Starting phenix.real_space_refine on Sat Apr 13 04:27:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d5a_27207/04_2024/8d5a_27207.pdb" } resolution = 3.1 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= -0.000 sd= 0.011 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 120 5.16 5 C 17622 2.51 5 N 4487 2.21 5 O 5482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27711 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8773 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 52, 'TRANS': 1065} Chain breaks: 4 Chain: "B" Number of atoms: 8822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8822 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 52, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8796 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "a" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 14.57, per 1000 atoms: 0.53 Number of scatterers: 27711 At special positions: 0 Unit cell: (146.08, 151.06, 205.84, 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 120 16.00 O 5482 8.00 N 4487 7.00 C 17622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.99 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.00 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG F 2 " - " MAN F 3 " " NAG H 2 " - " MAN H 3 " " NAG I 2 " - " MAN I 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 282 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1074 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.60 Conformation dependent library (CDL) restraints added in 4.8 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 45 sheets defined 27.1% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.619A pdb=" N LEU A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.602A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.802A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.735A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.593A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.544A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.971A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.743A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.449A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.803A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.313A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.580A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.336A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.452A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.569A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.248A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.248A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.762A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.842A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.680A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.203A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.885A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.713A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.913A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.543A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.657A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.310A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.654A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.123A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.626A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.829A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 removed outlier: 3.610A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.337A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.687A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.716A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.845A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.589A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 31 removed outlier: 3.533A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.813A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.772A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.834A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.022A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.765A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.253A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 20 through 31 removed outlier: 3.760A pdb=" N HIS B 66 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.672A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.817A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 141 through 146 removed outlier: 8.445A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.547A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.111A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.970A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.735A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.517A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.527A pdb=" N THR C 20 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 68 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.669A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.357A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.641A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.386A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.555A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.889A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 1112 hydrogen bonds defined for protein. 