlier: 4.614A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 4.056A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.515A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.564A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 417 removed outlier: 3.554A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.268A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.700A pdb=" N GLN C 819 " --> pdb=" O GLN C 815 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 820 " --> pdb=" O LYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.761A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 removed outlier: 4.003A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.508A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 5.205A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.402A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.042A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.274A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.687A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.759A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.736A pdb=" N SER A 215 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.483A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.167A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.898A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.086A pdb=" N CYS A 407 " --> pdb=" O CYS A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.535A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.496A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.651A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 4.541A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 796 removed outlier: 4.493A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 5.692A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.149A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.474A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AC7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.954A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.710A pdb=" N TRP D 33 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.477A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AD7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.161A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.031A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.562A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.584A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.514A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AE7, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.742A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.652A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.245A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.330A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.718A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 1184 through 1188 removed outlier: 4.698A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 785 through 796 removed outlier: 3.617A pdb=" N ASN B 785 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.931A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AF8, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.075A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.157A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AG3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.700A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.611A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AG6, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.938A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.671A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.233A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.538A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AH2, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.592A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.340A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.379A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AH6, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.058A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN C1163 " --> pdb=" O ASP C1157 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3063 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: 15.47 Time building geometry restraints manager: 15.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5851 1.32 - 1.45: 9056 1.45 - 1.58: 16515 1.58 - 1.71: 6 1.71 - 1.84: 206 Bond restraints: 31634 Sorted by residual: bond pdb=" CA PRO A1220 " pdb=" C PRO A1220 " ideal model delta sigma weight residual 1.517 1.581 -0.064 9.30e-03 1.16e+04 4.71e+01 bond pdb=" CA PRO C1220 " pdb=" C PRO C1220 " ideal model delta sigma weight residual 1.517 1.578 -0.061 9.30e-03 1.16e+04 4.31e+01 bond pdb=" CA PRO B1220 " pdb=" C PRO B1220 " ideal model delta sigma weight residual 1.517 1.573 -0.056 9.30e-03 1.16e+04 3.65e+01 bond pdb=" CA PRO B1219 " pdb=" C PRO B1219 " ideal model delta sigma weight residual 1.517 1.570 -0.053 9.30e-03 1.16e+04 3.23e+01 bond pdb=" N PRO C1221 " pdb=" CD PRO C1221 " ideal model delta sigma weight residual 1.473 1.402 0.071 1.40e-02 5.10e+03 2.59e+01 ... (remaining 31629 not shown) Histogram of bond angle deviations from ideal: 88.98 - 98.82: 5 98.82 - 108.67: 2403 108.67 - 118.52: 23039 118.52 - 128.37: 17452 128.37 - 138.21: 121 Bond angle restraints: 43020 Sorted by residual: angle pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta sigma weight residual 111.29 134.84 -23.55 1.64e+00 3.72e-01 2.06e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.21 -27.79 1.99e+00 2.53e-01 1.95e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 125.89 -15.61 1.48e+00 4.57e-01 1.11e+02 angle pdb=" N TYR C 905 " pdb=" CA TYR C 905 " pdb=" C TYR C 905 " ideal model delta sigma weight residual 110.80 88.98 21.82 2.13e+00 2.20e-01 1.05e+02 angle pdb=" CD1 LEU C 506 " pdb=" CG LEU C 506 " pdb=" CD2 LEU C 506 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.90e+01 ... (remaining 43015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 19758 22.11 - 44.22: 609 44.22 - 66.34: 149 66.34 - 88.45: 197 88.45 - 110.56: 120 Dihedral angle restraints: 20833 sinusoidal: 9953 harmonic: 10880 Sorted by residual: dihedral pdb=" C VAL B 711 " pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual -122.00 -158.42 36.42 0 2.50e+00 1.60e-01 2.12e+02 dihedral pdb=" N VAL B 711 " pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual 123.40 150.91 -27.51 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" CB CYS C 806 " pdb=" SG CYS C 806 " pdb=" SG CYS C 828 " pdb=" CB CYS C 828 " ideal model delta sinusoidal sigma weight residual 93.00 178.95 -85.95 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 20830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 5215 0.267 - 0.534: 58 0.534 - 0.802: 4 0.802 - 1.069: 0 1.069 - 1.336: 1 Chirality restraints: 5278 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.22e+01 chirality pdb=" C1 BMA o 3 " pdb=" O4 NAG o 2 " pdb=" C2 BMA o 3 " pdb=" O5 BMA o 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.77e+01 ... (remaining 5275 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.042 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 166 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.064 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 166 " 0.036 2.00e-02 2.50e+03 3.68e-02 1.70e+01 pdb=" CG ASN A 166 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 166 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 166 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 77 " 0.049 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 77 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 77 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 77 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 77 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 77 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 77 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 77 " 0.027 2.00e-02 2.50e+03 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 871 2.69 - 3.24: 29800 3.24 - 3.80: 48629 3.80 - 4.35: 63141 4.35 - 4.90: 102110 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OG SER C 419 " pdb=" OG1 THR C 483 " model vdw 2.139 2.440 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.238 2.440 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.253 2.520 nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 2.256 3.440 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.298 2.440 ... (remaining 244546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 18 through 1222 or resid 1423)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 2 through 124) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'l' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'n' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'd' selection = chain 'k' selection = chain 'q' selection = chain 'y' } 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 group one per residue 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: 2.570 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: 12.900 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 85.390 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.015 0.085 31634 Z= 0.940 Angle : 1.397 27.795 43020 Z= 0.858 Chirality : 0.090 1.336 5278 Planarity : 0.006 0.059 5317 Dihedral : 17.224 110.562 13752 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 0.41 % Allowed : 1.44 % Favored : 98.