Starting phenix.real_space_refine on Wed May 15 05:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1f_38834/05_2024/8y1f_38834.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 18729 2.51 5 N 4734 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "B PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 845": "OE1" <-> "OE2" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C ARG 932": "NH1" <-> "NH2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "C GLU 1112": "OE1" <-> "OE2" Residue "C PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 15.21, per 1000 atoms: 0.51 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.093, 160.876, 167.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 11.97 Conformation dependent library (CDL) restraints added in 5.3 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 71 sheets defined 24.1% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.594A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.594A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.670A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.512A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.857A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.974A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.539A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.691A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.563A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.865A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.767A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.605A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.539A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.792A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.929A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.614A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.972A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.696A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.797A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.622A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.207A pdb=" N PHE B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.044A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 400 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.611A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.751A pdb=" N ASN B 483 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.912A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.959A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.987A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.653A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 4.036A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.819A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.131A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.641A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.568A pdb=" N GLU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 4.027A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.559A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.994A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.947A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.752A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 862 removed outlier: 3.847A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.888A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.531A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.615A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 4.134A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.673A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.918A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 8.247A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.097A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 315 " --> pdb=" O CYS C 619 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 7.986A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.796A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N TYR A 158 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 175 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.534A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 146 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A 188 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 148 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 186 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 150 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.195A pdb=" N ALA A 315 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.673A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.783A pdb=" N SER A 422 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N CYS A 370 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 428 " --> pdb=" O HIS A 364 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS A 364 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AB5, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB7, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.367A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB9, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AC1, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.573A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.219A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 786 through 789 removed outlier: 7.300A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 793 through 804 removed outlier: 6.812A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A1140 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.378A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC7, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC8, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.655A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 59 through 67 removed outlier: 8.042A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.949A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.504A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD6, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD7, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD8, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.220A pdb=" N ALA B 315 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.713A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.549A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.576A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE4, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.442A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE7, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.417A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.005A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.866A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B1140 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.211A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AF3, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.552A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AF5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF6, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.595A