Starting phenix.real_space_refine on Wed May 15 05:05:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y19_38828/05_2024/8y19_38828.pdb" } resolution = 2.3 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= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 18729 2.51 5 N 4734 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" 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 GLU 930": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B GLU 635": "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 GLU 930": "OE1" <-> "OE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 845": "OE1" <-> "OE2" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C GLU 930": "OE1" <-> "OE2" Residue "C ARG 932": "NH1" <-> "NH2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "C GLU 1108": "OE1" <-> "OE2" Residue "C GLU 1112": "OE1" <-> "OE2" Time to flip residues: 0.06s 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: 13.98, per 1000 atoms: 0.47 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=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.93 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.93 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=2.04 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.04 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.93 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 5.0 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: 78 helices and 69 sheets defined 24.1% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.605A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.799A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.581A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.892A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.669A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.971A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 485 " --> pdb=" O VAL A 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 485' Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.566A 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 831 removed outlier: 3.976A pdb=" N GLU A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 863 removed outlier: 3.782A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.627A 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: 3.652A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.583A 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: 3.821A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.605A 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: 3.801A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.582A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.892A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.746A 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: 3.668A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.971A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 485 " --> pdb=" O VAL B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.566A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.977A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 863 removed outlier: 3.782A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.627A 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: 3.652A 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: 3.583A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.822A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.605A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.800A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.582A 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: 3.892A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.669A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.972A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 485 " --> pdb=" O VAL C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 485' Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.567A 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 831 removed outlier: 3.978A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.781A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.651A 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 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.584A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.822A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.677A 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: 8.123A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.890A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.110A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA C 315 " --> pdb=" O CYS C 619 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.992A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.490A pdb=" N LEU A 146 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 188 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 148 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 186 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.655A 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: 4.026A pdb=" N ALA A 315 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.501A 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: 6.602A 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: 6.581A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.581A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB6, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.359A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB8, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.562A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.326A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.865A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.294A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC7, first strand: chain 'A' and resid 1175 through 1180 removed outlier: 4.645A pdb=" N GLY A1188 " --> pdb=" O TYR A1193 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 removed outlier: 8.124A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 59 through 68 removed outlier: 3.891A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.992A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.489A pdb=" N LEU B 146 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 188 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 148 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 186 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 150 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD5, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD7, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.026A pdb=" N ALA B 315 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.602A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.581A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.581A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE3, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.359A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.561A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.303A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.864A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.295A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AF2, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AF3, first strand: chain 'B' and resid 1175 through 1180 removed outlier: 4.646A pdb=" N GLY B1188 " --> pdb=" O TYR B1193 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'C' and resid 38 through 39 removed outlier: 8.123A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 59 through 68 removed outlier: 3.891A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.993A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.490A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AG1, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG2, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG3, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.602A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.582A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.582A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG7, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.360A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AG9, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.561A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.866A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.293A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH5, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AH6, first strand: chain 'C' and resid 1175 through 1180 removed outlier: 4.644A pdb=" N GLY C1188 " --> pdb=" O TYR C1193 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3006 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: 14.81 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4717 1.32 - 1.45: 8887 1.45 - 1.58: 16423 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C VAL A 818 " pdb=" O VAL A 818 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.12e-02 7.97e+03 2.16e+01 bond pdb=" C VAL C 818 " pdb=" O VAL C 818 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.12e-02 7.97e+03 2.16e+01 bond pdb=" C VAL B 818 " pdb=" O VAL B 818 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.12e-02 7.97e+03 2.10e+01 bond pdb=" CA CYS C 819 " pdb=" C CYS C 819 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.29e-02 6.01e+03 1.89e+01 bond pdb=" CA CYS A 819 " pdb=" C CYS A 819 " ideal model delta sigma weight residual 1.521 1.466 0.056 1.29e-02 