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 3717 helix: 0.47 (0.19), residues: 682 sheet: 0.59 (0.16), residues: 897 loop : -0.27 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.006 TRP C1184 HIS 0.006 0.001 HIS A1138 PHE 0.030 0.004 PHE C 313 TYR 0.049 0.006 TYR A 77 ARG 0.006 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 839 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7676 (ttp) cc_final: 0.7233 (ttm) REVERT: A 444 ASP cc_start: 0.7617 (m-30) cc_final: 0.7276 (m-30) REVERT: A 817 CYS cc_start: 0.6670 (t) cc_final: 0.6431 (t) REVERT: H 83 LEU cc_start: 0.5935 (tp) cc_final: 0.5658 (tt) REVERT: H 88 LEU cc_start: 0.7166 (mt) cc_final: 0.6912 (mt) REVERT: H 92 ASP cc_start: 0.6545 (m-30) cc_final: 0.5164 (t70) REVERT: H 100 THR cc_start: 0.6187 (p) cc_final: 0.5960 (p) REVERT: H 108 TRP cc_start: 0.6890 (t-100) cc_final: 0.6405 (t60) REVERT: D 60 THR cc_start: 0.7052 (p) cc_final: 0.6763 (t) REVERT: D 62 TYR cc_start: 0.8067 (m-80) cc_final: 0.7688 (m-10) REVERT: D 72 LEU cc_start: 0.7149 (mp) cc_final: 0.6663 (tt) REVERT: D 95 VAL cc_start: 0.7588 (t) cc_final: 0.7384 (m) REVERT: E 64 PHE cc_start: 0.5375 (m-80) cc_final: 0.4594 (m-10) REVERT: E 97 SER cc_start: 0.8310 (m) cc_final: 0.7875 (p) REVERT: E 108 VAL cc_start: 0.6319 (t) cc_final: 0.6038 (t) REVERT: B 68 THR cc_start: 0.8641 (m) cc_final: 0.8338 (p) REVERT: B 220 ASN cc_start: 0.5262 (t0) cc_final: 0.4687 (t0) REVERT: B 677 VAL cc_start: 0.8872 (t) cc_final: 0.8591 (m) REVERT: B 816 LYS cc_start: 0.8229 (tptt) cc_final: 0.7762 (mmtt) REVERT: B 1054 ILE cc_start: 0.9101 (pt) cc_final: 0.8828 (mt) REVERT: C 84 MET cc_start: 0.7002 (ptm) cc_final: 0.6651 (ptm) REVERT: C 144 TYR cc_start: 0.7922 (m-80) cc_final: 0.7698 (m-10) REVERT: C 245 ILE cc_start: 0.8034 (mt) cc_final: 0.7814 (mt) REVERT: C 292 TYR cc_start: 0.8153 (m-80) cc_final: 0.7918 (m-10) REVERT: C 859 SER cc_start: 0.8795 (m) cc_final: 0.8515 (p) REVERT: C 1040 LEU cc_start: 0.8398 (tp) cc_final: 0.7853 (tp) outliers start: 13 outliers final: 1 residues processed: 848 average time/residue: 0.4141 time to fit residues: 556.1301 Evaluate side-chains 397 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 592 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 0.9980 chunk 281 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 chunk 216 optimal weight: 0.9980 chunk 336 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 522 GLN A 833 GLN A 857 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 119 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 277 ASN B 298 HIS B 346 GLN B 914 GLN ** B 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 60 GLN C 280 GLN C 421 ASN ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN C1056 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 31634 Z= 0.268 Angle : 0.703 8.815 43020 Z= 0.359 Chirality : 0.047 0.378 5278 Planarity : 0.005 0.057 5317 Dihedral : 13.637 86.426 7299 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 2.72 % Allowed : 8.74 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 3717 helix: 1.48 (0.20), residues: 698 sheet: 0.48 (0.16), residues: 933 loop : -0.31 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.009 0.002 HIS C 681 PHE 0.026 0.002 PHE A 977 TYR 0.023 0.002 TYR B 794 ARG 0.009 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 445 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7595 (ttp) cc_final: 0.7216 (ttm) REVERT: A 444 ASP cc_start: 0.7898 (m-30) cc_final: 0.7607 (m-30) REVERT: A 686 MET cc_start: 0.7960 (ttt) cc_final: 0.7599 (ttt) REVERT: A 1137 MET cc_start: 0.7885 (mpp) cc_final: 0.7488 (mtm) REVERT: H 89 LYS cc_start: 0.6928 (ttmt) cc_final: 0.6697 (ttmm) REVERT: H 92 ASP cc_start: 0.6703 (m-30) cc_final: 0.5263 (t70) REVERT: H 100 THR cc_start: 0.6306 (p) cc_final: 0.5904 (t) REVERT: D 28 THR cc_start: 0.8168 (t) cc_final: 0.7770 (t) REVERT: D 52 LYS cc_start: 0.8023 (mttp) cc_final: 0.7820 (mttp) REVERT: D 62 TYR cc_start: 0.8033 (m-80) cc_final: 0.7731 (m-10) REVERT: D 95 VAL cc_start: 0.7765 (t) cc_final: 0.7526 (m) REVERT: D 115 ASP cc_start: 0.7894 (p0) cc_final: 0.7598 (p0) REVERT: E 87 ASP cc_start: 0.7072 (m-30) cc_final: 0.6820 (m-30) REVERT: B 57 ILE cc_start: 0.8398 (mt) cc_final: 0.8186 (pt) REVERT: B 943 MET cc_start: 0.7542 (mtm) cc_final: 0.7237 (ttm) REVERT: B 1054 ILE cc_start: 0.9086 (pt) cc_final: 