pdb=" N ASP C 38 " --> pdb=" O PHE C 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 59 through 67 removed outlier: 8.062A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.925A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.882A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 221 through 227 removed outlier: 5.252A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 109 through 113 Processing sheet with id=AG3, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG4, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG5, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.852A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 345 through 349 Processing sheet with id=AG7, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.568A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.480A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AH2, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AH3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.541A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.964A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.964A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.313A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH8, first strand: chain 'C' and resid 1202 through 1205 1074 hydrogen bonds defined for protein. 2955 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.68 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9230 1.34 - 1.47: 7872 1.47 - 1.59: 12925 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.497 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA ASP B 250 " pdb=" C ASP B 250 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.34e-02 5.57e+03 1.29e+01 bond pdb=" CA ASP A 250 " pdb=" C ASP A 250 " ideal model delta sigma weight residual 1.523 1.569 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.484 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C5 MAN N 3 " pdb=" O5 MAN N 3 " ideal model delta sigma weight residual 1.418 1.478 -0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 755 106.62 - 113.47: 16789 113.47 - 120.32: 10728 120.32 - 127.17: 12650 127.17 - 134.01: 235 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 111.48 106.18 5.30 9.40e-01 1.13e+00 3.18e+01 angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 117.29 -6.59 1.22e+00 6.72e-01 2.91e+01 angle pdb=" C CYS A 819 " pdb=" N SER A 820 " pdb=" CA SER A 820 " ideal model delta sigma weight residual 121.19 129.44 -8.25 1.59e+00 3.96e-01 2.69e+01 angle pdb=" CA ASP A 250 " pdb=" C ASP A 250 " pdb=" O ASP A 250 " ideal model delta sigma weight residual 120.51 113.21 7.30 1.43e+00 4.89e-01 2.60e+01 angle pdb=" C CYS C 819 " pdb=" N SER C 820 " pdb=" CA SER C 820 " ideal model delta sigma weight residual 121.19 129.07 -7.88 1.59e+00 3.96e-01 2.46e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 18001 21.84 - 43.69: 922 43.69 - 65.53: 247 65.53 - 87.38: 45 87.38 - 109.22: 12 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA PRO C 969 " pdb=" C PRO C 969 " pdb=" N PRO C 970 " pdb=" CA PRO C 970 " ideal model delta harmonic sigma weight residual 180.00 144.21 35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA PRO B 969 " pdb=" C PRO B 969 " pdb=" N PRO B 970 " pdb=" CA PRO B 970 " ideal model delta harmonic sigma weight residual 180.00 145.82 34.18 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA PRO A 969 " pdb=" C PRO A 969 " pdb=" N PRO A 970 " pdb=" CA PRO A 970 " ideal model delta harmonic sigma weight residual 180.00 145.97 34.03 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4595 0.100 - 0.200: 299 0.200 - 0.300: 11 0.300 - 0.401: 1 0.401 - 0.501: 2 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 92 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 93 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 93 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 93 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.060 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7464 2.80 - 3.32: 23101 3.32 - 3.85: 47938 3.85 - 4.37: 55724 4.37 - 4.90: 98704 Nonbonded interactions: 232931 Sorted by model distance: nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.272 2.440 nonbonded pdb=" OG SER C 340 " pdb=" OD1 ASN C 343 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP C 523 " pdb=" OG SER C 526 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR B 448 " pdb=" O PHE B 473 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR A 625 " pdb=" OD1 ASP A 660 " model vdw 2.297 2.440 ... (remaining 232926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.020 Extract box with map and model: 14.810 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 81.680 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30225 Z= 0.350 Angle : 0.759 8.253 41157 Z= 0.420 Chirality : 0.052 0.501 4908 Planarity : 0.007 0.113 5172 Dihedral : 14.273 109.220 12183 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 6.87 % Allowed : 6.41 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.12), residues: 3618 helix: -1.82 (0.15), residues: 777 sheet: -1.02 (0.16), residues: 861 loop : -2.29 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 444 HIS 0.006 0.001 HIS C 201 PHE 0.023 0.002 PHE C 968 TYR 0.017 0.002 TYR C1148 ARG 0.004 0.001 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 372 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8866 (t) cc_final: 0.8578 (p) REVERT: A 83 LYS cc_start: 0.8164 (tttm) cc_final: 0.7957 (tttm) REVERT: A 84 TYR cc_start: 0.7870 (m-80) cc_final: 0.7580 (m-80) REVERT: A 113 VAL cc_start: 0.8315 (t) cc_final: 0.7892 (t) REVERT: A 187 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: A 206 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7261 (mtp85) REVERT: A 400 ASP cc_start: 0.8230 (m-30) cc_final: 0.7864 (m-30) REVERT: A 517 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6223 (ttp-170) REVERT: A 636 VAL cc_start: 0.8593 (p) cc_final: 0.8371 (m) REVERT: A 789 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8534 (mm-40) REVERT: A 828 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 835 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 912 LYS cc_start: 0.8435 (tttt) cc_final: 0.8231 (ttmt) REVERT: A 1066 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6273 (m-30) REVERT: A 1105 ARG cc_start: 0.7232 (ttt90) cc_final: 0.7018 (tpp80) REVERT: A 1131 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7892 (pp) REVERT: A 1219 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5269 (p90) REVERT: B 84 TYR cc_start: 0.7940 (m-80) cc_final: 0.7702 (m-80) REVERT: B 116 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 155 MET cc_start: 0.9175 (mmm) cc_final: 0.8628 (mmm) REVERT: B 241 THR cc_start: 0.8506 (m) cc_final: 0.8088 (p) REVERT: B 248 ASN cc_start: 0.7647 (p0) cc_final: 0.7404 (p0) REVERT: B 305 ASP cc_start: 0.7887 (m-30) cc_final: 0.7674 (m-30) REVERT: B 345 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7593 (mm-30) REVERT: B 500 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7906 (ptmm) REVERT: B 503 