6.01e+03 1.87e+01 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.71: 782 106.71 - 113.55: 16778 113.55 - 120.39: 11001 120.39 - 127.23: 12362 127.23 - 134.07: 234 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N ASN C 821 " pdb=" CA ASN C 821 " pdb=" C ASN C 821 " ideal model delta sigma weight residual 111.36 123.62 -12.26 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N ASN A 821 " pdb=" CA ASN A 821 " pdb=" C ASN A 821 " ideal model delta sigma weight residual 111.36 123.62 -12.26 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N ASN B 821 " pdb=" CA ASN B 821 " pdb=" C ASN B 821 " ideal model delta sigma weight residual 111.36 123.60 -12.24 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N TYR B 822 " pdb=" CA TYR B 822 " pdb=" C TYR B 822 " ideal model delta sigma weight residual 110.10 122.96 -12.86 1.49e+00 4.50e-01 7.45e+01 angle pdb=" N TYR C 822 " pdb=" CA TYR C 822 " pdb=" C TYR C 822 " ideal model delta sigma weight residual 110.10 122.92 -12.82 1.49e+00 4.50e-01 7.40e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 17916 20.77 - 41.55: 960 41.55 - 62.32: 285 62.32 - 83.10: 36 83.10 - 103.87: 30 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA SER A 929 " pdb=" C SER A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER B 929 " pdb=" C SER B 929 " pdb=" N GLU B 930 " pdb=" CA GLU B 930 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA SER C 929 " pdb=" C SER C 929 " pdb=" N GLU C 930 " pdb=" CA GLU C 930 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4318 0.089 - 0.179: 556 0.179 - 0.268: 22 0.268 - 0.358: 6 0.358 - 0.447: 6 Chirality restraints: 4908 Sorted by residual: chirality pdb=" CA TYR B 822 " pdb=" N TYR B 822 " pdb=" C TYR B 822 " pdb=" CB TYR B 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA TYR A 822 " pdb=" N TYR A 822 " pdb=" C TYR A 822 " pdb=" CB TYR A 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA TYR C 822 " pdb=" N TYR C 822 " pdb=" C TYR C 822 " pdb=" CB TYR C 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B 93 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 92 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C 93 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 93 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.057 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7542 2.80 - 3.33: 23409 3.33 - 3.85: 48665 3.85 - 4.38: 56808 4.38 - 4.90: 97695 Nonbonded interactions: 234119 Sorted by model distance: nonbonded pdb=" OD1 ASP C 523 " pdb=" OG SER C 526 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP A 523 " pdb=" OG SER A 526 " model vdw 2.279 2.440 nonbonded pdb=" OE2 GLU B 768 " pdb=" OH TYR C 958 " model vdw 2.337 2.440 nonbonded pdb=" OG SER A 405 " pdb=" O SER A 406 " model vdw 2.346 2.440 ... (remaining 234114 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.020 Check model and map are aligned: 0.240 Set scattering table: 0.240 Process input model: 77.130 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 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 : 0.006 0.081 30225 Z= 0.420 Angle : 0.826 12.858 41157 Z= 0.471 Chirality : 0.058 0.447 4908 Planarity : 0.007 0.103 5172 Dihedral : 14.345 103.873 12183 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.19 % Allowed : 5.45 % Favored : 88.35 % 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: -1.92 (0.12), residues: 3618 helix: -1.30 (0.15), residues: 786 sheet: -0.22 (0.17), residues: 864 loop : -1.78 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 174 HIS 0.006 0.001 HIS A 201 PHE 0.025 0.002 PHE A 968 TYR 0.020 0.002 TYR C 822 ARG 0.005 0.001 ARG C 986 *********************** 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 691 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 490 time to evaluate : 3.667 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 26 ASN cc_start: 0.8368 (t0) cc_final: 0.8028 (t0) REVERT: A 43 SER cc_start: 0.7974 (t) cc_final: 0.7425 (p) REVERT: A 69 LYS cc_start: 0.7389 (tttm) cc_final: 0.7185 (ttpm) REVERT: A 120 GLU cc_start: 0.6563 (tp30) cc_final: 0.6328 (tp30) REVERT: A 162 VAL cc_start: 0.7905 (t) cc_final: 0.7542 (m) REVERT: A 187 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6480 (ttmm) REVERT: A 213 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5169 (p90) REVERT: A 345 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 351 ASN cc_start: 0.7651 (m-40) cc_final: 0.7388 (t0) REVERT: A 418 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8131 (pt) REVERT: A 500 LYS cc_start: 0.7379 (mtmt) cc_final: 0.7121 (mttt) REVERT: A 613 GLU cc_start: 0.7233 (tp30) cc_final: 0.6880 (tp30) REVERT: A 630 GLN cc_start: 0.8039 (mt0) cc_final: 0.7724 (mt0) REVERT: A 634 LYS cc_start: 0.7925 (tttp) cc_final: 0.7580 (tttp) REVERT: A 655 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 738 MET cc_start: 0.7380 (mmm) cc_final: 0.6912 (mmm) REVERT: A 788 ILE cc_start: 0.7796 (tt) cc_final: 0.7553 (pt) REVERT: A 835 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6587 (t80) REVERT: A 862 MET cc_start: 0.7420 (mmm) cc_final: 0.6980 (mmm) REVERT: A 863 GLN cc_start: 0.6594 (tp40) cc_final: 0.6333 (tp40) REVERT: A 879 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7625 (p) REVERT: A 1050 LYS cc_start: 0.8016 (mttm) cc_final: 0.7795 (mttm) REVERT: A 1060 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6719 (mm-30) REVERT: A 1068 PRO cc_start: 0.7343 (Cg_exo) cc_final: 0.7031 (Cg_endo) REVERT: A 1071 GLN cc_start: 0.6943 (mt0) cc_final: 0.6509 (mp10) REVERT: A 1076 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6560 (mtm180) REVERT: A 1105 ARG cc_start: 0.6136 (ttt90) cc_final: 0.5885 (tpp80) REVERT: B 27 ASP cc_start: 0.6709 (p0) cc_final: 0.6439 (t0) REVERT: B 39 VAL cc_start: 0.7617 (t) cc_final: 0.7407 (p) REVERT: B 43 SER cc_start: 0.8224 (t) cc_final: 0.7902 (p) REVERT: B 52 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 69 LYS cc_start: 0.7226 (tttm) cc_final: 0.6779 (tttp) REVERT: B 118 TYR cc_start: 0.7351 (m-80) cc_final: 0.6926 (m-80) REVERT: B 155 MET cc_start: 0.8079 (mmm) cc_final: 0.7633 (mmm) REVERT: B 205 GLU cc_start: 0.6942 (tt0) cc_final: 0.6707 (tt0) REVERT: B 218 MET cc_start: 0.8017 (mtm) cc_final: 0.7697 (mtm) REVERT: B 241 THR cc_start: 0.8144 (m) cc_final: 0.7455 (p) REVERT: B 356 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 369 SER cc_start: 0.8034 (t) cc_final: 0.7559 (p) REVERT: B 399 ASP cc_start: 0.7413 (m-30) cc_final: 0.7198 (m-30) REVERT: B 402 GLN cc_start: 0.7585 (mm110) cc_final: 0.7359 (mm-40) REVERT: B 528 TYR cc_start: 0.7244 (m-80) cc_final: 0.7022 (m-10) REVERT: B 634 LYS cc_start: 0.7409 (tttp) cc_final: 0.7160 (tttp) REVERT: B 655 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 659 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7481 (ttpt) REVERT: B 712 TYR cc_start: 0.8248 (p90) cc_final: 0.7892 (p90) REVERT: B 731 VAL cc_start: 0.7866 (p) cc_final: 0.7635 (m) REVERT: B 780 GLU cc_start: 0.7583 (pm20) cc_final: 0.7291 (pm20) REVERT: B 835 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 863 GLN cc_start: 0.6793 (tp40) cc_final: 0.6340 (tm130) REVERT: B 865 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7640 (t) REVERT: B 879 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 891 LEU cc_start: 0.7905 (tt) cc_final: 0.7677 (tt) REVERT: B 912 LYS cc_start: 0.7897 (tttt) cc_final: 0.7696 (tptt) REVERT: B 967 MET cc_start: 0.7956 (mtp) cc_final: 0.7527 (mtp) REVERT: B 994 MET cc_start: 0.8067 (tpp) cc_final: 0.7665 (tpp) REVERT: B 1010 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7645 (tttt) REVERT: B 1024 SER cc_start: 0.8013 (m) cc_final: 0.7725 (t) REVERT: B 1038 GLN cc_start: 0.7015 (mm110) cc_final: 0.6357 (mt0) REVERT: B 1066 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.5895 (p0) REVERT: B 1076 ARG cc_start: 0.6696 (mtp180) cc_final: 0.6471 (mtp85) REVERT: B 1091 GLN cc_start: 0.6850 (tt0) cc_final: 0.6400 (tt0) REVERT: B 1095 ASP cc_start: 0.6594 (m-30) cc_final: 0.6302 (m-30) REVERT: B 1199 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7066 (p0) REVERT: C 58 ASN cc_start: 0.5843 (OUTLIER) cc_final: 0.5553 (m110) REVERT: C 88 LEU cc_start: 0.7756 (mt) cc_final: 0.7183 (pp) REVERT: C 120 GLU cc_start: 0.6548 (tp30) cc_final: 0.6288 (mm-30) REVERT: C 145 ILE cc_start: 0.7593 (mt) cc_final: 0.7155 (mp) REVERT: C 162 VAL cc_start: 0.7961 (t) cc_final: 0.7511 (m) REVERT: C 176 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7670 (mm) REVERT: C 187 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (mmmt) REVERT: C 205 GLU cc_start: 0.6353 (tt0) cc_final: 0.6077 (tt0) REVERT: C 206 ARG cc_start: 0.7390 (mtp85) cc_final: 0.6675 (mtp85) REVERT: C 213 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.5892 (p90) REVERT: C 218 MET cc_start: 0.7747 (mtm) cc_final: 0.7514 (mtm) REVERT: C 273 HIS cc_start: 0.7658 (m-70) cc_final: 0.7447 (m170) REVERT: C 356 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 402 GLN cc_start: 0.7062 (mm110) cc_final: 0.6784 (mm-40) REVERT: C 415 LYS cc_start: 0.7402 (tttt) cc_final: 0.6962 (ttmm) REVERT: C 503 HIS cc_start: 0.7818 (t70) cc_final: 0.7522 (t70) REVERT: C 511 TYR cc_start: 0.2434 (OUTLIER) cc_final: 0.1582 (m-80) REVERT: C 528 TYR cc_start: 0.7260 (m-80) cc_final: 0.6989 (m-10) REVERT: C 584 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6946 (t0) REVERT: C 630 GLN cc_start: 0.7276 (mt0) cc_final: 