0.8881 (mt) REVERT: B 1084 GLN cc_start: 0.8003 (tp40) cc_final: 0.7593 (tp40) REVERT: B 1186 TYR cc_start: 0.8454 (t80) cc_final: 0.8237 (t80) REVERT: C 84 MET cc_start: 0.6645 (ptm) cc_final: 0.6334 (ptm) REVERT: C 144 TYR cc_start: 0.7982 (m-80) cc_final: 0.7697 (m-10) REVERT: C 245 ILE cc_start: 0.7999 (mt) cc_final: 0.7769 (mt) REVERT: C 254 PHE cc_start: 0.8085 (t80) cc_final: 0.7838 (t80) REVERT: C 292 TYR cc_start: 0.8179 (m-80) cc_final: 0.7953 (m-10) REVERT: C 563 MET cc_start: 0.8061 (tpt) cc_final: 0.7800 (tpt) REVERT: C 580 ASP cc_start: 0.7203 (t70) cc_final: 0.6964 (t0) REVERT: C 910 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: C 970 ILE cc_start: 0.8590 (mm) cc_final: 0.8372 (mm) REVERT: C 1008 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6433 (tmm) outliers start: 87 outliers final: 52 residues processed: 502 average time/residue: 0.3763 time to fit residues: 311.8684 Evaluate side-chains 383 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 329 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 978 TYR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1008 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 337 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 300 optimal weight: 0.3980 chunk 334 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 421 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 993 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 927 GLN C1016 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31634 Z= 0.227 Angle : 0.632 11.511 43020 Z= 0.318 Chirality : 0.045 0.224 5278 Planarity : 0.004 0.053 5317 Dihedral : 10.840 80.812 7299 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 3.01 % Allowed : 10.64 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.13), residues: 3717 helix: 1.51 (0.21), residues: 710 sheet: 0.53 (0.16), residues: 942 loop : -0.39 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.006 0.001 HIS C 681 PHE 0.024 0.002 PHE C 850 TYR 0.028 0.001 TYR L 88 ARG 0.008 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 364 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7568 (ttp) cc_final: 0.7207 (ttm) REVERT: A 444 ASP cc_start: 0.7883 (m-30) cc_final: 0.7606 (m-30) REVERT: A 686 MET cc_start: 0.7884 (ttt) cc_final: 0.7432 (ttt) REVERT: A 850 PHE cc_start: 0.8377 (m-80) cc_final: 0.8006 (m-10) REVERT: A 871 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7620 (pp) REVERT: A 1020 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 1038 SER cc_start: 0.8918 (t) cc_final: 0.8690 (p) REVERT: L 47 LYS cc_start: 0.6802 (pttm) cc_final: 0.5595 (tppt) REVERT: H 51 ILE cc_start: 0.6630 (tp) cc_final: 0.6421 (tt) REVERT: H 100 THR cc_start: 0.6584 (p) cc_final: 0.6169 (t) REVERT: D 62 TYR cc_start: 0.8160 (m-80) cc_final: 0.7786 (m-10) REVERT: D 115 ASP cc_start: 0.8001 (p0) cc_final: 0.7646 (p0) REVERT: B 943 MET cc_start: 0.7336 (mtm) cc_final: 0.6984 (ttm) REVERT: B 1084 GLN cc_start: 0.8049 (tp40) cc_final: 0.7575 (tp40) REVERT: C 84 MET cc_start: 0.6646 (ptm) cc_final: 0.6366 (ptm) REVERT: C 144 TYR cc_start: 0.8306 (m-80) cc_final: 0.7834 (m-10) REVERT: C 563 MET cc_start: 0.8132 (tpt) cc_final: 0.7917 (tpt) REVERT: C 970 ILE cc_start: 0.8630 (mm) cc_final: 0.8404 (mm) outliers start: 96 outliers final: 64 residues processed: 434 average time/residue: 0.3733 time to fit residues: 271.5426 Evaluate side-chains 362 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 297 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 1016 ASN Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1125 SER Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 0.6980 chunk 253 optimal weight: 0.0670 chunk 175 optimal weight: 0.0370 chunk 37 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 358 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 321 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 421 ASN A 708 GLN A 842 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 ASN B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31634 Z= 0.183 Angle : 0.600 11.515 43020 Z= 0.301 Chirality : 0.044 0.306 5278 Planarity : 0.004 0.064 5317 Dihedral : 9.571 76.219 7299 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 2.91 % Allowed : 11.93 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3717 helix: 1.64 (0.21), residues: 697 sheet: 0.48 (0.16), residues: 919 loop : -0.37 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 36 HIS 0.006 0.001 HIS C1138 PHE 0.016 0.001 PHE C 850 TYR 0.031 0.001 TYR L 88 ARG 0.004 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 338 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7611 (ttp) cc_final: 0.7244 (ttm) REVERT: A 202 THR cc_start: 0.7766 (p) cc_final: 0.7347 (p) REVERT: A 686 MET cc_start: 0.8021 (ttt) cc_final: 0.7536 (ttt) REVERT: A 850 PHE cc_start: 0.8259 (m-80) cc_final: 0.7919 (m-10) REVERT: A 871 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7662 (pp) REVERT: A 1020 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 1038 SER cc_start: 0.8897 (t) cc_final: 0.8651 (p) REVERT: L 47 LYS cc_start: 0.6490 (pttm) cc_final: 0.5428 (tppt) REVERT: H 85 MET cc_start: 0.7027 (ptp) cc_final: 0.6771 (ptp) REVERT: H 101 LEU cc_start: 0.6844 (tp) cc_final: 0.6623 (tt) REVERT: D 62 TYR cc_start: 0.8269 (m-80) cc_final: 0.7921 (m-80) REVERT: D 115 ASP cc_start: 0.7995 (p0) cc_final: 0.7600 (p0) REVERT: E 47 LYS cc_start: 0.8369 (tttt) cc_final: 0.8045 (tttp) REVERT: B 943 MET cc_start: 0.7329 (mtm) cc_final: 0.6968 (ttm) REVERT: B 1084 GLN cc_start: 0.8053 (tp40) cc_final: 0.7578 (tp40) REVERT: B 1153 TYR cc_start: 0.8307 (m-80) cc_final: 0.7970 (m-80) REVERT: C 84 MET cc_start: 0.6636 (ptm) cc_final: 0.6342 (ptm) REVERT: C 970 ILE cc_start: 0.8600 (mm) cc_final: 0.8383 (mm) outliers start: 93 outliers final: 65 residues processed: 402 average time/residue: 0.3648 time to fit residues: 246.4003 Evaluate side-chains 367 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 301 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 321 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS L 39 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN B1129 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31634 Z= 0.204 Angle : 0.608 12.132 43020 Z= 0.302 Chirality : 0.045 0.365 5278 Planarity : 0.004 0.062 5317 Dihedral : 8.556 69.157 7299 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 3.32 % Allowed : 12.21 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3717 helix: 1.76 (0.21), residues: 683 sheet: 0.39 (0.16), residues: 957 loop : -0.43 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 36 HIS 0.007 0.001 HIS C1138 PHE 0.020 0.002 PHE H 29 TYR 0.020 0.001 TYR B1186 ARG 0.003 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 332 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7624 (ttp) cc_final: 0.7250 (ttm) REVERT: A 168 THR cc_start: 0.9135 (m) cc_final: 0.8860 (p) REVERT: A 202 THR cc_start: 0.7823 (p) cc_final: 0.7402 (p) REVERT: A 686 MET cc_start: 0.8052 (ttt) cc_final: 0.7585 (ttt) REVERT: A 850 PHE cc_start: 0.8268 (m-80) cc_final: 0.8014 (m-10) REVERT: A 871 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7746 (pp) REVERT: A 1020 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 1038 SER cc_start: 0.8868 (t) cc_final: 0.8629 (p) REVERT: D 62 TYR cc_start: 0.8261 (m-80) cc_final: 0.8026 (m-80) REVERT: D 115 ASP cc_start: 0.8002 (p0) cc_final: 0.7613 (p0) REVERT: E 47 LYS cc_start: 0.8365 (tttt) cc_final: 0.8038 (tttp) REVERT: E 84 ASP cc_start: 0.7450 (t0) cc_final: 0.7210 (t0) REVERT: B 943 MET cc_start: 0.7224 (mtm) cc_final: 0.6845 (ttm) REVERT: B 1084 GLN cc_start: 0.8069 (tp40) cc_final: 0.7575 (tp40) REVERT: C 84 MET cc_start: 0.6641 (ptm) cc_final: 0.6353 (ptm) REVERT: C 156 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: C 204 PHE cc_start: 0.6587 (p90) cc_final: 0.6362 (p90) REVERT: C 827 PHE cc_start: 0.7858 (t80) cc_final: 0.7603 (t80) REVERT: C 939 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7168 (ttm) REVERT: C 994 GLN cc_start: 0.6964 (pm20) cc_final: 0.6762 (pm20) outliers start: 106 outliers final: 71 residues processed: 403 average time/residue: 0.3708 time to fit residues: 251.2476 Evaluate side-chains 377 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 303 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 188 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 842 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B1042 ASN B1122 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31634 Z= 0.215 Angle : 0.610 10.388 43020 Z= 0.303 Chirality : 0.045 0.284 5278 Planarity : 0.004 0.064 5317 Dihedral : 7.845 63.514 7299 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.26 % Allowed : 12.52 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3717 helix: 1.78 (0.21), residues: 683 sheet: 0.37 (0.16), residues: 945 loop : -0.49 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.007 0.001 HIS C1138 PHE 0.022 0.002 PHE H 29 TYR 0.020 0.001 TYR B1186 ARG 0.003 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 321 time to evaluate : 3.313 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 84 MET cc_start: 0.7647 (ttp) cc_final: 0.7290 (ttm) REVERT: A 168 THR cc_start: 0.9128 (m) cc_final: 