HIS cc_start: 0.7537 (t70) cc_final: 0.7122 (t70) REVERT: B 511 TYR cc_start: 0.4097 (OUTLIER) cc_final: 0.3702 (m-80) REVERT: B 598 ASN cc_start: 0.8114 (m-40) cc_final: 0.7889 (m-40) REVERT: B 630 GLN cc_start: 0.8271 (mt0) cc_final: 0.7985 (mt0) REVERT: B 655 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (mt) REVERT: B 714 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 788 ILE cc_start: 0.8798 (tt) cc_final: 0.8470 (mt) REVERT: B 800 GLU cc_start: 0.8199 (pm20) cc_final: 0.7923 (pt0) REVERT: B 862 MET cc_start: 0.8310 (mmm) cc_final: 0.8050 (mmm) REVERT: B 912 LYS cc_start: 0.8431 (tttt) cc_final: 0.8185 (ttmt) REVERT: B 1001 GLN cc_start: 0.6907 (tt0) cc_final: 0.6454 (tm-30) REVERT: B 1060 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7276 (mm-30) REVERT: B 1091 GLN cc_start: 0.6953 (tt0) cc_final: 0.6593 (tm-30) REVERT: B 1105 ARG cc_start: 0.6917 (ttt90) cc_final: 0.6655 (tpp80) REVERT: B 1149 LYS cc_start: 0.8656 (tttt) cc_final: 0.8362 (tttp) REVERT: B 1167 ASP cc_start: 0.7504 (m-30) cc_final: 0.7020 (t70) REVERT: C 24 PHE cc_start: 0.7852 (m-80) cc_final: 0.7591 (m-80) REVERT: C 38 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: C 112 TYR cc_start: 0.7759 (m-80) cc_final: 0.7328 (m-80) REVERT: C 155 MET cc_start: 0.8789 (mmm) cc_final: 0.8351 (mmm) REVERT: C 187 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7408 (ttmm) REVERT: C 213 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7292 (p90) REVERT: C 356 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (mp) REVERT: C 374 ASP cc_start: 0.7206 (m-30) cc_final: 0.6166 (m-30) REVERT: C 402 GLN cc_start: 0.7661 (mm110) cc_final: 0.7333 (mm-40) REVERT: C 464 ASP cc_start: 0.7754 (m-30) cc_final: 0.7530 (m-30) REVERT: C 500 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7205 (mmtm) REVERT: C 655 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8818 (mt) REVERT: C 788 ILE cc_start: 0.8580 (tt) cc_final: 0.8204 (pt) REVERT: C 827 ASP cc_start: 0.7874 (m-30) cc_final: 0.7438 (m-30) REVERT: C 851 ASP cc_start: 0.7299 (m-30) cc_final: 0.7073 (m-30) REVERT: C 1091 GLN cc_start: 0.6951 (tt0) cc_final: 0.6578 (mt0) REVERT: C 1115 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8502 (mmmm) REVERT: C 1135 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8243 (mm110) REVERT: C 1219 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.5189 (m-80) outliers start: 223 outliers final: 72 residues processed: 554 average time/residue: 1.0126 time to fit residues: 698.0119 Evaluate side-chains 320 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 227 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 204 GLN A 384 ASN A 630 GLN A 876 HIS A1079 ASN A1136 ASN A1180 GLN B 204 GLN B 353 ASN B 561 ASN B 587 ASN B 630 GLN B 821 ASN B 872 ASN B 894 GLN B 984 GLN B1001 GLN B1079 ASN B1091 GLN C 204 GLN C 531 ASN C 552 ASN C 630 GLN C 799 HIS C 863 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C 984 GLN C1001 GLN C1059 GLN C1079 ASN C1091 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30225 Z= 0.166 Angle : 0.565 8.766 41157 Z= 0.300 Chirality : 0.048 0.711 4908 Planarity : 0.006 0.093 5172 Dihedral : 10.281 104.195 5996 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.59 % Allowed : 10.72 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3618 helix: 0.14 (0.18), residues: 789 sheet: -0.68 (0.17), residues: 822 loop : -1.95 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.005 0.001 HIS C 201 PHE 0.021 0.001 PHE A 968 TYR 0.017 0.001 TYR C1148 ARG 0.002 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 223 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8949 (t) cc_final: 0.8627 (p) REVERT: A 187 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7715 (ttmm) REVERT: A 400 ASP cc_start: 0.8044 (m-30) cc_final: 0.7569 (m-30) REVERT: A 517 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.6028 (ttp-170) REVERT: A 800 GLU cc_start: 0.7640 (pm20) cc_final: 0.7409 (pm20) REVERT: A 828 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 835 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 912 LYS cc_start: 0.8405 (tttt) cc_final: 0.8144 (ttmt) REVERT: A 1001 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: A 1066 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6223 (m-30) REVERT: A 1105 ARG cc_start: 0.7108 (ttt90) cc_final: 0.6890 (tpp80) REVERT: A 1219 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5257 (p90) REVERT: B 84 TYR cc_start: 0.7910 (m-80) cc_final: 0.7653 (m-10) REVERT: B 155 MET cc_start: 0.8951 (mmm) cc_final: 0.8687 (mmm) REVERT: B 241 THR cc_start: 0.8546 (m) cc_final: 0.8221 (p) REVERT: B 305 ASP cc_start: 0.7863 (m-30) cc_final: 0.7651 (m-30) REVERT: B 345 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7333 (mm-30) REVERT: B 500 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7894 (ptmm) REVERT: B 511 TYR cc_start: 0.4005 (OUTLIER) cc_final: 0.3690 (m-80) REVERT: B 598 ASN cc_start: 0.8135 (m-40) cc_final: 0.7919 (m-40) REVERT: B 630 GLN cc_start: 0.7986 (mt0) cc_final: 0.7707 (mt0) REVERT: B 655 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8837 (mt) REVERT: B 714 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: B 788 ILE cc_start: 0.8698 (tt) cc_final: 0.8214 (pp) REVERT: B 800 GLU cc_start: 0.8199 (pm20) cc_final: 0.7884 (pt0) REVERT: B 902 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7100 (mt) REVERT: B 912 LYS cc_start: 0.8400 (tttt) cc_final: 0.8158 (ttmt) REVERT: B 1001 GLN cc_start: 0.6900 (tt0) cc_final: 0.6290 (tm-30) REVERT: B 1091 GLN cc_start: 0.6995 (tt0) cc_final: 0.6430 (tm-30) REVERT: B 1105 ARG cc_start: 0.6866 (ttt90) cc_final: 0.6640 (tpp80) REVERT: B 1112 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: B 1149 LYS cc_start: 0.8594 (tttt) cc_final: 0.8241 (tttp) REVERT: B 1167 ASP cc_start: 0.7500 (m-30) cc_final: 0.7138 (t70) REVERT: C 112 TYR cc_start: 0.7515 (m-80) cc_final: 0.7124 (m-80) REVERT: C 155 MET cc_start: 0.8794 (mmm) cc_final: 0.8386 (mmm) REVERT: C 213 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7848 (p90) REVERT: C 374 ASP cc_start: 0.7372 (m-30) cc_final: 0.6283 (m-30) REVERT: C 402 GLN cc_start: 0.7640 (mm110) cc_final: 0.7329 (mm-40) REVERT: C 500 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7075 (mmtt) REVERT: C 655 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8809 (mt) REVERT: C 735 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7675 (p0) REVERT: C 788 ILE cc_start: 0.8570 (tt) cc_final: 0.8265 (pt) REVERT: C 827 ASP cc_start: 0.7793 (m-30) cc_final: 0.7389 (m-30) REVERT: C 977 VAL cc_start: 0.9094 (m) cc_final: 0.8892 (p) REVERT: C 994 MET cc_start: 0.8516 (tpp) cc_final: 0.8300 (tpt) REVERT: C 1003 LEU cc_start: 0.8052 (mm) cc_final: 0.7674 (tt) REVERT: C 1091 GLN cc_start: 0.7126 (tt0) cc_final: 0.6565 (mt0) REVERT: C 1219 TYR cc_start: 0.5385 (OUTLIER) cc_final: 0.5084 (m-80) outliers start: 149 outliers final: 83 residues processed: 341 average time/residue: 0.9797 time to fit residues: 419.7413 Evaluate side-chains 303 