0.6533 (mp10) REVERT: C 659 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6896 (tttt) REVERT: C 788 ILE cc_start: 0.7869 (tt) cc_final: 0.7372 (pp) REVERT: C 844 ASN cc_start: 0.7110 (m-40) cc_final: 0.6765 (m-40) REVERT: C 851 ASP cc_start: 0.6514 (m-30) cc_final: 0.6286 (m-30) REVERT: C 879 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8157 (m) REVERT: C 885 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7667 (tptp) REVERT: C 993 THR cc_start: 0.7839 (p) cc_final: 0.7604 (t) REVERT: C 1003 LEU cc_start: 0.7225 (mt) cc_final: 0.7016 (tt) REVERT: C 1013 LEU cc_start: 0.7933 (tp) cc_final: 0.7639 (tm) REVERT: C 1030 GLN cc_start: 0.6708 (mt0) cc_final: 0.6413 (tp40) REVERT: C 1069 GLU cc_start: 0.6929 (tp30) cc_final: 0.6688 (mp0) REVERT: C 1071 GLN cc_start: 0.6775 (mt0) cc_final: 0.6416 (mm-40) REVERT: C 1076 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6584 (mtm-85) REVERT: C 1091 GLN cc_start: 0.6893 (tt0) cc_final: 0.6077 (mt0) REVERT: C 1095 ASP cc_start: 0.6238 (m-30) cc_final: 0.5978 (m-30) REVERT: C 1096 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (tp) REVERT: C 1105 ARG cc_start: 0.6150 (ttt90) cc_final: 0.5928 (tpp80) REVERT: C 1118 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 1149 LYS cc_start: 0.7704 (tttt) cc_final: 0.7485 (tttm) REVERT: C 1181 ASN cc_start: 0.6573 (m-40) cc_final: 0.6368 (m-40) REVERT: C 1219 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4607 (p90) outliers start: 201 outliers final: 38 residues processed: 634 average time/residue: 1.1129 time to fit residues: 862.2977 Evaluate side-chains 376 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 310 time to evaluate : 3.195 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR 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 58 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 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: 3.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 630 GLN A 854 GLN A 876 HIS A 998 ASN A1079 ASN A1091 GLN A1174 GLN A1201 ASN B 204 GLN B 331 ASN B 353 ASN B 876 HIS B 998 ASN B1001 GLN B1091 GLN C 26 ASN C 204 GLN C 351 ASN C 531 ASN C 630 GLN C 876 HIS C 894 GLN C1001 GLN C1091 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 30225 Z= 0.253 Angle : 0.646 10.329 41157 Z= 0.346 Chirality : 0.049 0.827 4908 Planarity : 0.006 0.089 5172 Dihedral : 10.022 98.068 5951 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.22 % Allowed : 9.83 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.13), residues: 3618 helix: 0.70 (0.19), residues: 801 sheet: -0.08 (0.16), residues: 876 loop : -1.50 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 174 HIS 0.008 0.001 HIS C 799 PHE 0.021 0.002 PHE B 74 TYR 0.025 0.002 TYR B 212 ARG 0.004 0.001 ARG B 693 *********************** 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 471 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 334 time to evaluate : 3.248 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 26 ASN cc_start: 0.8459 (t0) cc_final: 0.8193 (t0) REVERT: A 43 SER cc_start: 0.7923 (t) cc_final: 0.7401 (p) REVERT: A 114 ASN cc_start: 0.4275 (m-40) cc_final: 0.4071 (m-40) REVERT: A 120 GLU cc_start: 0.6574 (tp30) cc_final: 0.6067 (tp30) REVERT: A 187 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6648 (tppt) REVERT: A 213 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5155 (p90) REVERT: A 273 HIS cc_start: 0.7028 (m-70) cc_final: 0.6732 (m-70) REVERT: A 345 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 351 ASN cc_start: 0.7736 (m-40) cc_final: 0.7372 (t0) REVERT: A 418 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8119 (pt) REVERT: A 494 ILE cc_start: 0.7937 (mt) cc_final: 0.7721 (mp) REVERT: A 500 LYS cc_start: 0.7229 (mtmt) cc_final: 0.6938 (mttt) REVERT: A 568 SER cc_start: 0.7507 (OUTLIER) cc_final: 0.7147 (p) REVERT: A 570 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7078 (p0) REVERT: A 613 GLU cc_start: 0.7322 (tp30) cc_final: 0.6910 (tp30) REVERT: A 630 GLN cc_start: 0.8068 (mt0) cc_final: 0.7714 (mt0) REVERT: A 634 LYS cc_start: 0.7770 (tttp) cc_final: 0.7505 (tttp) REVERT: A 788 ILE cc_start: 0.7710 (tt) cc_final: 0.7345 (pt) REVERT: A 835 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6126 (t80) REVERT: A 862 MET cc_start: 0.7164 (mmm) cc_final: 0.6876 (mmm) REVERT: A 1060 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6686 (mm-30) REVERT: A 1068 PRO cc_start: 0.7361 (Cg_exo) cc_final: 0.7068 (Cg_endo) REVERT: A 1071 GLN cc_start: 0.6779 (mt0) cc_final: 0.6383 (tt0) REVERT: A 1076 ARG cc_start: 0.6927 (mtp180) cc_final: 0.6459 (mtm180) REVERT: B 43 SER cc_start: 0.8197 (t) cc_final: 0.7868 (p) REVERT: B 69 LYS cc_start: 0.7198 (tttm) cc_final: 0.6755 (ttmp) REVERT: B 118 TYR cc_start: 0.7415 (m-80) cc_final: 0.7138 (m-80) REVERT: B 155 MET cc_start: 0.8019 (mmm) cc_final: 0.7468 (mmm) REVERT: B 205 GLU cc_start: 0.6990 (tt0) cc_final: 0.6775 (tt0) REVERT: B 218 MET cc_start: 0.7765 (mtm) cc_final: 0.7558 (mtm) REVERT: B 311 VAL cc_start: 0.7828 (t) cc_final: 0.7536 (m) REVERT: B 356 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7333 (mm) REVERT: B 369 SER cc_start: 0.8008 (t) cc_final: 0.7606 (p) REVERT: B 402 GLN cc_start: 0.7517 (mm110) cc_final: 0.7300 (mm-40) REVERT: B 528 TYR cc_start: 0.7214 (m-80) cc_final: 0.6982 (m-10) REVERT: B 634 LYS cc_start: 0.7323 (tttp) cc_final: 0.7084 (tttp) REVERT: B 712 TYR cc_start: 0.8242 (p90) cc_final: 0.8017 (p90) REVERT: B 780 GLU cc_start: 0.7428 (pm20) cc_final: 0.7217 (pm20) REVERT: B 835 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6466 (t80) REVERT: B 863 GLN cc_start: 0.6475 (tp40) cc_final: 0.6100 (tm130) REVERT: B 891 LEU cc_start: 0.8049 (tt) cc_final: 0.7823 (tt) REVERT: B 952 GLU cc_start: 0.5995 (mm-30) cc_final: 0.5742 (mm-30) REVERT: B 994 MET cc_start: 0.8042 (tpp) cc_final: 0.7829 (tpp) REVERT: B 1003 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6535 (tt) REVERT: B 1010 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7266 (tttt) REVERT: B 1038 GLN cc_start: 0.6594 (mm110) cc_final: 0.5961 (mt0) REVERT: B 1076 ARG cc_start: 0.6741 (mtp180) cc_final: 0.6508 (mtp85) REVERT: B 1091 GLN cc_start: 0.7038 (tt0) cc_final: 0.6375 (tt0) REVERT: B 1095 ASP cc_start: 0.6486 (m-30) cc_final: 0.6172 (m-30) REVERT: C 39 VAL cc_start: 0.8123 (t) cc_final: 0.7837 (p) REVERT: C 88 LEU cc_start: 0.7823 (mt) cc_final: 0.7197 (pp) REVERT: C 120 GLU cc_start: 0.6898 (tp30) cc_final: 0.6684 (mm-30) REVERT: C 162 VAL cc_start: 0.7896 (t) cc_final: 0.7155 (m) REVERT: C 164 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7031 (mptt) REVERT: C 176 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7769 (mm) REVERT: C 182 LEU cc_start: 0.8075 (mt) cc_final: 0.7873 (mp) REVERT: C 187 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6618 (mmtp) REVERT: C 205 GLU cc_start: 0.6275 (tt0) cc_final: 0.6011 (tt0) REVERT: C 206 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6742 (mtp85) REVERT: C 213 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.5735 (p90) REVERT: C 218 MET cc_start: 0.7557 (mtm) cc_final: 0.7322 (mtm) REVERT: C 402 GLN cc_start: 0.6957 (mm110) cc_final: 0.6605 (mm-40) REVERT: C 415 LYS cc_start: 0.7349 (tttt) cc_final: 0.6929 (ttmm) REVERT: C 511 TYR cc_start: 0.2447 (OUTLIER) cc_final: 0.1573 (m-80) REVERT: C 528 TYR cc_start: 0.7363 (m-80) cc_final: 0.6991 (m-10) REVERT: C 584 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 630 GLN cc_start: 0.7288 (mt0) cc_final: 0.6504 (mp10) REVERT: C 659 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6834 (tttt) REVERT: C 788 ILE cc_start: 0.7787 (tt) cc_final: 0.7378 (pp) REVERT: C 844 ASN cc_start: 0.6941 (m-40) cc_final: 0.6647 (m-40) REVERT: C 885 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7592 (tptp) REVERT: C 1030 GLN cc_start: 0.6670 (mt0) cc_final: 0.6435 (tp40) REVERT: C 1071 GLN cc_start: 0.6731 (mt0) cc_final: 0.6368 (mm-40) REVERT: C 1076 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6635 (mtm-85) REVERT: C 1091 GLN cc_start: 0.6982 (tt0) cc_final: 0.5962 (mt0) REVERT: C 1095 ASP cc_start: 0.6110 (m-30) cc_final: 0.5798 (m-30) REVERT: C 1149 LYS cc_start: 0.7740 (tttt) cc_final: 0.7539 (tttm) outliers start: 137 outliers final: 66 residues processed: 439 average time/residue: 1.0474 time to fit residues: 569.4907 Evaluate side-chains 377 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 294 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS 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 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 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 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1030 GLN 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 1200 LYS Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR 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 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 1024 SER 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 1199 ASP Chi-restraints excluded: chain C residue 1203 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: 0.7980 chunk 272 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 840 ASN A 854 GLN A1059 GLN A1091 GLN A1135 GLN A1174 GLN A1201 ASN B 384 ASN B 562 HIS B1001 GLN B1059 GLN B1135 GLN C 351 ASN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN C1023 ASN C1079 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30225 