3042 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: 12.08 Time building geometry restraints manager: 12.51 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: 5166 1.32 - 1.45: 7390 1.45 - 1.58: 15630 1.58 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 28336 Sorted by residual: bond pdb=" N PHE A 490 " pdb=" CA PHE A 490 " ideal model delta sigma weight residual 1.457 1.542 -0.085 1.41e-02 5.03e+03 3.61e+01 bond pdb=" C PHE A 490 " pdb=" N PRO A 491 " ideal model delta sigma weight residual 1.331 1.400 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 1.520 1.562 -0.042 8.80e-03 1.29e+04 2.27e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C5 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.413 1.505 -0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 28331 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.69: 428 104.69 - 112.80: 13337 112.80 - 120.91: 15863 120.91 - 129.02: 8817 129.02 - 137.13: 92 Bond angle restraints: 38537 Sorted by residual: angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 108.34 123.18 -14.84 1.64e+00 3.72e-01 8.19e+01 angle pdb=" OD1 ASN C 331 " pdb=" CG ASN C 331 " pdb=" ND2 ASN C 331 " ideal model delta sigma weight residual 122.60 113.60 9.00 1.00e+00 1.00e+00 8.09e+01 angle pdb=" C ASP A 215 " pdb=" N LEU A 216 " pdb=" CA LEU A 216 " ideal model delta sigma weight residual 122.28 129.94 -7.66 8.80e-01 1.29e+00 7.57e+01 angle pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " pdb=" CG ASN B 709 " ideal model delta sigma weight residual 112.60 120.60 -8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" N ARG A 34 " pdb=" CA ARG A 34 " pdb=" C ARG A 34 " ideal model delta sigma weight residual 110.53 120.95 -10.42 1.32e+00 5.74e-01 6.23e+01 ... (remaining 38532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 17141 24.73 - 49.46: 725 49.46 - 74.19: 163 74.19 - 98.91: 45 98.91 - 123.64: 52 Dihedral angle restraints: 18126 sinusoidal: 8316 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS B 617 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual -122.60 -140.64 18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual 122.80 139.82 -17.02 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 18123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 4601 0.368 - 0.737: 24 0.737 - 1.105: 2 1.105 - 1.474: 2 1.474 - 1.842: 2 Chirality restraints: 4631 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 ... (remaining 4628 not shown) Planarity restraints: 4883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.170 2.00e-02 2.50e+03 2.06e-01 5.29e+02 pdb=" CG ASN B 709 " 0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.338 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.156 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 709 " 0.109 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.297 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.020 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" CG ASN A 603 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.176 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.186 2.00e-02 2.50e+03 ... (remaining 4880 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 22 2.25 - 2.91: 10520 2.91 - 3.58: 37530 3.58 - 4.24: 63706 4.24 - 4.90: 106777 Nonbonded interactions: 218555 Sorted by model distance: nonbonded pdb=" CG2 THR A 20 " pdb=" OD2 ASP A 80 " model vdw 1.589 3.460 nonbonded pdb=" CE1 PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.646 3.760 nonbonded pdb=" CZ PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.685 3.760 nonbonded pdb=" OH TYR C 453 " pdb=" CD2 LEU C 492 " model vdw 1.903 3.460 nonbonded pdb=" O MET C 900 " pdb=" CD1 TYR C 904 " model vdw 1.925 3.340 ... (remaining 218550 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' and (resid 14 through 624 or resid 631 through 1162 or resid 1401 thr \ ough 1406)) selection = (chain 'B' and (resid 14 through 624 or resid 631 through 827 or resid 832 throu \ gh 1162 or resid 1401 through 1406)) selection = (chain 'C' and (resid 14 through 71 or resid 80 through 624 or resid 631 through \ 827 or resid 832 through 1162 or resid 1401 through 1406)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 23.640 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 76.110 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.016 0.095 28336 Z= 1.051 Angle : 1.998 14.843 38537 Z= 1.309 Chirality : 0.129 1.842 4631 Planarity : 0.014 0.124 4834 Dihedral : 16.442 123.642 11689 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 1.62 % Allowed : 6.68 % Favored : 91.70 % Rotamer: Outliers : 2.22 % Allowed : 6.14 % Favored : 91.64 % Cbeta Deviations : 0.54 % 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: -2.19 (0.13), residues: 3339 helix: -1.90 (0.15), residues: 777 sheet: 0.10 (0.20), residues: 601 loop : -1.82 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.025 TRP B 104 HIS 0.035 0.008 HIS A 69 PHE 0.114 0.016 PHE B 497 TYR 0.118 0.022 TYR C 449 ARG 0.028 0.002 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 167 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: A 29 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7587 (m) REVERT: A 152 TRP cc_start: 0.8752 (m100) cc_final: 0.7783 (m100) REVERT: A 429 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 814 LYS cc_start: 0.9118 (mttt) cc_final: 0.8852 (mmtt) REVERT: A 1029 MET cc_start: 0.9543 (tpp) cc_final: 0.9201 (tpt) REVERT: B 374 PHE cc_start: 0.7595 (p90) cc_final: 0.6898 (p90) REVERT: B 394 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 634 ARG cc_start: 0.7289 (ttp80) cc_final: 0.6558 (ttp80) REVERT: B 988 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: C 54 LEU cc_start: 0.8884 (mt) cc_final: 0.8648 (mt) REVERT: C 104 TRP cc_start: 0.6691 (m-90) cc_final: 0.6270 (m-90) REVERT: C 117 LEU cc_start: 0.7584 (tt) cc_final: 0.7155 (mm) REVERT: C 391 CYS cc_start: -0.2473 (OUTLIER) cc_final: -0.4090 (p) outliers start: 65 outliers final: 16 residues processed: 230 average time/residue: 0.4545 time to fit residues: 164.5649 Evaluate side-chains 108 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.7980 chunk 253 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 183 GLN A 394 ASN A 677 GLN B 52 GLN B 183 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 460 ASN B 506 GLN B 519 HIS B 762 GLN B 955 ASN B1002 GLN C 450 ASN C 762 GLN C 955 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28336 Z= 0.225 Angle : 0.753 10.906 38537 Z= 0.378 Chirality : 0.050 0.756 4631 Planarity : 0.005 0.071 4834 Dihedral : 13.380 115.104 5694 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.91 % Favored : 94.64 % Rotamer: Outliers : 2.12 % Allowed : 8.33 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3339 helix: 0.20 (0.18), residues: 793 sheet: 0.11 (0.19), residues: 715 loop : -1.57 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 633 HIS 0.006 0.001 HIS B1048 PHE 0.035 0.002 PHE B 374 TYR 0.027 0.002 TYR A 160 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 104 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 814 LYS cc_start: 0.9162 (mttt) cc_final: 0.8911 (mmtt) REVERT: A 867 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8222 (p0) REVERT: B 394 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.8018 (p0) REVERT: B 634 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6542 (ttp80) REVERT: B 902 MET cc_start: 0.9246 (mmt) cc_final: 0.8958 (mmt) REVERT: B 988 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: C 565 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6309 (p90) outliers start: 62 outliers final: 31 residues processed: 157 average time/residue: 0.4151 time to fit residues: 106.6761 Evaluate side-chains 120 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 703 ASN A1005 GLN B 787 GLN B1005 GLN C 66 HIS C 460 ASN C 519 HIS C 804 GLN C 914 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28336 Z= 0.251 Angle : 0.683 11.544 38537 Z= 0.330 Chirality : 0.047 0.549 4631 Planarity : 0.004 0.078 4834 Dihedral : 11.763 110.864 5682 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.05 % Favored : 93.59 % Rotamer: Outliers : 2.32 % Allowed : 9.49 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3339 helix: 0.86 (0.18), residues: 807 sheet: 0.30 (0.19), residues: 704 loop : -1.46 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 152 HIS 0.012 0.001 HIS A 245 PHE 0.031 0.002 PHE C 855 TYR 0.020 0.002 TYR C 495 ARG 0.012 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 98 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 177 MET cc_start: 0.8078 (ppp) cc_final: 0.7563 (ppp) REVERT: A 190 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7733 (mtp85) REVERT: A 429 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 814 LYS cc_start: 0.9208 (mttt) cc_final: 0.8955 (mmtt) REVERT: A 867 ASP cc_start: 0.8613 (m-30) cc_final: 0.8246 (p0) REVERT: B 515 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8670 (p90) REVERT: B 634 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6480 (ttp80) REVERT: B 636 TYR cc_start: 0.6711 (m-80) cc_final: 0.6414 (m-80) REVERT: B 988 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: C 102 ARG cc_start: 0.6811 (mmt-90) cc_final: 0.6104 (mmp-170) outliers start: 68 outliers final: 34 residues processed: 157 average time/residue: 0.3769 time to fit residues: 100.5829 Evaluate side-chains 124 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 121 ASN C 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 28336 Z= 0.396 Angle : 0.705 10.472 38537 Z= 0.340 Chirality : 0.048 0.537 4631 Planarity : 0.004 0.077 4834 Dihedral : 10.879 111.042 5672 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.60 % Favored : 94.07 % Rotamer: Outliers : 2.32 % Allowed : 10.72 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3339 helix: 0.87 (0.18), residues: 811 sheet: 0.16 (0.19), residues: 720 loop : -1.54 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 152 HIS 0.006 0.001 HIS C1058 PHE 0.024 0.002 PHE B 823 TYR 0.022 0.002 TYR C 495 ARG 0.008 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 87 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 633 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7689 (p-90) REVERT: A 636 TYR cc_start: 0.7297 (m-80) cc_final: 0.7086 (m-80) REVERT: A 814 LYS cc_start: 0.9205 (mttt) cc_final: 0.8940 (mmtt) REVERT: A 867 ASP cc_start: 0.8654 (m-30) cc_final: 0.8295 (p0) REVERT: A 1125 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.9041 (p0) REVERT: B 515 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8694 (p90) REVERT: B 634 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6481 (ttp80) REVERT: B 988 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: C 351 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.4921 (p90) REVERT: C 425 LEU cc_start: -0.2954 (OUTLIER) cc_final: -0.3259 (pp) outliers start: 68 outliers final: 40 residues processed: 146 average time/residue: 0.3857 time to fit residues: 95.1489 Evaluate side-chains 132 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 85 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 675 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28336 Z= 0.206 Angle : 0.630 9.693 38537 Z= 0.302 Chirality : 0.045 0.475 4631 Planarity : 0.004 0.078 4834 Dihedral : 10.160 108.693 5670 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.21 % Favored : 94.49 % Rotamer: Outliers : 2.22 % Allowed : 10.92 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3339 helix: 1.18 (0.19), residues: 806 sheet: 0.16 (0.19), residues: 739 loop : -1.44 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.020 0.001 PHE B 823 TYR 0.020 0.001 TYR C 495 ARG 0.006 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 95 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 633 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.7726 (p-90) REVERT: A 814 LYS cc_start: 0.9217 (mttt) cc_final: 0.8975 (mmtt) REVERT: A 867 ASP cc_start: 0.8618 (m-30) cc_final: 0.8196 (p0) REVERT: A 1125 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (p0) REVERT: B 634 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6408 (ttp80) REVERT: B 830 ASP cc_start: 0.8322 (t0) cc_final: 0.7788 (t70) REVERT: B 988 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: C 102 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6101 (mmp-170) REVERT: C 351 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.4902 (p90) REVERT: C 425 LEU cc_start: -0.3000 (OUTLIER) cc_final: -0.3287 (pp) outliers start: 65 outliers final: 41 residues processed: 149 average time/residue: 0.3858 time to fit residues: 98.9512 Evaluate side-chains 134 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 0.7980 chunk 291 optimal weight: 0.0980 chunk 64 optimal weight: 0.0970 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 324 optimal weight: 3.9990 chunk 269 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 121 ASN C 677 GLN C 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 28336 Z= 0.155 Angle : 0.608 9.364 38537 Z= 0.289 Chirality : 0.044 0.455 4631 Planarity : 0.004 0.082 4834 Dihedral : 9.598 105.846 5670 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.06 % Favored : 94.64 % Rotamer: Outliers : 2.42 % Allowed : 10.89 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3339 helix: 1.36 (0.19), residues: 799 sheet: 0.23 (0.19), residues: 726 loop : -1.36 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE B 375 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 94 time to evaluate : 2.960 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 118 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 177 MET cc_start: 0.8087 (ppp) cc_final: 0.7133 (ppp) REVERT: A 179 LEU cc_start: 0.3125 (OUTLIER) cc_final: 0.2859 (pp) REVERT: A 190 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7728 (mtp-110) REVERT: A 571 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 633 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7634 (p-90) REVERT: A 814 LYS cc_start: 0.9167 (mttt) cc_final: 0.8950 (mmtt) REVERT: A 867 ASP cc_start: 0.8606 (m-30) cc_final: 0.8197 (p0) REVERT: A 1125 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8862 (p0) REVERT: B 634 ARG cc_start: 0.7111 (ttp80) cc_final: 0.6370 (ttp80) REVERT: B 830 ASP cc_start: 0.8212 (t0) cc_final: 0.7697 (t70) REVERT: B 988 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: C 102 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6081 (mmp-170) REVERT: C 351 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.4837 (p90) REVERT: C 425 LEU cc_start: -0.2878 (OUTLIER) cc_final: -0.3143 (pp) outliers start: 71 outliers final: 46 residues processed: 154 average time/residue: 0.3739 