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 204 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 0.0470 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 984 GLN B 872 ASN B 894 GLN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN C1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30225 Z= 0.283 Angle : 0.609 10.725 41157 Z= 0.319 Chirality : 0.047 0.768 4908 Planarity : 0.006 0.097 5172 Dihedral : 9.604 100.168 5946 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.87 % Allowed : 11.21 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3618 helix: 0.96 (0.20), residues: 771 sheet: -0.56 (0.17), residues: 840 loop : -1.77 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 444 HIS 0.007 0.001 HIS B 799 PHE 0.018 0.002 PHE B 968 TYR 0.019 0.002 TYR C1148 ARG 0.005 0.001 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 214 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9027 (t) cc_final: 0.8619 (p) REVERT: A 187 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7688 (ttmm) REVERT: A 400 ASP cc_start: 0.8109 (m-30) cc_final: 0.7632 (m-30) REVERT: A 659 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8194 (ttpt) REVERT: A 828 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8536 (tp) REVERT: A 835 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 900 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7807 (ptt180) REVERT: A 912 LYS cc_start: 0.8407 (tttt) cc_final: 0.8171 (ttmt) REVERT: A 1066 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6140 (m-30) REVERT: A 1105 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6903 (tpp80) REVERT: A 1219 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5253 (p90) REVERT: B 84 TYR cc_start: 0.7963 (m-80) cc_final: 0.7691 (m-10) REVERT: B 116 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 241 THR cc_start: 0.8738 (m) cc_final: 0.8311 (p) REVERT: B 345 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7405 (mm-30) REVERT: B 500 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7855 (ptmm) REVERT: B 511 TYR cc_start: 0.4198 (OUTLIER) cc_final: 0.3815 (m-80) REVERT: B 598 ASN cc_start: 0.8115 (m-40) cc_final: 0.7890 (m-40) REVERT: B 630 GLN cc_start: 0.8111 (mt0) cc_final: 0.7826 (mt0) REVERT: B 655 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8768 (mt) REVERT: B 714 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: B 788 ILE cc_start: 0.8672 (tt) cc_final: 0.8445 (mt) REVERT: B 800 GLU cc_start: 0.8237 (pm20) cc_final: 0.7932 (pt0) REVERT: B 894 GLN cc_start: 0.5841 (OUTLIER) cc_final: 0.5376 (pm20) REVERT: B 902 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 903 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 912 LYS cc_start: 0.8461 (tttt) cc_final: 0.8192 (ttmt) REVERT: B 1001 GLN cc_start: 0.6978 (tt0) cc_final: 0.6436 (tm-30) REVERT: B 1091 GLN cc_start: 0.7032 (tt0) cc_final: 0.6778 (tt0) REVERT: B 1105 ARG cc_start: 0.6957 (ttt90) cc_final: 0.6687 (tpp80) REVERT: B 1112 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 1149 LYS cc_start: 0.8624 (tttt) cc_final: 0.8268 (tttp) REVERT: B 1167 ASP cc_start: 0.7413 (m-30) cc_final: 0.7017 (t70) REVERT: C 38 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: C 112 TYR cc_start: 0.7634 (m-80) cc_final: 0.7226 (m-80) REVERT: C 155 MET cc_start: 0.8841 (mmm) cc_final: 0.8404 (mmm) REVERT: C 213 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7840 (p90) REVERT: C 374 ASP cc_start: 0.7422 (m-30) cc_final: 0.6351 (m-30) REVERT: C 402 GLN cc_start: 0.7710 (mm110) cc_final: 0.7415 (mm-40) REVERT: C 500 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7227 (mmtm) REVERT: C 655 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 735 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7646 (p0) REVERT: C 827 ASP cc_start: 0.7754 (m-30) cc_final: 0.7319 (m-30) REVERT: C 845 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6870 (mm-30) REVERT: C 934 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 1003 LEU cc_start: 0.8054 (mm) cc_final: 0.7693 (tt) REVERT: C 1091 GLN cc_start: 0.7162 (tt0) cc_final: 0.6610 (mt0) REVERT: C 1219 TYR cc_start: 0.5314 (OUTLIER) cc_final: 0.4858 (m-80) outliers start: 158 outliers final: 102 residues processed: 337 average time/residue: 0.9807 time to fit residues: 417.1824 Evaluate side-chains 325 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 202 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 967 MET Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 0.0770 chunk 156 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN B 483 ASN B 872 ASN B 894 GLN C 531 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30225 Z= 0.260 Angle : 0.584 11.311 41157 Z= 0.307 Chirality : 0.047 0.813 4908 Planarity : 0.005 0.092 5172 Dihedral : 8.992 96.275 5933 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.93 % Allowed : 11.98 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3618 helix: 1.23 (0.20), residues: 774 sheet: -0.46 (0.17), residues: 840 loop : -1.69 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 515 HIS 0.006 0.001 HIS B 799 PHE 0.016 0.001 PHE C 968 TYR 0.018 0.001 TYR C1148 ARG 0.004 0.000 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 202 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9002 (t) cc_final: 0.8580 (p) REVERT: A 187 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7699 (ttmm) REVERT: A 206 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: A 221 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 255 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: A 400 ASP cc_start: 0.8113 (m-30) cc_final: 0.7641 (m-30) REVERT: A 659 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8193 (ttpt) REVERT: A 828 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 835 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 900 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7799 (ptt180) REVERT: A 912 LYS cc_start: 0.8400 (tttt) cc_final: 0.8165 (ttmt) REVERT: A 1066 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: A 1105 ARG cc_start: 0.7183 (ttt90) cc_final: 0.6945 (tpp80) REVERT: A 1219 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5296 (p90) REVERT: B 84 TYR cc_start: 0.7957 (m-80) cc_final: 0.7673 (m-10) REVERT: B 213 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7547 (p90) REVERT: B 241 THR cc_start: 0.8710 (m) cc_final: 0.8240 (p) REVERT: B 345 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7393 (mm-30) REVERT: B 500 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7838 (ptmm) REVERT: B 511 TYR cc_start: 0.4191 (OUTLIER) cc_final: 0.3659 (m-80) REVERT: B 598 ASN cc_start: 0.8092 (m-40) cc_final: 0.7864 (m-40) REVERT: B 630 GLN cc_start: 0.8109 (mt0) cc_final: 0.7786 (mt0) REVERT: B 655 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 714 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: B 788 ILE cc_start: 0.8665 (tt) cc_final: 0.8444 (mt) REVERT: B 800 GLU cc_start: 0.8242 (pm20) cc_final: 0.7944 (pt0) REVERT: B 894 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5295 (pm20) REVERT: B 902 