0.8858 (p) REVERT: A 202 THR cc_start: 0.7889 (p) cc_final: 0.7487 (p) REVERT: A 731 LEU cc_start: 0.8564 (mp) cc_final: 0.8316 (mp) REVERT: A 850 PHE cc_start: 0.8417 (m-80) cc_final: 0.8168 (m-10) REVERT: A 871 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7688 (pp) REVERT: A 1038 SER cc_start: 0.8902 (t) cc_final: 0.8658 (p) REVERT: L 47 LYS cc_start: 0.6370 (pttm) cc_final: 0.5196 (tppt) REVERT: L 54 ILE cc_start: 0.7438 (tp) cc_final: 0.7021 (mm) REVERT: H 27 LEU cc_start: 0.1672 (OUTLIER) cc_final: 0.1372 (pp) REVERT: H 34 MET cc_start: 0.5794 (mmm) cc_final: 0.5374 (mmm) REVERT: D 34 MET cc_start: 0.5363 (ptt) cc_final: 0.5116 (ptt) REVERT: D 43 LYS cc_start: 0.6833 (ptmt) cc_final: 0.6598 (ptmt) REVERT: D 52 LYS cc_start: 0.7934 (mttp) cc_final: 0.7363 (mmtp) REVERT: D 62 TYR cc_start: 0.8156 (m-80) cc_final: 0.7943 (m-80) REVERT: D 85 MET cc_start: 0.3987 (mtt) cc_final: 0.3715 (mtt) REVERT: D 115 ASP cc_start: 0.7974 (p0) cc_final: 0.7626 (p0) REVERT: E 47 LYS cc_start: 0.8459 (tttt) cc_final: 0.8159 (tttp) REVERT: E 84 ASP cc_start: 0.7557 (t0) cc_final: 0.7209 (t0) REVERT: B 943 MET cc_start: 0.7396 (mtm) cc_final: 0.7014 (ttm) REVERT: B 1019 PHE cc_start: 0.7913 (t80) cc_final: 0.7697 (t80) REVERT: B 1084 GLN cc_start: 0.8083 (tp40) cc_final: 0.7575 (tp40) REVERT: C 84 MET cc_start: 0.6675 (ptm) cc_final: 0.6389 (ptm) REVERT: C 156 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5125 (m-10) REVERT: C 827 PHE cc_start: 0.7862 (t80) cc_final: 0.7524 (t80) REVERT: C 858 SER cc_start: 0.8286 (t) cc_final: 0.7793 (p) REVERT: C 939 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7161 (ttm) outliers start: 104 outliers final: 79 residues processed: 392 average time/residue: 0.3783 time to fit residues: 246.6773 Evaluate side-chains 372 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 289 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1214 ILE Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31634 Z= 0.243 Angle : 0.629 13.340 43020 Z= 0.312 Chirality : 0.045 0.245 5278 Planarity : 0.004 0.061 5317 Dihedral : 7.597 60.680 7299 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 3.44 % Allowed : 12.81 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3717 helix: 1.72 (0.21), residues: 683 sheet: 0.24 (0.16), residues: 961 loop : -0.56 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 36 HIS 0.007 0.001 HIS C1138 PHE 0.024 0.002 PHE H 29 TYR 0.032 0.001 TYR L 88 ARG 0.003 0.000 ARG B 822 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 303 time to evaluate : 3.731 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 84 MET cc_start: 0.7630 (ttp) cc_final: 0.7265 (ttm) REVERT: A 168 THR cc_start: 0.9123 (m) cc_final: 0.8860 (p) REVERT: A 202 THR cc_start: 0.7935 (p) cc_final: 0.7547 (p) REVERT: A 731 LEU cc_start: 0.8694 (mp) cc_final: 0.8471 (mp) REVERT: A 850 PHE cc_start: 0.8403 (m-80) cc_final: 0.8123 (m-10) REVERT: A 871 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7732 (pp) REVERT: A 1038 SER cc_start: 0.8948 (t) cc_final: 0.8726 (p) REVERT: L 47 LYS cc_start: 0.6361 (pttm) cc_final: 0.5304 (tppt) REVERT: L 54 ILE cc_start: 0.7478 (tp) cc_final: 0.7123 (mm) REVERT: H 27 LEU cc_start: 0.1781 (OUTLIER) cc_final: 0.1456 (pp) REVERT: D 80 THR cc_start: 0.4642 (OUTLIER) cc_final: 0.4283 (t) REVERT: D 115 ASP cc_start: 0.7849 (p0) cc_final: 0.7533 (p0) REVERT: E 16 GLN cc_start: 0.8129 (mp10) cc_final: 0.7845 (mp10) REVERT: E 47 LYS cc_start: 0.8471 (tttt) cc_final: 0.8226 (tttp) REVERT: E 84 ASP cc_start: 0.7676 (t0) cc_final: 0.7333 (t0) REVERT: B 78 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8176 (tp-100) REVERT: B 943 MET cc_start: 0.7422 (mtm) cc_final: 0.7022 (ttm) REVERT: B 1084 GLN cc_start: 0.8103 (tp40) cc_final: 0.7581 (tp40) REVERT: C 84 MET cc_start: 0.6709 (ptm) cc_final: 0.6415 (ptm) REVERT: C 156 PHE cc_start: 0.5658 (OUTLIER) cc_final: 0.5216 (m-10) REVERT: C 939 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7329 (ttm) REVERT: C 1200 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8072 (mm) outliers start: 110 outliers final: 89 residues processed: 381 average time/residue: 0.3603 time to fit residues: 231.5405 Evaluate side-chains 392 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 296 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 740 ASP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1214 ILE Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 213 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 33 optimal weight: 0.0060 chunk 281 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31634 Z= 0.222 Angle : 