time to fit residues: 98.1409 Evaluate side-chains 147 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 91 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 675 GLN B 409 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28336 Z= 0.294 Angle : 0.632 9.143 38537 Z= 0.302 Chirality : 0.045 0.469 4631 Planarity : 0.004 0.074 4834 Dihedral : 9.357 104.757 5670 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.69 % Favored : 93.98 % Rotamer: Outliers : 2.49 % Allowed : 11.02 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3339 helix: 1.19 (0.18), residues: 813 sheet: 0.14 (0.18), residues: 747 loop : -1.42 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 258 HIS 0.004 0.001 HIS B 245 PHE 0.018 0.001 PHE B 375 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 96 time to evaluate : 3.119 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 118 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 177 MET cc_start: 0.8153 (ppp) cc_final: 0.7821 (ppp) REVERT: A 571 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 633 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.7773 (p-90) REVERT: A 814 LYS cc_start: 0.9177 (mttt) cc_final: 0.8944 (mmtt) REVERT: A 867 ASP cc_start: 0.8698 (m-30) cc_final: 0.8273 (p0) REVERT: A 1125 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8927 (p0) REVERT: B 515 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8740 (p90) REVERT: B 586 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: B 634 ARG cc_start: 0.7155 (ttp80) cc_final: 0.6413 (ttp80) REVERT: B 830 ASP cc_start: 0.8290 (t0) cc_final: 0.7788 (t70) REVERT: B 988 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: C 102 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6184 (mmp-170) REVERT: C 220 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7746 (t80) REVERT: C 351 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.4775 (p90) REVERT: C 425 LEU cc_start: -0.2879 (OUTLIER) cc_final: -0.3136 (pp) REVERT: C 633 TRP cc_start: 0.8410 (OUTLIER) cc_final: 0.8108 (p-90) REVERT: C 830 ASP cc_start: 0.8163 (t0) cc_final: 0.7947 (t0) outliers start: 73 outliers final: 50 residues processed: 156 average time/residue: 0.3794 time to fit residues: 100.7956 Evaluate side-chains 149 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 87 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 253 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 121 ASN C 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28336 Z= 0.164 Angle : 0.595 9.211 38537 Z= 0.282 Chirality : 0.044 0.409 4631 Planarity : 0.004 0.073 4834 Dihedral : 9.057 102.806 5670 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.00 % Favored : 94.67 % Rotamer: Outliers : 2.25 % Allowed : 11.43 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3339 helix: 1.34 (0.19), residues: 815 sheet: 0.19 (0.19), residues: 731 loop : -1.33 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 PHE 0.020 0.001 PHE B 375 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 91 time to evaluate : 3.466 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 118 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 135 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: A 177 MET cc_start: 0.8053 (ppp) cc_final: 0.7818 (ppp) REVERT: A 571 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7956 (t0) REVERT: A 633 TRP cc_start: 0.8394 (OUTLIER) cc_final: 0.7698 (p-90) REVERT: A 636 TYR cc_start: 0.7202 (m-80) cc_final: 0.6877 (m-80) REVERT: A 814 LYS cc_start: 0.9163 (mttt) cc_final: 0.8950 (mmtt) REVERT: A 867 ASP cc_start: 0.8652 (m-30) cc_final: 0.8198 (p0) REVERT: A 1125 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8855 (p0) REVERT: B 586 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 830 ASP cc_start: 0.8202 (t0) cc_final: 0.7698 (t70) REVERT: B 988 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: C 102 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6136 (mmp-170) REVERT: C 220 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7699 (t80) REVERT: C 351 TYR cc_start: 0.5287 (OUTLIER) cc_final: 0.4785 (p90) REVERT: C 425 LEU cc_start: -0.2782 (OUTLIER) cc_final: -0.3013 (pp) REVERT: C 633 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.8121 (p-90) REVERT: C 830 ASP cc_start: 0.8073 (t0) cc_final: 0.7842 (t0) REVERT: C 1155 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.3596 (m-10) outliers start: 66 outliers final: 48 residues processed: 147 average time/residue: 0.3537 time to fit residues: 89.9966 Evaluate side-chains 147 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 86 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 0.9980 chunk 309 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 0.0370 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 284 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28336 Z= 0.197 Angle : 0.594 10.610 38537 Z= 0.281 Chirality : 0.044 0.419 4631 Planarity : 0.004 0.069 4834 Dihedral : 8.752 101.451 5670 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.27 % Favored : 94.43 % Rotamer: Outliers : 2.25 % Allowed : 11.40 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3339 helix: 1.39 (0.19), residues: 815 sheet: 0.20 (0.19), residues: 732 loop : -1.32 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 152 HIS 0.004 0.001 HIS B 245 PHE 0.020 0.001 PHE B 375 TYR 0.021 0.001 TYR C 904 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 86 time to evaluate : 3.541 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 118 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 135 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: A 177 MET cc_start: 0.8103 (ppp) cc_final: 0.7870 (ppp) REVERT: A 571 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 633 TRP cc_start: 0.8388 (OUTLIER) cc_final: 0.7510 (p-90) REVERT: A 636 TYR cc_start: 0.7202 (m-80) cc_final: 0.6872 (m-80) REVERT: A 814 LYS cc_start: 0.9146 (mttt) cc_final: 0.8942 (mmtt) REVERT: A 1125 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8839 (p0) REVERT: B 586 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: B 830 ASP cc_start: 0.8222 (t0) cc_final: 0.7720 (t70) REVERT: B 988 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: C 102 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6142 (mmp-170) REVERT: C 220 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 351 TYR cc_start: 0.5314 (OUTLIER) cc_final: 0.4824 (p90) REVERT: C 425 LEU cc_start: -0.2776 (OUTLIER) cc_final: -0.3004 (pp) REVERT: C 633 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.8120 (p-90) REVERT: C 1155 TYR cc_start: 0.3967 (OUTLIER) cc_final: 0.3621 (m-10) outliers start: 66 outliers final: 47 residues processed: 142 average time/residue: 0.3561 time to fit residues: 87.9112 Evaluate side-chains 144 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 84 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 150 optimal weight: 0.0570 chunk 221 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 99 ASN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28336 Z= 0.194 Angle : 0.586 10.041 38537 Z= 0.277 Chirality : 0.044 0.413 4631 Planarity : 0.003 0.068 4834 Dihedral : 8.222 100.042 5670 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.18 % Favored : 94.55 % Rotamer: Outliers : 2.18 % Allowed : 11.47 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3339 helix: 1.43 (0.19), residues: 821 sheet: 0.22 (0.19), residues: 727 loop : -1.28 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.004 0.001 HIS B 245 PHE 0.021 0.001 PHE B 375 TYR 0.028 0.001 TYR C 904 ARG 0.007 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 95 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 177 MET cc_start: 0.8093 (ppp) cc_final: 0.7863 (ppp) REVERT: A 571 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (t0) REVERT: A 633 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7463 (p-90) REVERT: A 636 TYR cc_start: 0.7168 (m-80) cc_final: 0.6856 (m-80) REVERT: A 1125 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8617 (p0) REVERT: B 586 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: B 830 ASP cc_start: 0.8260 (t0) cc_final: 0.7761 (t70) REVERT: B 988 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: C 102 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6112 (mmp-170) REVERT: C 186 PHE cc_start: 0.6248 (p90) cc_final: 0.5646 (p90) REVERT: C 220 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 351 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.4686 (p90) REVERT: C 633 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.8075 (p-90) REVERT: C 636 TYR cc_start: 0.7698 (m-80) cc_final: 0.7442 (m-80) REVERT: C 1155 TYR cc_start: 0.3945 (OUTLIER) cc_final: 0.3569 (m-10) outliers start: 64 outliers final: 46 residues processed: 148 average time/residue: 0.3674 time to fit residues: 93.0163 Evaluate side-chains 140 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 83 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 0.0570 chunk 283 optimal weight: 0.0970 chunk 81 optimal weight: 0.0970 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 266 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.102965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064507 restraints weight = 80751.010| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.93 r_work: 0.3111 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28336 Z= 0.140 Angle : 0.581 13.878 38537 Z= 0.273 Chirality : 0.043 0.393 4631 Planarity : 0.003 0.069 4834 Dihedral : 7.738 98.642 5670 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.03 % Favored : 94.73 % Rotamer: Outliers : 1.98 % Allowed : 11.81 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3339 helix: 1.64 (0.19), residues: 801 sheet: 0.30 (0.19), residues: 721 loop : -1.22 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 633 HIS 0.004 0.000 HIS B 245 PHE 0.022 0.001 PHE B 375 TYR 0.027 0.001 TYR C 904 ARG 0.009 0.000 ARG C 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5308.13 seconds wall clock time: 99 minutes 42.50 seconds (5982.50 seconds total)