Z= 0.323 Angle : 0.708 14.031 41157 Z= 0.380 Chirality : 0.051 0.814 4908 Planarity : 0.006 0.085 5172 Dihedral : 9.514 94.682 5921 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 4.47 % Allowed : 10.54 % Favored : 85.00 % Cbeta Deviations : 0.03 % 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: -0.75 (0.13), residues: 3618 helix: 1.14 (0.19), residues: 801 sheet: -0.13 (0.16), residues: 837 loop : -1.39 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 444 HIS 0.007 0.001 HIS C 799 PHE 0.022 0.002 PHE A 764 TYR 0.024 0.002 TYR B 212 ARG 0.007 0.001 ARG B 693 *********************** 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 441 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 296 time to evaluate : 3.013 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: 0.8030 (t) cc_final: 0.7405 (p) REVERT: A 69 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7076 (ttpp) REVERT: A 120 GLU cc_start: 0.6780 (tp30) cc_final: 0.6085 (tp30) REVERT: A 187 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6690 (ttmm) REVERT: A 273 HIS cc_start: 0.7038 (m-70) cc_final: 0.6700 (m-70) REVERT: A 345 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6873 (mt-10) REVERT: A 351 ASN cc_start: 0.7797 (m-40) cc_final: 0.7361 (t0) REVERT: A 494 ILE cc_start: 0.7822 (mt) cc_final: 0.7608 (mp) REVERT: A 500 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6897 (mttt) REVERT: A 568 SER cc_start: 0.7516 (OUTLIER) cc_final: 0.7157 (p) REVERT: A 570 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7072 (p0) REVERT: A 613 GLU cc_start: 0.7391 (tp30) cc_final: 0.6972 (tp30) REVERT: A 630 GLN cc_start: 0.8145 (mt0) cc_final: 0.7791 (mt0) REVERT: A 788 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7189 (pt) REVERT: A 835 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6284 (t80) REVERT: A 1060 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7120 (tt0) REVERT: A 1071 GLN cc_start: 0.6817 (mt0) cc_final: 0.6362 (tt0) REVERT: A 1076 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6517 (mtm180) REVERT: B 43 SER cc_start: 0.8065 (t) cc_final: 0.7635 (p) REVERT: B 57 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8235 (mp) REVERT: B 69 LYS cc_start: 0.7224 (tttm) cc_final: 0.6723 (ttmp) REVERT: B 118 TYR cc_start: 0.7534 (m-80) cc_final: 0.7000 (m-80) REVERT: B 205 GLU cc_start: 0.6981 (tt0) cc_final: 0.6749 (tt0) REVERT: B 206 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7306 (mtt90) REVERT: B 218 MET cc_start: 0.7734 (mtm) cc_final: 0.7511 (mtm) REVERT: B 311 VAL cc_start: 0.7971 (t) cc_final: 0.7764 (m) REVERT: B 356 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7346 (mm) REVERT: B 369 SER cc_start: 0.7951 (t) cc_final: 0.7590 (p) REVERT: B 402 GLN cc_start: 0.7596 (mm110) cc_final: 0.7371 (mm-40) REVERT: B 634 LYS cc_start: 0.7345 (tttp) cc_final: 0.7130 (tttp) REVERT: B 780 GLU cc_start: 0.7509 (pm20) cc_final: 0.7252 (pm20) REVERT: B 835 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6440 (t80) REVERT: B 863 GLN cc_start: 0.6552 (tp40) cc_final: 0.6178 (tm130) REVERT: B 891 LEU cc_start: 0.8052 (tt) cc_final: 0.7845 (tt) REVERT: B 952 GLU cc_start: 0.6245 (mm-30) cc_final: 0.6007 (mm-30) REVERT: B 994 MET cc_start: 0.8101 (tpp) cc_final: 0.7773 (tpt) REVERT: B 1003 LEU cc_start: 0.6928 (mm) cc_final: 0.6528 (tt) REVERT: B 1010 LYS cc_start: 0.7413 (ttmm) cc_final: 0.7109 (tttt) REVERT: B 1038 GLN cc_start: 0.6468 (mm110) cc_final: 0.5922 (mt0) REVERT: B 1071 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6082 (mp10) REVERT: B 1076 ARG cc_start: 0.6853 (mtp180) cc_final: 0.6517 (mtp85) REVERT: B 1091 GLN cc_start: 0.6943 (tt0) cc_final: 0.6577 (tt0) REVERT: C 39 VAL cc_start: 0.8108 (t) cc_final: 0.7792 (p) REVERT: C 88 LEU cc_start: 0.7809 (mt) cc_final: 0.7088 (pt) REVERT: C 120 GLU cc_start: 0.7055 (tp30) cc_final: 0.6772 (mm-30) REVERT: C 164 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.6916 (mptt) REVERT: C 176 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7734 (mm) REVERT: C 182 LEU cc_start: 0.7984 (mt) cc_final: 0.7570 (tp) REVERT: C 187 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6452 (mmtp) REVERT: C 205 GLU cc_start: 0.6235 (tt0) cc_final: 0.5947 (tt0) REVERT: C 206 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6591 (mtp85) REVERT: C 213 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5572 (p90) REVERT: C 218 MET cc_start: 0.7606 (mtm) cc_final: 0.7350 (mtm) REVERT: C 241 THR cc_start: 0.8178 (m) cc_final: 0.7460 (p) REVERT: C 402 GLN cc_start: 0.7066 (mm110) cc_final: 0.6717 (mm-40) REVERT: C 415 LYS cc_start: 0.7351 (tttt) cc_final: 0.6933 (ttmm) REVERT: C 511 TYR cc_start: 0.2501 (OUTLIER) cc_final: 0.1898 (m-80) REVERT: C 528 TYR cc_start: 0.7433 (m-80) cc_final: 0.6894 (m-80) REVERT: C 584 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7179 (t0) REVERT: C 630 GLN cc_start: 0.7384 (mt0) cc_final: 0.6610 (mp10) REVERT: C 659 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6897 (tttt) REVERT: C 788 ILE cc_start: 0.7790 (tt) cc_final: 0.7351 (pp) REVERT: C 844 ASN cc_start: 0.6903 (m-40) cc_final: 0.6654 (m-40) REVERT: C 885 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7582 (tptp) REVERT: C 1066 ASP cc_start: 0.6200 (p0) cc_final: 0.5992 (p0) REVERT: C 1071 GLN cc_start: 0.6833 (mt0) cc_final: 0.6397 (mp-120) REVERT: C 1076 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6729 (mtt-85) REVERT: C 1091 GLN cc_start: 0.7143 (tt0) cc_final: 0.6062 (mp10) REVERT: C 1095 ASP cc_start: 0.6218 (m-30) cc_final: 0.5956 (m-30) REVERT: C 1115 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7798 (mmmm) REVERT: C 1149 LYS cc_start: 0.7854 (tttt) cc_final: 0.7645 (tttm) outliers start: 145 outliers final: 79 residues processed: 407 average time/residue: 1.0749 time to fit residues: 541.1281 Evaluate side-chains 380 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 281 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 432 VAL 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 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1071 GLN 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 1205 MET Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR 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 162 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1203 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: 2.9990 chunk 246 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A1091 GLN B 838 ASN B 984 GLN B 998 ASN B1045 GLN B1059 GLN C 351 ASN C 998 ASN C1001 GLN C1122 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30225 Z= 0.344 Angle : 0.722 14.146 41157 Z= 0.386 Chirality : 0.054 1.268 4908 Planarity : 0.006 0.084 5172 Dihedral : 9.440 93.549 5919 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 4.81 % Allowed : 10.75 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.70 (0.13), residues: 3618 helix: 1.20 (0.19), residues: 801 sheet: -0.11 (0.16), residues: 837 loop : -1.36 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 444 HIS 0.009 0.001 HIS C 799 PHE 0.022 0.003 PHE A 764 TYR 0.022 0.002 TYR B 212 ARG 0.008 0.001 ARG B 693 *********************** 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 443 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 287 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8036 (t) cc_final: 0.7373 (p) REVERT: A 120 GLU cc_start: 0.6779 (tp30) cc_final: 0.6093 (tp30) REVERT: A 187 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6724 (ttmm) REVERT: A 273 HIS cc_start: 0.7046 (m-70) cc_final: 0.6683 (m-70) REVERT: A 351 ASN cc_start: 0.7770 (m-40) cc_final: 0.7418 (t0) REVERT: A 457 SER cc_start: 0.7017 (p) cc_final: 0.6764 (t) REVERT: A 570 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 613 GLU cc_start: 0.7392 (tp30) cc_final: 0.6928 (mp0) REVERT: A 630 GLN cc_start: 0.8134 (mt0) cc_final: 0.7771 (mt0) REVERT: A 735 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6291 (p0) REVERT: A 788 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6996 (pt) REVERT: A 1060 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7098 (tt0) REVERT: A 1071 GLN cc_start: 0.6810 (mt0) cc_final: 0.6354 (tt0) REVERT: A 1076 ARG cc_start: 0.6911 (mtp180) cc_final: 0.6473 (mtm180) REVERT: B 43 SER cc_start: 0.8080 (t) cc_final: 0.7603 (p) REVERT: B 69 LYS cc_start: 0.7218 (tttm) cc_final: 0.6719 (ttmp) REVERT: B 118 TYR cc_start: 0.7430 (m-80) cc_final: 0.6995 (m-80) REVERT: B 205 GLU cc_start: 0.6983 (tt0) cc_final: 0.6756 (tt0) REVERT: B 206 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7304 (mtt90) REVERT: B 218 MET cc_start: 0.7714 (mtm) cc_final: 0.7478 (mtm) REVERT: B 245 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6968 (tt) REVERT: B 356 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7364 (mm) REVERT: B 369 SER cc_start: 0.7977 (t) cc_final: 0.7639 (p) REVERT: B 402 GLN cc_start: 0.7633 (mm110) cc_final: 0.7413 (mm-40) REVERT: B 745 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: B 780 GLU cc_start: 0.7497 (pm20) cc_final: 0.7232 (pm20) REVERT: B 835 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6509 (t80) REVERT: B 863 GLN cc_start: 0.6586 (tp40) cc_final: 0.6212 (tm-30) REVERT: B 891 LEU cc_start: 0.8031 (tt) cc_final: 0.7801 (tt) REVERT: B 952 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5934 (mm-30) REVERT: B 994 MET cc_start: 0.8071 (tpp) cc_final: 0.7723 (tpt) REVERT: B 1003 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6487 (tt) REVERT: B 1010 LYS cc_start: 0.7386 (ttmm) cc_final: 0.7065 (tttt) REVERT: B 1038 GLN cc_start: 0.6461 (mm110) cc_final: 0.5878 (mt0) REVERT: B 1071 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6028 (mp10) REVERT: B 1076 ARG cc_start: 0.6832 (mtp180) cc_final: 0.6507 (mtp85) REVERT: B 1091 GLN cc_start: 0.6884 (tt0) cc_final: 0.6520 (tt0) REVERT: C 117 LEU cc_start: 0.8384 (tp) cc_final: 0.8056 (tm) REVERT: C 120 GLU cc_start: 0.7132 (tp30) cc_final: 0.6852 (mm-30) REVERT: C 162 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7622 (m) REVERT: C 164 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.6930 (mptt) REVERT: C 176 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7769 (mm) REVERT: C 187 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6489 (mmtp) REVERT: C 206 ARG cc_start: 0.7394 (mtp85) cc_final: 0.6718 (mtp85) REVERT: C 213 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.5579 (p90) REVERT: C 241 THR cc_start: 0.8133 (m) cc_final: 0.7455 (p) REVERT: C 402 GLN cc_start: 0.7271 (mm110) cc_final: 0.6887 (mm-40) REVERT: C 415 LYS cc_start: 0.7413 (tttt) cc_final: 0.6982 (ttmm) REVERT: C 511 TYR cc_start: 0.2604 (OUTLIER) cc_final: 0.1918 (m-80) REVERT: C 528 TYR cc_start: 0.7614 (m-80) cc_final: 0.7015 (m-80) REVERT: C 573 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7783 (mp) REVERT: C 584 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7171 (t0) REVERT: C 630 GLN cc_start: 0.7383 (mt0) cc_final: 0.6592 (mp10) REVERT: C 659 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6931 (tttt) REVERT: C 844 ASN cc_start: 0.6955 (m-40) cc_final: 0.6707 (m-40) REVERT: C 885 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7517 (tptp) REVERT: C 1071 GLN cc_start: 0.6831 (mt0) cc_final: 0.6371 (mp-120) REVERT: C 1076 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6678 (mtt-85) REVERT: C 1091 GLN cc_start: 0.7110 (tt0) cc_final: 0.6019 (mp10) REVERT: C 1115 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7813 (mmmm) REVERT: C 1149 LYS cc_start: 0.7859 (tttt) cc_final: 0.7638 (tttp) outliers start: 156 outliers final: 89 residues processed: 407 average time/residue: 1.0671 time to fit residues: 536.9893 Evaluate side-chains 384 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 273 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 432 VAL 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 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1071 GLN 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 1205 MET Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER 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 58 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1203 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: 10.0000 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A1079 ASN A1091 GLN B1059 GLN C 351 ASN C 598 ASN C1001 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30225 Z= 0.232 Angle : 0.634 12.413 41157 Z= 0.339 Chirality : 0.048 0.739 4908 Planarity : 0.005 0.075 5172 Dihedral : 8.862 92.671 5916 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.47 % Allowed : 11.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3618 helix: 1.47 (0.20), residues: 801 sheet: 0.01 (0.16), residues: 873 loop : -1.24 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.007 0.001 HIS C 799 PHE 0.017 0.002 PHE B 968 TYR 0.020 0.002 TYR B 212 ARG 0.004 0.000 ARG B 693 *********************** 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 430 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 285 time to evaluate : 3.523 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: 0.8043 (t) cc_final: 0.7403 (p) REVERT: A 114 ASN cc_start: 0.4236 (m-40) cc_final: 0.4003 (m-40) REVERT: A 120 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6038 (tp30) REVERT: A 187 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6690 (tppt) REVERT: A 273 HIS cc_start: 0.7017 (m-70) cc_final: 0.6652 (m-70) REVERT: A 351 ASN cc_start: 0.7749 (m-40) cc_final: 0.7430 (t0) REVERT: A 568 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 570 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7053 (p0) REVERT: A 613 GLU cc_start: 0.7398 (tp30) cc_final: 0.6986 (mp0) REVERT: A 630 GLN cc_start: 0.8067 (mt0) cc_final: 0.7703 (mt0) REVERT: A 788 ILE cc_start: 0.7637 (tt) cc_final: 0.7193 (pt) REVERT: A 920 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6969 (mm-30) REVERT: A 1060 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7095 (tt0) REVERT: A 1076 ARG cc_start: 0.6726 (mtp180) cc_final: 0.6281 (mtm180) REVERT: A 1097 THR cc_start: 0.7059 (m) cc_final: 0.6760 (p) REVERT: B 43 SER cc_start: 0.8050 (t) cc_final: 0.7645 (p) REVERT: B 69 LYS cc_start: 0.7147 (tttm) cc_final: 0.6680 (ttmp) REVERT: B 118 TYR cc_start: 0.7416 (m-80) cc_final: 0.7032 (m-80) REVERT: B 205 GLU cc_start: 0.6955 (tt0) cc_final: 0.6734 (tt0) REVERT: B 206 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7308 (mtt90) REVERT: B 218 MET cc_start: 0.7699 (mtm) cc_final: 0.7491 (mtm) REVERT: B 245 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6979 (tt) REVERT: B 356 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7334 (mm) REVERT: B 369 SER cc_start: 0.7895 (t) cc_final: 0.7526 (p) REVERT: B 402 GLN cc_start: 0.7616 (mm110) cc_final: 0.7414 (mm-40) REVERT: B 745 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: B 780 GLU cc_start: 0.7447 (pm20) cc_final: 0.7223 (pm20) REVERT: B 835 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6510 (t80) REVERT: B 863 GLN cc_start: 0.6589 (tp40) cc_final: 0.6142 (tm130) REVERT: B 1003 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6434 (tt) REVERT: B 1010 LYS cc_start: 0.7381 (ttmm) cc_final: 0.7058 (tttt) REVERT: B 1038 GLN cc_start: 0.6468 (mm110) cc_final: 0.5882 (mt0) REVERT: B 1071 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: B 1076 ARG cc_start: 0.6764 (mtp180) cc_final: 0.6470 (mtp85) REVERT: B 1091 GLN cc_start: 0.6953 (tt0) cc_final: 0.6589 (tt0) REVERT: C 39 VAL cc_start: 0.8067 (t) cc_final: 0.7730 (p) REVERT: C 117 LEU cc_start: 0.8379 (tp) cc_final: 0.8071 (tm) REVERT: C 120 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: C 162 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7847 (m) REVERT: C 187 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6511 (mmtp) REVERT: C 205 GLU cc_start: 0.6395 (tt0) cc_final: 0.5992 (tt0) REVERT: C 206 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6689 (mtp85) REVERT: C 213 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.5602 (p90) REVERT: C 402 GLN cc_start: 0.7312 (mm110) cc_final: 0.6909 (mm-40) REVERT: C 415 LYS cc_start: 0.7390 (tttt) cc_final: 0.6983 (ttmm) REVERT: C 500 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7235 (mttm) REVERT: C 511 TYR cc_start: 0.2561 (OUTLIER) cc_final: 0.1836 (m-80) REVERT: C 528 TYR cc_start: 0.7589 (m-80) cc_final: 0.7021 (m-80) REVERT: C 573 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 584 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7217 (t0) REVERT: C 630 GLN cc_start: 0.7290 (mt0) cc_final: 0.6483 (mp10) REVERT: C 844 ASN cc_start: 0.6876 (m-40) cc_final: 0.6639 (m-40) REVERT: C 885 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7616 (tptp) REVERT: C 1071 GLN cc_start: 0.6813 (mt0) cc_final: 0.6384 (mp-120) REVERT: C 1076 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6689 (mtt-85) REVERT: C 1091 GLN cc_start: 0.7049 (tt0) cc_final: 0.6041 (mp10) REVERT: C 1149 LYS cc_start: 0.7847 (tttt) cc_final: 0.7625 (tttp) outliers start: 145 outliers final: 79 residues processed: 388 average time/residue: 1.0821 time to fit residues: 520.3494 Evaluate side-chains 370 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 271 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 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 518 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1071 GLN 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 1205 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR 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 58 ASN Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU 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 1199 ASP 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: 0.7980 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 GLN A1079 ASN A1091 GLN B 22 ASN B1059 GLN C 351 ASN C1001 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30225 Z= 0.384 Angle : 0.756 13.694 41157 Z= 0.406 Chirality : 0.053 0.669 4908 Planarity : 0.006 0.078 5172 Dihedral : 9.238 94.177 5909 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 4.90 % Allowed : 11.21 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.66 (0.13), residues: 3618 helix: 1.20 (0.19), residues: 801 sheet: -0.13 (0.16), residues: 837 loop : -1.30 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 515 HIS 0.008 0.001 HIS C 799 PHE 0.023 0.003 PHE A 764 TYR 0.023 0.003 TYR B 212 ARG 0.009 0.001 ARG B 693 *********************** 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 437 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 278 time to evaluate : 3.447 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: 0.8030 (t) cc_final: 0.7380 (p) REVERT: A 114 ASN cc_start: 0.4245 (m-40) cc_final: 0.4004 (m-40) REVERT: A 120 