0.622 11.133 43020 Z= 0.307 Chirality : 0.045 0.585 5278 Planarity : 0.004 0.064 5317 Dihedral : 7.399 58.386 7299 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 3.29 % Allowed : 13.34 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3717 helix: 1.78 (0.21), residues: 683 sheet: 0.21 (0.16), residues: 967 loop : -0.58 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.006 0.001 HIS C1138 PHE 0.019 0.002 PHE B 786 TYR 0.036 0.001 TYR L 88 ARG 0.005 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 301 time to evaluate : 3.826 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 84 MET cc_start: 0.7628 (ttp) cc_final: 0.7260 (ttm) REVERT: A 168 THR cc_start: 0.9119 (m) cc_final: 0.8853 (p) REVERT: A 202 THR cc_start: 0.7979 (p) cc_final: 0.7608 (p) REVERT: A 686 MET cc_start: 0.8507 (tpp) cc_final: 0.8208 (tpp) REVERT: A 731 LEU cc_start: 0.8714 (mp) cc_final: 0.8462 (mp) REVERT: A 850 PHE cc_start: 0.8386 (m-80) cc_final: 0.8099 (m-10) REVERT: A 871 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7710 (pp) REVERT: A 1038 SER cc_start: 0.8937 (t) cc_final: 0.8720 (p) REVERT: L 47 LYS cc_start: 0.6310 (pttm) cc_final: 0.5296 (tppt) REVERT: L 54 ILE cc_start: 0.7478 (tp) cc_final: 0.7153 (mm) REVERT: L 88 TYR cc_start: 0.6815 (m-80) cc_final: 0.6615 (m-80) REVERT: H 27 LEU cc_start: 0.1599 (OUTLIER) cc_final: 0.1257 (pp) REVERT: D 52 LYS cc_start: 0.7942 (mttp) cc_final: 0.7597 (mtmt) REVERT: D 62 TYR cc_start: 0.7500 (m-80) cc_final: 0.7083 (m-10) REVERT: D 80 THR cc_start: 0.4651 (OUTLIER) cc_final: 0.4279 (t) REVERT: E 47 LYS cc_start: 0.8459 (tttt) cc_final: 0.8203 (tttp) REVERT: E 84 ASP cc_start: 0.7762 (t0) cc_final: 0.7383 (t0) REVERT: B 240 MET cc_start: 0.7169 (ttt) cc_final: 0.6183 (ttt) REVERT: B 943 MET cc_start: 0.7475 (mtm) cc_final: 0.7043 (ttm) REVERT: B 1019 PHE cc_start: 0.7945 (t80) cc_final: 0.7741 (t80) REVERT: B 1084 GLN cc_start: 0.8087 (tp40) cc_final: 0.7579 (tp40) REVERT: C 84 MET cc_start: 0.6700 (ptm) cc_final: 0.6416 (ptm) REVERT: C 156 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5217 (m-10) REVERT: C 939 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7345 (ttm) outliers start: 105 outliers final: 89 residues processed: 373 average time/residue: 0.3724 time to fit residues: 233.1390 Evaluate side-chains 379 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 285 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 740 ASP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 689 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 2.9990 chunk 342 optimal weight: 0.5980 chunk 312 optimal weight: 0.5980 chunk 333 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 145 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 332 optimal weight: 0.3980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 842 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31634 Z= 0.191 Angle : 0.616 10.885 43020 Z= 0.303 Chirality : 0.045 0.397 5278 Planarity : 0.004 0.062 5317 Dihedral : 7.163 56.713 7299 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 13.87 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3717 helix: 1.84 (0.21), residues: 683 sheet: 0.24 (0.16), residues: 946 loop : -0.55 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 36 HIS 0.005 0.001 HIS C1138 PHE 0.022 0.001 PHE H 29 TYR 0.029 0.001 TYR L 88 ARG 0.013 0.000 ARG C 629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 312 time to evaluate : 3.203 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 84 MET cc_start: 0.7563 (ttp) cc_final: 0.7180 (ttm) REVERT: A 202 THR cc_start: 0.7997 (p) cc_final: 0.7639 (p) REVERT: A 686 MET cc_start: 0.8588 (tpp) cc_final: 0.8330 (tpp) REVERT: A 731 LEU cc_start: 0.8721 (mp) cc_final: 0.8501 (mp) REVERT: A 850 PHE cc_start: 0.8347 (m-80) cc_final: 0.8082 (m-10) REVERT: A 871 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7771 (pp) REVERT: A 1038 SER cc_start: 0.8895 (t) cc_final: 0.8674 (p) REVERT: L 47 LYS cc_start: 0.6208 (pttm) cc_final: 0.5231 (tppt) REVERT: L 54 ILE cc_start: 0.7581 (tp) cc_final: 0.7318 (mm) REVERT: H 27 LEU cc_start: 0.2118 (OUTLIER) cc_final: 0.1658 (pp) REVERT: D 62 TYR cc_start: 0.7517 (m-80) cc_final: 0.7091 (m-10) REVERT: D 70 PHE cc_start: 0.7799 (m-10) cc_final: 0.7384 (m-10) REVERT: E 47 LYS cc_start: 0.8445 (tttt) cc_final: 0.8213 (tttp) REVERT: E 84 ASP cc_start: 0.7757 (t0) cc_final: 0.7419 (t0) REVERT: B 78 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8360 (tp-100) REVERT: B 846 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 943 MET cc_start: 0.7419 (mtm) cc_final: 0.7011 (ttm) REVERT: B 1084 