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7328 (mt) REVERT: B 903 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 912 LYS cc_start: 0.8462 (tttt) cc_final: 0.8193 (ttmt) REVERT: B 1001 GLN cc_start: 0.6937 (tt0) cc_final: 0.6448 (tm-30) REVERT: B 1091 GLN cc_start: 0.7022 (tt0) cc_final: 0.6741 (tt0) REVERT: B 1105 ARG cc_start: 0.6918 (ttt90) cc_final: 0.6641 (tpp80) REVERT: B 1112 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 1149 LYS cc_start: 0.8626 (tttt) cc_final: 0.8254 (tttp) REVERT: B 1167 ASP cc_start: 0.7399 (m-30) cc_final: 0.7032 (t70) REVERT: C 112 TYR cc_start: 0.7595 (m-80) cc_final: 0.7202 (m-80) REVERT: C 155 MET cc_start: 0.8865 (mmm) cc_final: 0.8415 (mmm) REVERT: C 213 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7821 (p90) REVERT: C 374 ASP cc_start: 0.7407 (m-30) cc_final: 0.6367 (m-30) REVERT: C 402 GLN cc_start: 0.7647 (mm110) cc_final: 0.7356 (mm-40) REVERT: C 500 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7005 (mmtm) REVERT: C 655 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 735 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7663 (p0) REVERT: C 827 ASP cc_start: 0.7782 (m-30) cc_final: 0.7348 (m-30) REVERT: C 1003 LEU cc_start: 0.8091 (mm) cc_final: 0.7730 (tt) REVERT: C 1028 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7997 (tttt) REVERT: C 1091 GLN cc_start: 0.7162 (tt0) cc_final: 0.6607 (mt0) REVERT: C 1131 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7894 (pp) REVERT: C 1185 MET cc_start: 0.7956 (mtt) cc_final: 0.7582 (mmm) REVERT: C 1219 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4719 (m-80) outliers start: 160 outliers final: 107 residues processed: 333 average time/residue: 1.0080 time to fit residues: 419.0391 Evaluate side-chains 326 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 195 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 894 GLN C 531 ASN C 587 ASN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30225 Z= 0.411 Angle : 0.667 11.469 41157 Z= 0.345 Chirality : 0.049 0.547 4908 Planarity : 0.006 0.100 5172 Dihedral : 9.028 94.379 5933 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.79 % Allowed : 11.92 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3618 helix: 1.14 (0.20), residues: 768 sheet: -0.40 (0.16), residues: 924 loop : -1.72 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 344 HIS 0.008 0.001 HIS C 201 PHE 0.019 0.002 PHE C 968 TYR 0.020 0.002 TYR C1148 ARG 0.007 0.001 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 199 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9010 (t) cc_final: 0.8536 (p) REVERT: A 187 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7603 (ttmm) REVERT: A 205 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: A 206 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: A 221 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7873 (t) REVERT: A 255 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: A 263 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8263 (ttt180) REVERT: A 400 ASP cc_start: 0.8152 (m-30) cc_final: 0.7692 (m-30) REVERT: A 828 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 835 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6787 (t80) REVERT: A 891 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 912 LYS cc_start: 0.8392 (tttt) cc_final: 0.8159 (ttmt) REVERT: A 1066 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6250 (m-30) REVERT: A 1091 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: A 1095 ASP cc_start: 0.7395 (m-30) cc_final: 0.7013 (m-30) REVERT: A 1105 ARG cc_start: 0.7285 (ttt90) cc_final: 0.7040 (tpp80) REVERT: A 1219 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5379 (p90) REVERT: B 84 TYR cc_start: 0.7918 (m-80) cc_final: 0.7614 (m-10) REVERT: B 213 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7702 (p90) REVERT: B 241 THR cc_start: 0.8727 (m) cc_final: 0.8322 (p) REVERT: B 345 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7392 (mm-30) REVERT: B 503 HIS cc_start: 0.7823 (t70) cc_final: 0.7548 (t70) REVERT: B 511 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3669 (m-80) REVERT: B 598 ASN cc_start: 0.8058 (m-40) cc_final: 0.7833 (m-40) REVERT: B 630 GLN cc_start: 0.8187 (mt0) cc_final: 0.7848 (mt0) REVERT: B 655 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 714 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: B 735 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 788 ILE cc_start: 0.8697 (tt) cc_final: 0.8486 (mt) REVERT: B 800 GLU cc_start: 0.8320 (pm20) cc_final: 0.7953 (pt0) REVERT: B 894 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: B 903 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8221 (mp) REVERT: B 912 LYS cc_start: 0.8423 (tttt) cc_final: 0.8165 (ttmt) REVERT: B 1001 GLN cc_start: 0.7020 (tt0) cc_final: 0.6474 (tm-30) REVERT: B 1091 GLN cc_start: 0.7036 (tt0) cc_final: 0.6801 (tt0) REVERT: B 1105 ARG cc_start: 0.6886 (ttt90) cc_final: 0.6539 (tpp80) REVERT: B 1112 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: B 1149 LYS cc_start: 0.8631 (tttt) cc_final: 0.8265 (tttp) REVERT: C 38 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: C 112 TYR cc_start: 0.7678 (m-80) cc_final: 0.7284 (m-80) REVERT: C 155 MET cc_start: 0.8867 (mmm) cc_final: 0.8367 (mmm) REVERT: C 213 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7631 (p90) REVERT: C 374 ASP cc_start: 0.7338 (m-30) cc_final: 0.6153 (m-30) REVERT: C 402 GLN cc_start: 0.7696 (mm110) cc_final: 0.7348 (mm-40) REVERT: C 500 LYS cc_start: 0.7722 (mtmt) cc_final: 0.6972 (mmtm) REVERT: C 655 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8652 (mt) REVERT: C 735 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7563 (p0) REVERT: C 827 ASP cc_start: 0.7808 (m-30) cc_final: 0.7363 (m-30) REVERT: C 934 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7887 (mm) REVERT: C 1003 LEU cc_start: 0.8201 (mm) cc_final: 0.7818 (tt) REVERT: C 1028 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7987 (tttt) REVERT: C 1071 GLN cc_start: 0.7198 (mt0) cc_final: 0.6833 (mm-40) REVERT: C 1091 GLN cc_start: 0.7180 (tt0) cc_final: 0.6644 (mt0) REVERT: C 1185 MET cc_start: 0.8043 (mtt) cc_final: 0.7641 (mmm) REVERT: C 1219 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4702 (m-80) outliers start: 188 outliers final: 118 residues processed: 354 average time/residue: 1.0124 time to fit residues: 450.5830 Evaluate side-chains 337 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 192 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1014 SER Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 chunk 289 optimal weight: 0.0000 chunk 161 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 872 ASN A1122 ASN B 872 ASN B 894 GLN C 531 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30225 Z= 0.141 Angle : 0.535 11.066 41157 Z= 0.280 Chirality : 0.045 0.554 4908 Planarity : 0.005 0.087 5172 Dihedral : 8.096 93.967 5930 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.57 % Allowed : 13.96 % Favored : 82.