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6156 (tp30) REVERT: A 187 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6708 (tppt) REVERT: A 457 SER cc_start: 0.6945 (p) cc_final: 0.6712 (t) REVERT: A 568 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7135 (p) REVERT: A 570 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7078 (p0) REVERT: A 576 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7643 (t) REVERT: A 613 GLU cc_start: 0.7397 (tp30) cc_final: 0.6964 (mp0) REVERT: A 630 GLN cc_start: 0.8145 (mt0) cc_final: 0.7778 (mt0) REVERT: A 788 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6924 (pt) REVERT: A 835 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6682 (t80) REVERT: A 891 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7897 (tt) REVERT: A 1060 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7096 (tt0) REVERT: A 1071 GLN cc_start: 0.6832 (mt0) cc_final: 0.6358 (tt0) REVERT: A 1076 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6393 (mtm-85) REVERT: B 43 SER cc_start: 0.8093 (t) cc_final: 0.7646 (p) REVERT: B 69 LYS cc_start: 0.7216 (tttm) cc_final: 0.6762 (tttp) REVERT: B 118 TYR cc_start: 0.7488 (m-80) cc_final: 0.7036 (m-80) REVERT: B 205 GLU cc_start: 0.6981 (tt0) cc_final: 0.6756 (tt0) REVERT: B 206 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7302 (mtt90) REVERT: B 213 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.5284 (p90) REVERT: B 218 MET cc_start: 0.7720 (mtm) cc_final: 0.7481 (mtm) REVERT: B 245 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.6988 (tt) REVERT: B 356 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7350 (mm) REVERT: B 369 SER cc_start: 0.8015 (t) cc_final: 0.7690 (p) REVERT: B 745 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: B 835 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6468 (t80) REVERT: B 863 GLN cc_start: 0.6648 (tp40) cc_final: 0.6223 (tm-30) REVERT: B 1003 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6487 (tt) REVERT: B 1010 LYS cc_start: 0.7395 (ttmm) cc_final: 0.7080 (tttt) REVERT: B 1038 GLN cc_start: 0.6395 (mm110) cc_final: 0.5805 (mt0) REVERT: B 1050 LYS cc_start: 0.7892 (mttm) cc_final: 0.7623 (mtpp) REVERT: B 1071 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6053 (mp10) REVERT: B 1076 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6531 (mtp85) REVERT: B 1091 GLN cc_start: 0.6888 (tt0) cc_final: 0.6528 (tt0) REVERT: B 1108 GLU cc_start: 0.6444 (tt0) cc_final: 0.6140 (mt-10) REVERT: C 117 LEU cc_start: 0.8389 (tp) cc_final: 0.8136 (tt) REVERT: C 120 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: C 162 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7836 (m) REVERT: C 176 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 187 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6483 (mmtp) REVERT: C 206 ARG cc_start: 0.7364 (mtp85) cc_final: 0.6682 (mtp85) REVERT: C 213 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.5545 (p90) REVERT: C 241 THR cc_start: 0.8163 (m) cc_final: 0.7617 (p) REVERT: C 252 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6116 (mm-30) REVERT: C 272 GLU cc_start: 0.6375 (mp0) cc_final: 0.6108 (mp0) REVERT: C 399 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: C 402 GLN cc_start: 0.7233 (mm110) cc_final: 0.6820 (mm-40) REVERT: C 415 LYS cc_start: 0.7390 (tttt) cc_final: 0.6923 (ttmm) REVERT: C 511 TYR cc_start: 0.2456 (OUTLIER) cc_final: 0.1753 (m-80) REVERT: C 528 TYR cc_start: 0.7547 (m-80) cc_final: 0.6950 (m-80) REVERT: C 531 ASN cc_start: 0.8871 (m-40) cc_final: 0.8636 (m110) REVERT: C 573 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7769 (mp) REVERT: C 584 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7196 (t0) REVERT: C 630 GLN cc_start: 0.7394 (mt0) cc_final: 0.6590 (mp10) REVERT: C 644 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.7127 (p-90) REVERT: C 844 ASN cc_start: 0.6758 (m-40) cc_final: 0.6542 (m-40) REVERT: C 885 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7525 (tptp) REVERT: C 920 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6720 (mt-10) REVERT: C 1071 GLN cc_start: 0.6908 (mt0) cc_final: 0.6444 (mp10) REVERT: C 1076 ARG cc_start: 0.6881 (mtp180) cc_final: 0.6485 (mtt-85) REVERT: C 1091 GLN cc_start: 0.7045 (tt0) cc_final: 0.6060 (mp10) REVERT: C 1115 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7795 (mmmm) REVERT: C 1149 LYS cc_start: 0.7920 (tttt) cc_final: 0.7700 (tttp) outliers start: 159 outliers final: 89 residues processed: 392 average time/residue: 1.0709 time to fit residues: 521.4332 Evaluate side-chains 382 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 265 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 432 VAL 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 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1071 GLN 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 1205 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 644 TRP Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1199 ASP 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: 0.5980 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN A1091 GLN B 22 ASN B 248 ASN B 838 ASN B1059 GLN B1079 ASN C 351 ASN C 353 ASN C1001 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30225 Z= 0.192 Angle : 0.611 10.590 41157 Z= 0.325 Chirality : 0.047 0.574 4908 Planarity : 0.005 0.071 5172 Dihedral : 8.765 99.176 5907 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.85 % Allowed : 12.45 % Favored : 83.70 % 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: -0.35 (0.14), residues: 3618 helix: 1.57 (0.20), residues: 807 sheet: 0.04 (0.17), residues: 822 loop : -1.14 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 515 HIS 0.007 0.001 HIS C 799 PHE 0.015 0.002 PHE B 968 TYR 0.017 0.001 TYR B 212 ARG 0.003 0.000 ARG B 693 *********************** 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 401 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 276 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8014 (t) cc_final: 0.7385 (p) REVERT: A 114 ASN cc_start: 0.4206 (m-40) cc_final: 0.3952 (m-40) REVERT: A 120 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6033 (tp30) REVERT: A 187 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6695 (tppt) REVERT: A 206 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: A 351 ASN cc_start: 0.7759 (m-40) cc_final: 0.7426 (t0) REVERT: A 568 SER cc_start: 0.7503 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 570 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7051 (p0) REVERT: A 613 GLU cc_start: 0.7393 (tp30) cc_final: 0.7000 (mp0) REVERT: A 630 GLN cc_start: 0.8019 (mt0) cc_final: 0.7647 (mt0) REVERT: A 788 ILE cc_start: 0.7561 (tt) cc_final: 0.7102 (pt) REVERT: A 835 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 891 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 920 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7063 (mm-30) REVERT: A 1060 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7089 (tt0) REVERT: A 1076 ARG cc_start: 0.6701 (mtp180) cc_final: 0.6240 (mtm180) REVERT: A 1097 THR cc_start: 0.7007 (m) cc_final: 0.6784 (p) REVERT: B 43 SER cc_start: 0.8067 (t) cc_final: 0.7654 (p) REVERT: B 69 LYS cc_start: 0.7133 (tttm) cc_final: 0.6686 (ttmp) REVERT: B 118 TYR cc_start: 0.7475 (m-80) cc_final: 0.7042 (m-80) REVERT: B 205 GLU cc_start: 0.6957 (tt0) cc_final: 0.6720 (tt0) REVERT: B 206 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7328 (mtt90) REVERT: B 218 MET cc_start: 0.7657 (mtm) cc_final: 0.7431 (mtm) REVERT: B 245 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7018 (tt) REVERT: B 356 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7376 (mm) REVERT: B 369 SER cc_start: 0.7890 (t) cc_final: 0.7510 (p) REVERT: B 745 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: B 780 GLU cc_start: 0.7494 (pm20) cc_final: 0.7290 (pm20) REVERT: B 835 PHE cc_start: 0.7101 (t80) cc_final: 0.6525 (t80) REVERT: B 863 GLN cc_start: 0.6627 (tp40) cc_final: 0.6134 (tm130) REVERT: B 1003 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6447 (tt) REVERT: B 1010 LYS cc_start: 0.7373 (ttmm) cc_final: 0.7049 (tttt) REVERT: B 1038 GLN cc_start: 0.6339 (mm110) cc_final: 0.5784 (mt0) REVERT: B 1071 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: B 1076 ARG cc_start: 0.6729 (mtp180) cc_final: 0.6505 (mtp85) REVERT: B 1091 GLN cc_start: 0.6923 (tt0) cc_final: 0.6568 (tt0) REVERT: C 117 LEU cc_start: 0.8358 (tp) cc_final: 0.8080 (tm) REVERT: C 120 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: C 162 VAL cc_start: 0.8209 (t) cc_final: 0.7802 (m) REVERT: C 176 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7762 (mm) REVERT: C 187 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6534 (mmtp) REVERT: C 205 GLU cc_start: 0.6279 (tt0) cc_final: 0.6008 (tt0) REVERT: C 206 ARG cc_start: 0.7380 (mtp85) cc_final: 0.6702 (mtp85) REVERT: C 213 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.5642 (p90) REVERT: C 252 GLU cc_start: 0.6646 (mm-30) cc_final: 0.5942 (mm-30) REVERT: C 272 GLU cc_start: 0.6574 (mp0) cc_final: 0.6299 (mp0) REVERT: C 402 GLN cc_start: 0.7201 (mm110) cc_final: 0.6795 (mm-40) REVERT: C 415 LYS cc_start: 0.7389 (tttt) cc_final: 0.6935 (ttmm) REVERT: C 511 TYR cc_start: 0.2354 (OUTLIER) cc_final: 0.1613 (m-80) REVERT: C 528 TYR cc_start: 0.7538 (m-80) cc_final: 0.6980 (m-10) REVERT: C 573 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7734 (mp) REVERT: C 584 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7214 (t0) REVERT: C 630 GLN cc_start: 0.7258 (mt0) cc_final: 0.6448 (mp10) REVERT: C 844 ASN cc_start: 0.6820 (m-40) cc_final: 0.6569 (m-40) REVERT: C 885 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7632 (tptp) REVERT: C 920 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6698 (mt-10) REVERT: C 1069 GLU cc_start: 0.7359 (mp0) cc_final: 0.6801 (tp30) REVERT: C 1071 GLN cc_start: 0.6835 (mt0) cc_final: 0.6383 (mp-120) REVERT: C 1076 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6634 (mtt-85) REVERT: C 1091 GLN cc_start: 0.6936 (tt0) cc_final: 0.5958 (mp10) REVERT: C 1149 LYS cc_start: 0.7819 (tttt) cc_final: 0.7611 (tttp) outliers start: 125 outliers final: 70 residues processed: 372 average time/residue: 1.0891 time to fit residues: 499.4175 Evaluate side-chains 358 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 267 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1071 GLN 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 C residue 14 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU 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 1199 ASP 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: 4.9990 chunk 138 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 272 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1079 ASN A1091 GLN A1201 ASN B 22 ASN B1059 GLN C 26 ASN C 351 ASN C1001 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30225 Z= 0.347 Angle : 0.730 12.621 41157 Z= 0.390 Chirality : 0.052 0.544 4908 Planarity : 0.006 0.075 5172 Dihedral : 8.924 94.320 5902 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 3.88 % Allowed : 12.51 % Favored : 83.61 % 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: -0.55 (0.13), residues: 3618 helix: 1.31 (0.19), residues: 801 sheet: -0.05 (0.17), residues: 837 loop : -1.24 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 515 HIS 0.009 0.001 HIS C 799 PHE 0.022 0.003 PHE A 764 TYR 0.024 0.002 TYR B 212 ARG 0.008 0.001 ARG B 693 *********************** 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 403 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 277 time to evaluate : 3.254 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: 0.8077 (t) cc_final: 0.7397 (p) REVERT: A 114 ASN cc_start: 0.4271 (m-40) cc_final: 0.4034 (m-40) REVERT: A 120 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6115 (tp30) REVERT: A 187 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6676 (tppt) REVERT: A 206 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7476 (mtt180) REVERT: A 272 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: A 457 SER cc_start: 0.6991 (p) cc_final: 0.6752 (t) REVERT: A 568 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7103 (p) REVERT: A 570 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 576 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7656 (t) REVERT: A 613 GLU cc_start: 0.7302 (tp30) cc_final: 0.6926 (mp0) REVERT: A 630 GLN cc_start: 0.8130 (mt0) cc_final: 0.7758 (mt0) REVERT: A 788 ILE cc_start: 0.7453 (tt) cc_final: 0.6898 (pt) REVERT: A 891 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 920 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7075 (mm-30) REVERT: A 1071 GLN cc_start: 0.6814 (mt0) cc_final: 0.6343 (tt0) REVERT: A 1076 ARG cc_start: 0.6865 (mtp180) cc_final: 0.6319 (mtm180) REVERT: B 43 SER cc_start: 0.8035 (t) cc_final: 0.7605 (p) REVERT: B 69 LYS cc_start: 0.7208 (tttm) cc_final: 0.6727 (ttmp) REVERT: B 118 TYR cc_start: 0.7505 (m-80) cc_final: 0.7093 (m-80) REVERT: B 205 GLU cc_start: 0.6967 (tt0) cc_final: 0.6737 (tt0) REVERT: B 206 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7304 (mtt90) REVERT: B 218 MET cc_start: 0.7721 (mtm) cc_final: 0.7484 (mtm) REVERT: B 245 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.6999 (tt) REVERT: B 356 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7344 (mm) REVERT: B 369 SER cc_start: 0.8003 (t) cc_final: 0.7661 (p) REVERT: B 745 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: B 835 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6727 (t80) REVERT: B 863 GLN cc_start: 0.6639 (tp40) cc_final: 0.6137 (tm130) REVERT: B 1003 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6478 (tt) REVERT: B 1010 LYS cc_start: 0.7396 (ttmm) cc_final: 0.7078 (tttt) REVERT: B 1038 GLN cc_start: 0.6353 (mm110) cc_final: 0.5787 (mt0) REVERT: B 1050 LYS cc_start: 0.7866 (mttm) cc_final: 0.7609 (mtpp) REVERT: B 1071 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: B 1076 ARG cc_start: 0.6828 (mtp180) cc_final: 0.6525 (mtp85) REVERT: B 1091 GLN cc_start: 0.6846 (tt0) cc_final: 0.6492 (tt0) REVERT: B 1108 GLU cc_start: 0.6463 (tt0) cc_final: 0.6217 (mt-10) REVERT: C 117 LEU cc_start: 0.8382 (tp) cc_final: 0.8074 (tm) REVERT: C 120 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: C 162 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7747 (m) REVERT: C 176 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7851 (mm) REVERT: C 187 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6470 (mmtp) REVERT: C 205 GLU cc_start: 0.6294 (tt0) cc_final: 0.6040 (tt0) REVERT: C 206 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6708 (mtp85) REVERT: C 213 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5581 (p90) REVERT: C 252 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6180 (mm-30) REVERT: C 272 GLU cc_start: 0.6578 (mp0) cc_final: 0.6308 (mp0) REVERT: C 402 GLN cc_start: 0.7231 (mm110) cc_final: 0.6809 (mm-40) REVERT: C 415 LYS cc_start: 0.7387 (tttt) cc_final: 0.6917 (ttmm) REVERT: C 500 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7212 (mttm) REVERT: C 511 TYR cc_start: 0.2310 (OUTLIER) cc_final: 0.1598 (m-80) REVERT: C 528 TYR cc_start: 0.7554 (m-80) cc_final: 0.6961 (m-10) REVERT: C 573 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7768 (mp) REVERT: C 584 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7199 (t0) REVERT: C 630 GLN cc_start: 0.7369 (mt0) cc_final: 0.6555 (mp10) REVERT: C 844 ASN cc_start: 0.6961 (m-40) cc_final: 0.6735 (m-40) REVERT: C 885 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7561 (tptp) REVERT: C 920 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6719 (mt-10) REVERT: C 1069 GLU cc_start: 0.7428 (mp0) cc_final: 0.6874 (tp30) REVERT: C 1071 GLN cc_start: 0.6887 (mt0) cc_final: 0.6429 (mp10) REVERT: C 1076 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6676 (mtt-85) REVERT: C 1091 GLN cc_start: 0.7029 (tt0) cc_final: 0.6059 (mp10) REVERT: C 1149 LYS cc_start: 0.7901 (tttt) cc_final: 0.7687 (tttp) outliers start: 126 outliers final: 83 residues processed: 374 average time/residue: 1.1090 time to fit residues: 514.5008 Evaluate side-chains 371 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 263 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1071 GLN 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 1199 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1199 ASP Chi-restraints excluded: chain C residue 1219 TYR 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: 0.6980 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 0.9990 chunk 194 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 322 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1091 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B1059 GLN B1221 ASN C 26 ASN C 351 ASN C 531 ASN C1001 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30225 Z= 0.168 Angle : 0.604 11.866 41157 Z= 0.319 Chirality : 0.047 0.477 4908 Planarity : 0.005 0.068 5172 Dihedral : 8.680 100.906 5900 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.11 % Allowed : 13.37 % Favored : 83.52 % 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: -0.24 (0.14), residues: 3618 helix: 1.69 (0.20), residues: 810 sheet: 0.09 (0.17), residues: 822 loop : -1.09 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 515 HIS 0.007 0.001 HIS C 799 PHE 0.015 0.001 PHE A 968 TYR 0.018 0.001 TYR A 682 ARG 0.003 0.000 ARG A1081 *********************** 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 375 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 274 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.7992 (t) cc_final: 0.7359 (p) REVERT: A 114 ASN cc_start: 0.4228 (m-40) cc_final: 0.3986 (m-40) REVERT: A 120 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6009 (tp30) REVERT: A 187 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6638 (tppt) REVERT: A 206 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7477 (mtt180) REVERT: A 272 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: A 351 ASN cc_start: 0.7713 (m-40) cc_final: 0.7387 (t0) REVERT: A 568 SER cc_start: 0.7515 (OUTLIER) cc_final: 0.7130 (p) REVERT: A 570 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7054 (p0) REVERT: A 613 GLU cc_start: 0.7285 (tp30) cc_final: 0.6925 (mp0) REVERT: A 630 GLN cc_start: 0.7947 (mt0) cc_final: 0.7568 (mt0) REVERT: A 788 ILE cc_start: 0.7564 (tt) cc_final: 0.7088 (pt) REVERT: A 1066 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6026 (p0) REVERT: A 1076 ARG cc_start: 0.6597 (mtp180) cc_final: 0.6129 (mtm180) REVERT: B 43 SER cc_start: 0.8088 (t) cc_final: 0.7692 (p) REVERT: B 69 LYS cc_start: 0.7168 (tttm) cc_final: 0.6696 (ttmp) REVERT: B 118 TYR cc_start: 0.7447 (m-80) cc_final: 0.7033 (m-80) REVERT: B 205 GLU cc_start: 0.6932 (tt0) cc_final: 