Starting phenix.real_space_refine on Thu May 16 22:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1d_38832/05_2024/8y1d_38832.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.111 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 217 5.16 5 C 22133 2.51 5 N 5668 2.21 5 O 6903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B GLU 800": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "B TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 904": "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" Residue "C TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ARG 409": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 34921 Number of models: 1 Model: "" Number of chains: 23 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': 2, 'PTRANS': 50, '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: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2690 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain: "E" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2690 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 328} Chain: "F" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 17.96, per 1000 atoms: 0.51 Number of scatterers: 34921 At special positions: 0 Unit cell: (159.789, 168.485, 243.488, 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 217 16.00 O 6903 8.00 N 5668 7.00 C 22133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, 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=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.02 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.02 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 241 " distance=2.04 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 297 " distance=2.02 Simple disulfide: pdb=" SG CYS D 410 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 437 " - pdb=" SG CYS D 465 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 241 " distance=2.04 Simple disulfide: pdb=" SG CYS E 244 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 297 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 465 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " MAN K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " " MAN P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " ALPHA1-4 " NAG F 2 " - " MAN F 3 " " NAG K 2 " - " MAN K 3 " " NAG P 2 " - " MAN P 3 " ALPHA1-6 " MAN F 3 " - " MAN F 4 " " MAN K 3 " - " MAN K 4 " " MAN P 3 " - " MAN P 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-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 F 1 " - " ASN A 132 " " NAG G 1 " - " ASN A 188 " " NAG H 1 " - " ASN A 335 " " NAG I 1 " - " ASN A 355 " " NAG J 1 " - " ASN A 664 " " NAG K 1 " - " ASN B 132 " " NAG L 1 " - " ASN B 188 " " NAG M 1 " - " ASN B 335 " " NAG N 1 " - " ASN B 355 " " NAG O 1 " - " ASN B 664 " " NAG P 1 " - " ASN C 132 " " NAG Q 1 " - " ASN C 188 " " NAG R 1 " - " ASN C 335 " " NAG S 1 " - " ASN C 355 " " NAG T 1 " - " ASN C 664 " Time building additional restraints: 14.62 Conformation dependent library (CDL) restraints added in 6.2 seconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 79 sheets defined 21.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.888A 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 329 through 334 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.168A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 394 through 402 removed outlier: 5.079A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.927A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.026A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.089A pdb=" N THR A 527 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 863 Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 933 through 940 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 Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.828A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.793A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.610A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 4.393A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.086A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.587A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 376 through 381 removed outlier: 4.171A pdb=" N GLY B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 381' Processing helix chain 'B' and resid 394 through 402 removed outlier: 5.080A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 447 removed outlier: 3.928A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.025A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.090A pdb=" N THR B 527 " --> pdb=" O PRO B 524 " (cutoff:3.500A) 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 830 Processing helix chain 'B' and resid 835 through 863 removed outlier: 3.643A 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 924 removed outlier: 4.038A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.574A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.808A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.718A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.601A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 4.082A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.622A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.758A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.531A 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 395 through 402 removed outlier: 4.009A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.577A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.655A 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 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.551A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.533A pdb=" N LEU C 888 " --> pdb=" O LYS C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.904A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.774A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.528A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.628A 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: 3.845A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.676A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1058 through 1063 Processing helix chain 'C' and resid 1069 through 1113 removed outlier: 3.944A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.682A pdb=" N HIS D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.742A pdb=" N CYS D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 488 through 492 removed outlier: 4.135A pdb=" N ASP D 491 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY D 492 " --> pdb=" O ARG D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 492' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.683A pdb=" N HIS E 307 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.745A pdb=" N CYS E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 483 through 487 Processing helix chain 'E' and resid 488 through 492 removed outlier: 4.135A pdb=" N ASP E 491 " --> pdb=" O MET E 488 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY E 492 " --> pdb=" O ARG E 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 492' 