GLN cc_start: 0.8101 (tp40) cc_final: 0.7587 (tp40) REVERT: C 84 MET cc_start: 0.6694 (ptm) cc_final: 0.6426 (ptm) REVERT: C 156 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: C 224 SER cc_start: 0.8850 (m) cc_final: 0.8529 (p) REVERT: C 254 PHE cc_start: 0.8320 (t80) cc_final: 0.8062 (t80) REVERT: C 628 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: C 939 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7339 (ttm) outliers start: 99 outliers final: 80 residues processed: 383 average time/residue: 0.3678 time to fit residues: 237.2052 Evaluate side-chains 385 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 298 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 740 ASP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 815 GLN Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 681 HIS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 369 optimal weight: 0.6980 chunk 340 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 836 HIS B1042 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31634 Z= 0.278 Angle : 0.665 11.064 43020 Z= 0.329 Chirality : 0.046 0.358 5278 Planarity : 0.004 0.067 5317 Dihedral : 7.302 58.035 7299 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.51 % Rotamer: Outliers : 3.01 % Allowed : 14.31 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3717 helix: 1.64 (0.21), residues: 683 sheet: 0.16 (0.16), residues: 941 loop : -0.69 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.007 0.001 HIS C1138 PHE 0.022 0.002 PHE B 786 TYR 0.022 0.002 TYR E 89 ARG 0.006 0.000 ARG L 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 303 time to evaluate : 3.010 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 84 MET cc_start: 0.7617 (ttp) cc_final: 0.7235 (ttm) REVERT: A 202 THR cc_start: 0.8016 (p) cc_final: 0.7671 (p) REVERT: A 731 LEU cc_start: 0.8775 (mp) cc_final: 0.8515 (mp) REVERT: A 850 PHE cc_start: 0.8391 (m-80) cc_final: 0.8090 (m-10) REVERT: A 871 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7734 (pp) REVERT: L 54 ILE cc_start: 0.7617 (tp) cc_final: 0.7336 (mm) REVERT: H 27 LEU cc_start: 0.1656 (OUTLIER) cc_final: 0.1191 (pp) REVERT: D 52 LYS cc_start: 0.7983 (mttp) cc_final: 0.7756 (mtmt) REVERT: D 62 TYR cc_start: 0.7584 (m-80) cc_final: 0.7214 (m-10) REVERT: D 70 PHE cc_start: 0.8107 (m-10) cc_final: 0.7835 (m-80) REVERT: E 47 LYS cc_start: 0.8456 (tttt) cc_final: 0.8206 (tttp) REVERT: B 78 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8065 (tp-100) REVERT: B 303 ILE cc_start: 0.6651 (pp) cc_final: 0.6349 (mm) REVERT: B 943 MET cc_start: 0.7407 (mtm) cc_final: 0.7027 (ttm) REVERT: B 1084 GLN cc_start: 0.8125 (tp40) cc_final: 0.7585 (tp40) REVERT: C 84 MET cc_start: 0.6768 (ptm) cc_final: 0.6485 (ptm) REVERT: C 156 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.5273 (m-10) REVERT: C 224 SER cc_start: 0.8899 (m) cc_final: 0.8586 (p) REVERT: C 452 MET cc_start: 0.8323 (mtm) cc_final: 0.8086 (mtp) REVERT: C 757 MET cc_start: 0.7789 (mtp) cc_final: 0.7405 (mtp) REVERT: C 939 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7382 (ttm) outliers start: 96 outliers final: 83 residues processed: 373 average time/residue: 0.3649 time to fit residues: 227.4869 Evaluate side-chains 377 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 289 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 108 TRP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 740 ASP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 689 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 0.1980 chunk 313 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B1042 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.141997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113080 restraints weight = 59941.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116116 restraints weight = 35810.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116230 restraints weight = 24710.997| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31634 Z= 0.239 Angle : 0.644 11.009 43020 Z= 0.318 Chirality : 0.045 0.322 5278 Planarity : 0.004 0.062 5317 Dihedral : 7.222 58.947 7299 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 3.01 % Allowed : 14.62 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3717 helix: 1.67 (0.21), residues: 683 sheet: 0.12 (0.16), residues: 948 loop : -0.71 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.006 0.001 HIS C1138 PHE 0.022 0.002 PHE L 64 TYR 0.037 0.001 TYR D 82 ARG 0.007 0.000 ARG C 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6147.94 seconds wall clock time: 112 minutes 35.92 seconds (6755.92 seconds total)