0.6694 (tt0) REVERT: B 206 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7382 (mtt90) REVERT: B 245 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7078 (tt) REVERT: B 356 LEU cc_start: 0.7630 (tp) cc_final: 0.7385 (mm) REVERT: B 369 SER cc_start: 0.7886 (t) cc_final: 0.7502 (p) REVERT: B 745 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: B 780 GLU cc_start: 0.7408 (pm20) cc_final: 0.7199 (pm20) REVERT: B 835 PHE cc_start: 0.7381 (t80) cc_final: 0.6840 (t80) REVERT: B 863 GLN cc_start: 0.6608 (tp40) cc_final: 0.6129 (tm130) REVERT: B 1003 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6436 (tt) REVERT: B 1010 LYS cc_start: 0.7356 (ttmm) cc_final: 0.7039 (tttt) REVERT: B 1038 GLN cc_start: 0.6339 (mm110) cc_final: 0.5783 (mt0) REVERT: B 1071 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: B 1076 ARG cc_start: 0.6685 (mtp180) cc_final: 0.6484 (mtp85) REVERT: B 1091 GLN cc_start: 0.6919 (tt0) cc_final: 0.6556 (tt0) REVERT: C 117 LEU cc_start: 0.8368 (tp) cc_final: 0.8095 (tm) REVERT: C 120 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6735 (mm-30) REVERT: C 162 VAL cc_start: 0.8122 (t) cc_final: 0.7710 (m) REVERT: C 176 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7752 (mm) REVERT: C 187 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6519 (mmtp) REVERT: C 205 GLU cc_start: 0.6271 (tt0) cc_final: 0.6018 (tt0) REVERT: C 206 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6701 (mtp85) REVERT: C 213 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5643 (p90) REVERT: C 252 GLU cc_start: 0.6645 (mm-30) cc_final: 0.5966 (mm-30) REVERT: C 272 GLU cc_start: 0.6651 (mp0) cc_final: 0.6407 (mp0) REVERT: C 402 GLN cc_start: 0.7200 (mm110) cc_final: 0.6785 (mm-40) REVERT: C 415 LYS cc_start: 0.7415 (tttt) cc_final: 0.6974 (ttmm) REVERT: C 511 TYR cc_start: 0.2448 (OUTLIER) cc_final: 0.1688 (m-80) REVERT: C 528 TYR cc_start: 0.7575 (m-80) cc_final: 0.7013 (m-10) REVERT: C 573 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 584 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7197 (t0) REVERT: C 630 GLN cc_start: 0.7208 (mt0) cc_final: 0.6405 (mp10) REVERT: C 835 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: C 844 ASN cc_start: 0.6811 (m-40) cc_final: 0.6558 (m-40) REVERT: C 920 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6703 (mt-10) REVERT: C 1069 GLU cc_start: 0.7422 (mp0) cc_final: 0.6867 (tp30) REVERT: C 1071 GLN cc_start: 0.6841 (mt0) cc_final: 0.6403 (mp-120) REVERT: C 1076 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6602 (mtt-85) REVERT: C 1091 GLN cc_start: 0.6889 (tt0) cc_final: 0.5921 (mp10) REVERT: C 1149 LYS cc_start: 0.7811 (tttt) cc_final: 0.7603 (tttp) outliers start: 101 outliers final: 58 residues processed: 351 average time/residue: 1.1348 time to fit residues: 491.8626 Evaluate side-chains 340 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 262 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1071 GLN 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 C residue 14 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 964 VAL 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 1199 ASP Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 285 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1079 ASN A1091 GLN A1201 ASN B 22 ASN B 26 ASN C 26 ASN C 351 ASN C 531 ASN C1001 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.2714 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= 0.241 Angle : 0.663 11.992 41157 Z= 0.354 Chirality : 0.051 1.170 4908 Planarity : 0.005 0.068 5172 Dihedral : 8.580 102.397 5893 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.90 % Allowed : 13.65 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.29 (0.14), residues: 3618 helix: 1.63 (0.20), residues: 804 sheet: 0.08 (0.17), residues: 858 loop : -1.13 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 515 HIS 0.008 0.001 HIS C 799 PHE 0.018 0.002 PHE A 764 TYR 0.020 0.002 TYR B 212 ARG 0.005 0.000 ARG B 693 ********************** 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 366 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 272 time to evaluate : 3.280 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: 0.8001 (t) cc_final: 0.7352 (p) REVERT: A 114 ASN cc_start: 0.4291 (m-40) cc_final: 0.4063 (m-40) REVERT: A 120 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6041 (tp30) REVERT: A 187 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6648 (tppt) REVERT: A 206 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7480 (mtt180) REVERT: A 272 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: A 351 ASN cc_start: 0.7784 (m-40) cc_final: 0.7402 (t0) REVERT: A 570 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 613 GLU cc_start: 0.7310 (tp30) cc_final: 0.6958 (mp0) REVERT: A 630 GLN cc_start: 0.8062 (mt0) cc_final: 0.7688 (mt0) REVERT: A 788 ILE cc_start: 0.7487 (tt) cc_final: 0.6967 (pt) REVERT: A 1076 ARG cc_start: 0.6752 (mtp180) cc_final: 0.6320 (mtm-85) REVERT: B 43 SER cc_start: 0.8087 (t) cc_final: 0.7616 (p) REVERT: B 69 LYS cc_start: 0.7185 (tttm) cc_final: 0.6720 (ttmp) REVERT: B 118 TYR cc_start: 0.7460 (m-80) cc_final: 0.7080 (m-80) REVERT: B 205 GLU cc_start: 0.6962 (tt0) cc_final: 0.6718 (tt0) REVERT: B 206 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7315 (mtt90) REVERT: B 213 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.5211 (p90) REVERT: B 245 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7180 (tt) REVERT: B 369 SER cc_start: 0.7950 (t) cc_final: 0.7582 (p) REVERT: B 745 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: B 835 PHE cc_start: 0.7394 (t80) cc_final: 0.6807 (t80) REVERT: B 863 GLN cc_start: 0.6645 (tp40) cc_final: 0.6154 (tm130) REVERT: B 1003 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6389 (tt) REVERT: B 1010 LYS cc_start: 0.7384 (ttmm) cc_final: 0.7060 (tttt) REVERT: B 1038 GLN cc_start: 0.6358 (mm110) cc_final: 0.5798 (mt0) REVERT: B 1071 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6119 (mp10) REVERT: B 1076 ARG cc_start: 0.6775 (mtp180) cc_final: 0.6479 (mtp85) REVERT: B 1091 GLN cc_start: 0.6933 (tt0) cc_final: 0.6563 (tt0) REVERT: C 117 LEU cc_start: 0.8383 (tp) cc_final: 0.8108 (tm) REVERT: C 120 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: C 162 VAL cc_start: 0.8148 (t) cc_final: 0.7729 (m) REVERT: C 176 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7807 (mm) REVERT: C 187 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6474 (mmtp) REVERT: C 205 GLU cc_start: 0.6288 (tt0) cc_final: 0.6037 (tt0) REVERT: C 206 ARG cc_start: 0.7365 (mtp85) cc_final: 0.6697 (mtp85) REVERT: C 213 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.5593 (p90) REVERT: C 252 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6056 (mm-30) REVERT: C 272 GLU cc_start: 0.6704 (mp0) cc_final: 0.6495 (mp0) REVERT: C 402 GLN cc_start: 0.7246 (mm110) cc_final: 0.6815 (mm-40) REVERT: C 415 LYS cc_start: 0.7423 (tttt) cc_final: 0.6968 (ttmm) REVERT: C 511 TYR cc_start: 0.2412 (OUTLIER) cc_final: 0.1659 (m-80) REVERT: C 528 TYR cc_start: 0.7556 (m-80) cc_final: 0.7000 (m-10) REVERT: C 573 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7741 (mp) REVERT: C 584 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7184 (t0) REVERT: C 630 GLN cc_start: 0.7311 (mt0) cc_final: 0.6491 (mp10) REVERT: C 844 ASN cc_start: 0.6895 (m-40) cc_final: 0.6669 (m-40) REVERT: C 903 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7023 (tt) REVERT: C 920 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6695 (mt-10) REVERT: C 1069 GLU cc_start: 0.7443 (mp0) cc_final: 0.6878 (tp30) REVERT: C 1071 GLN cc_start: 0.6868 (mt0) cc_final: 0.6410 (mp-120) REVERT: C 1076 ARG cc_start: 0.6971 (mtp180) cc_final: 0.6652 (mtt-85) REVERT: C 1091 GLN cc_start: 0.6999 (tt0) cc_final: 0.6042 (mp10) REVERT: C 1149 LYS cc_start: 0.7811 (tttt) cc_final: 0.7604 (tttp) outliers start: 94 outliers final: 67 residues processed: 342 average time/residue: 1.1162 time to fit residues: 468.8832 Evaluate side-chains 346 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 260 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1071 GLN 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 C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 964 VAL 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 1199 ASP Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1079 ASN A1091 GLN A1201 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B1059 GLN B1221 ASN C 26 ASN C 351 ASN C 531 ASN C1001 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107457 restraints weight = 31036.164| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.89 r_work: 0.3098 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30225 Z= 0.193 Angle : 0.613 11.899 41157 Z= 0.326 Chirality : 0.048 0.927 4908 Planarity : 0.005 0.067 5172 Dihedral : 8.289 103.671 5891 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.14 % Allowed : 13.65 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.18 (0.14), residues: 3618 helix: 1.74 (0.20), residues: 807 sheet: 0.18 (0.17), residues: 852 loop : -1.08 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 515 HIS 0.008 0.001 HIS C 799 PHE 0.017 0.002 PHE A 74 TYR 0.017 0.001 TYR B 212 ARG 0.003 0.000 ARG B 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10248.19 seconds wall clock time: 184 minutes 41.05 seconds (11081.05 seconds total)