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3618 helix: 1.67 (0.20), residues: 768 sheet: -0.33 (0.17), residues: 840 loop : -1.54 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 444 HIS 0.006 0.001 HIS B 799 PHE 0.016 0.001 PHE A 968 TYR 0.015 0.001 TYR B 203 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 216 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8926 (t) cc_final: 0.8521 (p) REVERT: A 187 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7697 (ttmm) REVERT: A 206 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7306 (mtp85) REVERT: A 305 ASP cc_start: 0.8148 (m-30) cc_final: 0.7936 (m-30) REVERT: A 351 ASN cc_start: 0.8371 (t0) cc_final: 0.7725 (t0) REVERT: A 400 ASP cc_start: 0.7991 (m-30) cc_final: 0.7508 (m-30) REVERT: A 468 SER cc_start: 0.8145 (t) cc_final: 0.7803 (p) REVERT: A 835 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 912 LYS cc_start: 0.8405 (tttt) cc_final: 0.8159 (ttmt) REVERT: A 1066 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6208 (m-30) REVERT: A 1091 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: A 1095 ASP cc_start: 0.7205 (m-30) cc_final: 0.6827 (m-30) REVERT: A 1219 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5318 (p90) REVERT: B 64 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8100 (m) REVERT: B 84 TYR cc_start: 0.7944 (m-80) cc_final: 0.7616 (m-10) REVERT: B 241 THR cc_start: 0.8688 (m) cc_final: 0.8274 (p) REVERT: B 345 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7282 (mm-30) REVERT: B 500 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7792 (ptmm) REVERT: B 503 HIS cc_start: 0.7774 (t70) cc_final: 0.7458 (t70) REVERT: B 511 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3662 (m-80) REVERT: B 537 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7932 (tttt) REVERT: B 630 GLN cc_start: 0.8020 (mt0) cc_final: 0.7703 (mt0) REVERT: B 655 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 714 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 788 ILE cc_start: 0.8698 (tt) cc_final: 0.8485 (mt) REVERT: B 800 GLU cc_start: 0.8262 (pm20) cc_final: 0.7884 (pt0) REVERT: B 912 LYS cc_start: 0.8422 (tttt) cc_final: 0.8150 (ttmt) REVERT: B 1001 GLN cc_start: 0.6888 (tt0) cc_final: 0.6425 (tm-30) REVERT: B 1069 GLU cc_start: 0.7422 (mp0) cc_final: 0.7179 (mp0) REVERT: B 1091 GLN cc_start: 0.6871 (tt0) cc_final: 0.6399 (tm-30) REVERT: B 1105 ARG cc_start: 0.6804 (ttt90) cc_final: 0.6537 (tpp80) REVERT: B 1149 LYS cc_start: 0.8574 (tttt) cc_final: 0.8246 (tttp) REVERT: C 155 MET cc_start: 0.8879 (mmm) cc_final: 0.8411 (mmm) REVERT: C 213 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (p90) REVERT: C 374 ASP cc_start: 0.7289 (m-30) cc_final: 0.6359 (m-30) REVERT: C 402 GLN cc_start: 0.7659 (mm110) cc_final: 0.7302 (mm-40) REVERT: C 500 LYS cc_start: 0.7685 (mtmt) cc_final: 0.6927 (mmtm) REVERT: C 655 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 735 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7637 (p0) REVERT: C 827 ASP cc_start: 0.7768 (m-30) cc_final: 0.7322 (m-30) REVERT: C 1003 LEU cc_start: 0.8094 (mm) cc_final: 0.7734 (tt) REVERT: C 1091 GLN cc_start: 0.7035 (tt0) cc_final: 0.6550 (mt0) REVERT: C 1096 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7937 (tp) REVERT: C 1219 TYR cc_start: 0.5199 (OUTLIER) cc_final: 0.4912 (m-80) outliers start: 116 outliers final: 73 residues processed: 314 average time/residue: 1.0047 time to fit residues: 398.3226 Evaluate side-chains 286 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 197 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.0030 chunk 39 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 ASN B1038 GLN C 531 ASN C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30225 Z= 0.207 Angle : 0.568 14.264 41157 Z= 0.294 Chirality : 0.045 0.538 4908 Planarity : 0.005 0.083 5172 Dihedral : 8.127 93.600 5921 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 3.79 % Allowed : 14.17 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.72 (0.14), residues: 3618 helix: 1.64 (0.20), residues: 780 sheet: -0.30 (0.17), residues: 840 loop : -1.48 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 444 HIS 0.009 0.001 HIS B 799 PHE 0.015 0.001 PHE B 968 TYR 0.017 0.001 TYR C1148 ARG 0.002 0.000 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 197 time to evaluate : 3.528 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 43 SER cc_start: 0.8920 (t) cc_final: 0.8485 (p) REVERT: A 187 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7685 (ttmm) REVERT: A 206 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7317 (mtp85) REVERT: A 305 ASP cc_start: 0.8190 (m-30) cc_final: 0.7967 (m-30) REVERT: A 351 ASN cc_start: 0.8427 (t0) cc_final: 0.7785 (t0) REVERT: A 400 ASP cc_start: 0.8005 (m-30) cc_final: 0.7533 (m-30) REVERT: A 468 SER cc_start: 0.8202 (t) cc_final: 0.7835 (p) REVERT: A 835 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 912 LYS cc_start: 0.8388 (tttt) cc_final: 0.8159 (ttmt) REVERT: A 1066 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: A 1091 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 1219 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5359 (p90) REVERT: B 84 TYR cc_start: 0.7954 (m-80) cc_final: 0.7621 (m-10) REVERT: B 116 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8101 (p) REVERT: B 241 THR cc_start: 0.8695 (m) cc_final: 0.8293 (p) REVERT: B 345 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7297 (mm-30) REVERT: B 500 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7861 (ptmm) REVERT: B 503 HIS cc_start: 0.7894 (t70) cc_final: 0.7531 (t70) REVERT: B 511 TYR cc_start: 0.4394 (OUTLIER) cc_final: 0.3897 (m-80) REVERT: B 537 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7936 (tttt) REVERT: B 630 GLN cc_start: 0.8073 (mt0) cc_final: 0.7746 (mt0) REVERT: B 655 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 714 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: B 788 ILE cc_start: 0.8688 (tt) cc_final: 0.8487 (mt) REVERT: B 800 GLU cc_start: 0.8262 (pm20) cc_final: 0.7895 (pt0) REVERT: B 845 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: B 912 LYS cc_start: 0.8425 (tttt) cc_final: 0.8141 (ttmt) REVERT: B 1001 GLN cc_start: 0.6882 (tt0) cc_final: 0.6370 (tm-30) REVERT: B 1069 GLU cc_start: 0.7490 (mp0) cc_final: 0.7160 (mp0) REVERT: B 1091 GLN cc_start: 0.7052 (tt0) cc_final: 0.6526 (tm-30) REVERT: B 1105 ARG cc_start: 0.6845 (ttt90) cc_final: 0.6558 (tpp80) REVERT: B 1112 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: B 1149 LYS cc_start: 0.8576 (tttt) cc_final: 0.8259 (tttp) REVERT: C 155 MET cc_start: 0.8887 (mmm) cc_final: 0.8421 (mmm) REVERT: C 213 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7894 (p90) REVERT: C 374 ASP cc_start: 0.7333 (m-30) cc_final: 0.6348 (m-30) REVERT: C 402 GLN cc_start: 0.7645 (mm110) cc_final: 0.7292 (mm110) REVERT: C 500 LYS cc_start: 0.7682 (mtmt) cc_final: 0.6915 (mmtm) REVERT: C 655 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 735 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7428 (p0) REVERT: C 827 ASP cc_start: 0.7758 (m-30) cc_final: 0.7326 (m-30) REVERT: C 934 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7767 (mm) REVERT: C 1003 LEU cc_start: 0.8118 (mm) cc_final: 0.7700 (tt) REVERT: C 1028 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7970 (tttt) REVERT: C 1091 GLN cc_start: 0.7101 (tt0) cc_final: 0.6570 (mt0) REVERT: C 1096 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7944 (tp) REVERT: C 1185 MET cc_start: 0.7943 (mtt) cc_final: 0.7685 (mmm) REVERT: C 1219 TYR cc_start: 0.5013 (OUTLIER) cc_final: 0.4785 (m-80) outliers start: 123 outliers final: 89 residues processed: 300 average time/residue: 1.0223 time to fit residues: 383.9249 Evaluate side-chains 302 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 193 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 872 ASN B 894 GLN C 531 ASN C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30225 Z= 0.187 Angle : 0.544 11.357 41157 Z= 0.283 Chirality : 0.044 0.551 4908 Planarity : 0.005 0.076 5172 Dihedral : 7.938 92.919 5918 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.91 % Allowed : 13.99 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3618 helix: 1.70 (0.20), residues: 783 sheet: -0.30 (0.17), residues: 861 loop : -1.41 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 444 HIS 0.009 0.001 HIS B 799 PHE 0.023 0.001 PHE A 770 TYR 0.016 0.001 TYR C1148 ARG 0.002 0.000 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 201 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8901 (t) cc_final: 0.8475 (p) REVERT: A 187 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7695 (ttmm) REVERT: A 206 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: A 305 ASP cc_start: 0.8174 (m-30) cc_final: 0.7919 (m-30) REVERT: A 351 ASN cc_start: 0.8444 (t0) cc_final: 0.7842 (t0) REVERT: A 400 ASP cc_start: 0.8017 (m-30) cc_final: 0.7535 (m-30) REVERT: A 468 SER cc_start: 0.8214 (t) cc_final: 0.7866 (p) REVERT: A 835 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6641 (t80) REVERT: A 912 LYS cc_start: 0.8388 (tttt) cc_final: 0.8143 (ttmt) REVERT: A 1066 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6207 (m-30) REVERT: A 1091 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: A 1219 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.5327 (p90) REVERT: B 64 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 84 TYR cc_start: 0.7941 (m-80) cc_final: 0.7619 (m-10) REVERT: B 116 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8132 (p) REVERT: B 241 THR cc_start: 0.8714 (m) cc_final: 0.8312 (p) REVERT: B 345 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7274 (mm-30) REVERT: B 500 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7895 (ptmm) REVERT: B 503 HIS cc_start: 0.7846 (t70) cc_final: 0.7468 (t70) REVERT: B 511 TYR cc_start: 0.4691 (OUTLIER) cc_final: 0.4191 (m-80) REVERT: B 537 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7921 (tttt) REVERT: B 630 GLN cc_start: 0.8035 (mt0) cc_final: 0.7719 (mt0) REVERT: B 655 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 714 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 800 GLU cc_start: 0.8248 (pm20) cc_final: 0.7888 (pt0) REVERT: B 912 LYS cc_start: 0.8385 (tttt) cc_final: 0.8091 (ttmt) REVERT: B 1001 GLN cc_start: 0.6841 (tt0) cc_final: 0.6450 (tm-30) REVERT: B 1091 GLN cc_start: 0.7037 (tt0) cc_final: 0.6523 (tm-30) REVERT: B 1105 ARG cc_start: 0.6850 (ttt90) cc_final: 0.6593 (tpp80) REVERT: B 1149 LYS cc_start: 0.8580 (tttt) cc_final: 0.8261 (tttp) REVERT: C 155 MET cc_start: 0.8898 (mmm) cc_final: 0.8329 (mmm) REVERT: C 213 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7908 (p90) REVERT: C 374 ASP cc_start: 0.7287 (m-30) cc_final: 0.6304 (m-30) REVERT: C 402 GLN cc_start: 0.7622 (mm110) cc_final: 0.7279 (mm110) REVERT: C 500 LYS cc_start: 0.7689 (mtmt) cc_final: 0.6914 (mmtm) REVERT: C 655 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 735 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7382 (p0) REVERT: C 788 ILE cc_start: 0.8515 (tt) cc_final: 0.8305 (pt) REVERT: C 827 ASP cc_start: 0.7756 (m-30) cc_final: 0.7329 (m-30) REVERT: C 835 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7573 (t80) REVERT: C 934 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7739 (mm) REVERT: C 1003 LEU cc_start: 0.8103 (mm) cc_final: 0.7693 (tt) REVERT: C 1028 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7979 (tttt) REVERT: C 1091 GLN cc_start: 0.7080 (tt0) cc_final: 0.6574 (mt0) REVERT: C 1096 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7942 (tp) REVERT: C 1185 MET cc_start: 0.7934 (mtt) cc_final: 0.7699 (mmm) outliers start: 127 outliers final: 90 residues processed: 309 average time/residue: 1.0289 time to fit residues: 399.6815 Evaluate side-chains 300 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 191 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 292 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30225 Z= 0.273 Angle : 0.591 12.664 41157 Z= 0.308 Chirality : 0.046 0.565 4908 Planarity : 0.005 0.080 5172 Dihedral : 7.936 93.295 5916 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.97 % Allowed : 13.96 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3618 helix: 1.42 (0.20), residues: 795 sheet: -0.31 (0.17), residues: 861 loop : -1.45 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 515 HIS 0.008 0.001 HIS B 799 PHE 0.016 0.002 PHE C 968 TYR 0.018 0.002 TYR C1148 ARG 0.004 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 197 time to evaluate : 3.304 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 43 SER cc_start: 0.8931 (t) cc_final: 0.8495 (p) REVERT: A 187 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7681 (ttmm) REVERT: A 206 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: A 305 ASP cc_start: 0.8214 (m-30) cc_final: 0.7996 (m-30) REVERT: A 351 ASN cc_start: 0.8525 (t0) cc_final: 0.7892 (t0) REVERT: A 400 ASP cc_start: 0.8029 (m-30) cc_final: 0.7583 (m-30) REVERT: A 468 SER cc_start: 0.8264 (t) cc_final: 0.7904 (p) REVERT: A 835 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 912 LYS cc_start: 0.8391 (tttt) cc_final: 0.8146 (ttmt) REVERT: A 1066 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6227 (m-30) REVERT: A 1091 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: A 1131 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7946 (pp) REVERT: A 1219 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5327 (p90) REVERT: B 84 TYR cc_start: 0.7956 (m-80) cc_final: 0.7604 (m-10) REVERT: B 213 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7590 (p90) REVERT: B 241 THR cc_start: 0.8741 (m) cc_final: 0.8368 (p) REVERT: B 345 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7312 (mm-30) REVERT: B 500 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7875 (ptmm) REVERT: B 503 HIS cc_start: 0.7899 (t70) cc_final: 0.7616 (t70) REVERT: B 511 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.4166 (m-80) REVERT: B 537 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7932 (tttt) REVERT: B 630 GLN cc_start: 0.8107 (mt0) cc_final: 0.7785 (mt0) REVERT: B 655 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8766 (mt) REVERT: B 714 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 800 GLU cc_start: 0.8301 (pm20) cc_final: 0.7912 (pt0) REVERT: B 845 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6968 (pt0) REVERT: B 912 LYS cc_start: 0.8406 (tttt) cc_final: 0.8094 (ttmt) REVERT: B 1001 GLN cc_start: 0.6906 (tt0) cc_final: 0.6416 (tm-30) REVERT: B 1091 GLN cc_start: 0.7019 (tt0) cc_final: 0.6745 (tt0) REVERT: B 1105 ARG cc_start: 0.6891 (ttt90) cc_final: 0.6504 (tpp80) REVERT: B 1112 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: B 1149 LYS cc_start: 0.8640 (tttt) cc_final: 0.8266 (tttp) REVERT: C 14 VAL cc_start: 0.6987 (t) cc_final: 0.6515 (p) REVERT: C 155 MET cc_start: 0.8895 (mmm) cc_final: 0.8432 (mmm) REVERT: C 213 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7613 (p90) REVERT: C 374 ASP cc_start: 0.7368 (m-30) cc_final: 0.6180 (OUTLIER) REVERT: C 402 GLN cc_start: 0.7650 (mm110) cc_final: 0.7375 (mm-40) REVERT: C 500 LYS cc_start: 0.7723 (mtmt) cc_final: 0.6854 (mmtt) REVERT: C 655 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8694 (mt) REVERT: C 735 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7436 (p0) REVERT: C 827 ASP cc_start: 0.7777 (m-30) cc_final: 0.7349 (m-30) REVERT: C 835 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7560 (t80) REVERT: C 934 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7836 (mm) REVERT: C 1028 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (tttt) REVERT: C 1091 GLN cc_start: 0.7131 (tt0) cc_final: 0.6623 (mt0) REVERT: C 1096 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7971 (tp) outliers start: 129 outliers final: 96 residues processed: 304 average time/residue: 1.0263 time to fit residues: 392.5571 Evaluate side-chains 306 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 190 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 GLN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 0.0670 chunk 330 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30225 Z= 0.147 Angle : 0.530 11.867 41157 Z= 0.276 Chirality : 0.044 0.565 4908 Planarity : 0.004 0.072 5172 Dihedral : 7.520 92.493 5914 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.11 % Allowed : 14.91 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3618 helix: 1.77 (0.20), residues: 786 sheet: -0.25 (0.17), residues: 858 loop : -1.33 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 444 HIS 0.009 0.001 HIS B 799 PHE 0.013 0.001 PHE A 770 TYR 0.015 0.001 TYR B 203 ARG 0.001 0.000 ARG A1105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 199 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8875 (t) cc_final: 0.8484 (p) REVERT: A 187 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7756 (ttmm) REVERT: A 206 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7350 (mtp85) REVERT: A 305 ASP cc_start: 0.8165 (m-30) cc_final: 0.7891 (m-30) REVERT: A 351 ASN cc_start: 0.8408 (t0) cc_final: 0.7853 (t0) REVERT: A 400 ASP cc_start: 0.8016 (m-30) cc_final: 0.7536 (m-30) REVERT: A 468 SER cc_start: 0.8217 (t) cc_final: 0.7867 (p) REVERT: A 835 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6579 (t80) REVERT: A 912 LYS cc_start: 0.8360 (tttt) cc_final: 0.8127 (ttmt) REVERT: A 1066 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6289 (m-30) REVERT: A 1219 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5401 (p90) REVERT: B 64 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8283 (m) REVERT: B 84 TYR cc_start: 0.7942 (m-80) cc_final: 0.7609 (m-10) REVERT: B 116 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 241 THR cc_start: 0.8702 (m) cc_final: 0.8319 (p) REVERT: B 289 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: B 345 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7215 (mm-30) REVERT: B 500 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7897 (ptmm) REVERT: B 503 HIS cc_start: 0.7928 (t70) cc_final: 0.7553 (t70) REVERT: B 537 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7911 (tttt) REVERT: B 630 GLN cc_start: 0.8016 (mt0) cc_final: 0.7719 (mt0) REVERT: B 655 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8809 (mt) REVERT: B 714 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: B 729 TYR cc_start: 0.7425 (t80) cc_final: 0.7196 (t80) REVERT: B 800 GLU cc_start: 0.8238 (pm20) cc_final: 0.7871 (pt0) REVERT: B 912 LYS cc_start: 0.8384 (tttt) cc_final: 0.8079 (ttmt) REVERT: B 1001 GLN cc_start: 0.6799 (tt0) cc_final: 0.6423 (tm-30) REVERT: B 1091 GLN cc_start: 0.6946 (tt0) cc_final: 0.6437 (tm-30) REVERT: B 1105 ARG cc_start: 0.6792 (ttt90) cc_final: 0.6498 (tpp80) REVERT: B 1112 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: B 1149 LYS cc_start: 0.8586 (tttt) cc_final: 0.8281 (tttp) REVERT: C 14 VAL cc_start: 0.6855 (t) cc_final: 0.6476 (p) REVERT: C 155 MET cc_start: 0.8907 (mmm) cc_final: 0.8346 (mmm) REVERT: C 213 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7940 (p90) REVERT: C 374 ASP cc_start: 0.7287 (m-30) cc_final: 0.6351 (m-30) REVERT: C 402 GLN cc_start: 0.7609 (mm110) cc_final: 0.7340 (mm-40) REVERT: C 500 LYS cc_start: 0.7699 (mtmt) cc_final: 0.6821 (mmtt) REVERT: C 655 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8703 (mt) REVERT: C 735 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7366 (p0) REVERT: C 827 ASP cc_start: 0.7747 (m-30) cc_final: 0.7317 (m-30) REVERT: C 934 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7709 (mm) REVERT: C 1028 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7962 (tttt) REVERT: C 1091 GLN cc_start: 0.7054 (tt0) cc_final: 0.6556 (mt0) REVERT: C 1096 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7913 (tp) REVERT: C 1185 MET cc_start: 0.7916 (mtt) cc_final: 0.7675 (mmm) outliers start: 101 outliers final: 74 residues processed: 285 average time/residue: 0.9834 time to fit residues: 354.1747 Evaluate side-chains 284 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 192 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1155 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1076 ARG Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 286 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091005 restraints weight = 41536.379| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.55 r_work: 0.2886 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30225 Z= 0.160 Angle : 0.529 9.650 41157 Z= 0.275 Chirality : 0.044 0.594 4908 Planarity : 0.004 0.072 5172 Dihedral : 7.302 91.881 5909 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.05 % Allowed : 15.06 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3618 helix: 1.70 (0.20), residues: 798 sheet: -0.24 (0.17), residues: 858 loop : -1.31 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 444 HIS 0.009 0.001 HIS B 799 PHE 0.013 0.001 PHE A 770 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG C 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8695.35 seconds wall clock time: 157 minutes 43.88 seconds (9463.88 seconds total)