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: 3.833A pdb=" N ASP A 38 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.057A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 3.922A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.953A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.585A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (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 307 removed outlier: 7.671A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.680A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AB2, first strand: chain 'A' and resid 382 through 383 removed outlier: 3.640A pdb=" N THR A 602 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.619A pdb=" N ASP A 578 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 576 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB5, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB7, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AB8, first strand: chain 'A' and resid 619 through 624 removed outlier: 3.973A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.623A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 736 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.388A 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: 6.853A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.723A 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: 4.406A 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 Processing sheet with id=AC8, first strand: chain 'B' and resid 59 through 64 removed outlier: 7.803A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AD1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.604A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 146 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 188 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 148 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 186 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 150 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.778A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 307 removed outlier: 7.603A pdb=" N ARG B 676 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 693 " --> pdb=" O ARG B 676 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 318 through 319 removed outlier: 5.478A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.680A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 347 through 349 Processing sheet with id=AD8, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.639A pdb=" N THR B 602 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.619A pdb=" N ASP B 578 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 576 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AE2, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AE3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE4, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AE5, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.527A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 773 through 775 Processing sheet with id=AE7, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.849A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.849A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.328A 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 'C' and resid 59 through 67 removed outlier: 4.033A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.642A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.692A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 306 Processing sheet with id=AF9, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.521A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.569A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG4, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.646A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 473 through 477 removed outlier: 3.867A pdb=" N ARG C 502 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS C 476 " --> pdb=" O ARG C 502 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AG7, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.563A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.853A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.853A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.320A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH4, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AH5, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.519A pdb=" N SER D 167 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.610A pdb=" N SER D 196 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN D 198 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 200 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AH8, first strand: chain 'D' and resid 279 through 281 Processing sheet with id=AH9, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AI1, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.534A pdb=" N GLY D 457 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR D 447 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 455 " --> pdb=" O THR D 447 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.520A pdb=" N SER E 167 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 196 through 200 removed outlier: 3.611A pdb=" N SER E 196 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 198 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 200 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 209 through 212 Processing sheet with id=AI5, first strand: chain 'E' and resid 279 through 281 Processing sheet with id=AI6, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AI7, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.534A pdb=" N GLY E 457 " --> pdb=" O LEU E 445 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 447 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU E 455 " --> pdb=" O THR E 447 " (cutoff:3.500A) 1121 hydrogen bonds defined for protein. 2991 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: 18.60 Time building geometry restraints manager: 15.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10066 1.33 - 1.46: 9092 1.46 - 1.58: 16329 1.58 - 1.71: 0 1.71 - 1.83: 262 Bond restraints: 35749 Sorted by residual: bond pdb=" N PRO A 325 " pdb=" CD PRO A 325 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.10e+01 bond pdb=" C LEU A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.331 1.387 -0.055 1.28e-02 6.10e+03 1.88e+01 bond pdb=" N PRO B 325 " pdb=" CD PRO B 325 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C5 MAN P 3 " pdb=" O5 MAN P 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 MAN K 3 " pdb=" O5 MAN K 3 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 35744 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.75: 1051 106.75 - 114.77: 21052 114.77 - 122.79: 22617 122.79 - 130.81: 3816 130.81 - 138.83: 135 Bond angle restraints: 48671 Sorted by residual: angle pdb=" N PRO A 969 " pdb=" CA PRO A 969 " pdb=" C PRO A 969 " ideal model delta sigma weight residual 110.70 119.52 -8.82 1.22e+00 6.72e-01 5.23e+01 angle pdb=" C SER B 604 " pdb=" CA SER B 604 " pdb=" CB SER B 604 " ideal model delta sigma weight residual 109.80 121.07 -11.27 1.64e+00 3.72e-01 4.73e+01 angle pdb=" N PRO C 969 " pdb=" CA PRO C 969 " pdb=" C PRO C 969 " ideal model delta sigma weight residual 110.70 119.06 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N LYS E 340 " pdb=" CA LYS E 340 " pdb=" C LYS E 340 " ideal model delta sigma weight residual 111.36 117.68 -6.32 1.09e+00 8.42e-01 3.36e+01 ... (remaining 48666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 20526 22.98 - 45.96: 1487 45.96 - 68.94: 418 68.94 - 91.92: 56 91.92 - 114.90: 6 Dihedral angle restraints: 22493 sinusoidal: 9877 harmonic: 12616 Sorted by residual: dihedral pdb=" CA GLN E 327 " pdb=" C GLN E 327 " pdb=" N VAL E 328 " pdb=" CA VAL E 328 " ideal model delta harmonic sigma weight residual -180.00 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA GLN D 327 " pdb=" C GLN D 327 " pdb=" N VAL D 328 " pdb=" CA VAL D 328 " ideal model delta harmonic sigma weight residual -180.00 -139.80 -40.20 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA PRO A 969 " pdb=" C PRO A 969 " pdb=" N PRO A 970 " pdb=" CA PRO A 970 " ideal model delta harmonic sigma weight residual 180.00 142.58 37.42 0 5.00e+00 4.00e-02 5.60e+01 ... (remaining 22490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 5613 0.156 - 0.311: 79 0.311 - 0.467: 6 0.467 - 0.622: 3 0.622 - 0.778: 3 Chirality restraints: 5704 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 19 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.74e+00 ... (remaining 5701 not shown) Planarity restraints: 6206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 171 " 0.206 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" CG ASN B 171 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN B 171 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 171 " -0.361 2.00e-02 2.50e+03 pdb=" C1 NAG B2005 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 188 " -0.180 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" CG ASN C 188 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 188 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN C 188 " 0.395 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 132 " -0.038 2.00e-02 2.50e+03 4.40e-02 2.42e+01 pdb=" CG ASN C 132 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 132 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 132 " 0.074 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.051 2.00e-02 2.50e+03 ... (remaining 6203 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7329 2.77 - 3.30: 29185 3.30 - 3.84: 57563 3.84 - 4.37: 66019 4.37 - 4.90: 115743 Nonbonded interactions: 275839 Sorted by model distance: nonbonded pdb=" O SER A 604 " pdb=" OG SER A 604 " model vdw 2.238 2.440 nonbonded pdb=" O SER C 740 " pdb=" OG SER C 740 " model vdw 2.245 2.440 nonbonded pdb=" CZ PHE B 354 " pdb=" OG SER B 604 " model vdw 2.264 3.340 nonbonded pdb=" O SER D 448 " pdb=" OG SER D 448 " model vdw 2.267 2.440 nonbonded pdb=" O SER E 448 " pdb=" OG SER E 448 " model vdw 2.267 2.440 ... (remaining 275834 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 'E' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 3.470 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: 0.060 Extract box with map and model: 15.270 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 98.180 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 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 : 0.011 0.135 35749 Z= 0.689 Angle : 1.042 13.830 48671 Z= 0.573 Chirality : 0.066 0.778 5704 Planarity : 0.008 0.111 6140 Dihedral : 17.059 114.899 14153 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.01 % Favored : 89.94 % Rotamer: Outliers : 13.49 % Allowed : 11.80 % Favored : 74.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 2.66 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.11), residues: 4304 helix: -1.91 (0.15), residues: 772 sheet: -1.54 (0.16), residues: 934 loop : -3.15 (0.10), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 515 HIS 0.012 0.002 HIS A 201 PHE 0.032 0.004 PHE A 391 TYR 0.031 0.003 TYR B 203 ARG 0.007 0.001 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 517 poor density : 276 time to evaluate : 3.892 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 155 MET cc_start: 0.7411 (mmm) cc_final: 0.6627 (mmm) REVERT: A 187 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7456 (mtpm) REVERT: A 190 THR cc_start: 0.8296 (p) cc_final: 0.8080 (t) REVERT: A 206 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7128 (mtp180) REVERT: A 213 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7263 (p90) REVERT: A 218 MET cc_start: 0.8236 (mtm) cc_final: 0.7964 (mtp) REVERT: A 262 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 318 TYR cc_start: 0.7266 (t80) cc_final: 0.6791 (t80) REVERT: A 371 ASN cc_start: 0.4212 (OUTLIER) cc_final: 0.3898 (p0) REVERT: A 431 LEU cc_start: 0.1207 (OUTLIER) cc_final: 0.0380 (mm) REVERT: A 437 ASN cc_start: 0.1869 (OUTLIER) cc_final: -0.0211 (p0) REVERT: A 706 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4443 (t80) REVERT: A 714 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 726 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 789 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: A 827 ASP cc_start: 0.7918 (m-30) cc_final: 0.7716 (m-30) REVERT: A 831 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7461 (mp0) REVERT: A 952 GLU cc_start: 0.7257 (tp30) cc_final: 0.6962 (tp30) REVERT: A 1003 LEU cc_start: 0.8411 (mt) cc_final: 0.7906 (tt) REVERT: A 1059 GLN cc_start: 0.8614 (tp40) cc_final: 0.8272 (tp40) REVERT: A 1086 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7989 (m-40) REVERT: A 1095 ASP cc_start: 0.7030 (m-30) cc_final: 0.6391 (t0) REVERT: A 1105 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6540 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6712 (tt0) cc_final: 0.6431 (tt0) REVERT: B 182 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4702 (tp) REVERT: B 256 TYR cc_start: 0.8142 (t80) cc_final: 0.7783 (t80) REVERT: B 412 SER cc_start: 0.4828 (OUTLIER) cc_final: 0.4221 (m) REVERT: B 484 SER cc_start: 0.0088 (OUTLIER) cc_final: -0.0322 (t) REVERT: B 835 PHE cc_start: 0.8075 (t80) cc_final: 0.6732 (t80) REVERT: B 862 MET cc_start: 0.7995 (mmm) cc_final: 0.7685 (mmp) REVERT: B 902 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8216 (tt) REVERT: B 906 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 1010 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7592 (tttp) REVERT: B 1012 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 1030 GLN cc_start: 0.7389 (mt0) cc_final: 0.7047 (tp40) REVERT: B 1210 VAL cc_start: 0.9116 (m) cc_final: 0.8885 (p) REVERT: C 204 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: C 289 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 384 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8164 (t0) REVERT: C 494 ILE cc_start: 0.6114 (mt) cc_final: 0.5870 (mt) REVERT: C 598 ASN cc_start: 0.7953 (m110) cc_final: 0.7732 (m110) REVERT: C 599 SER cc_start: 0.7653 (t) cc_final: 0.7228 (p) REVERT: C 640 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.5902 (p90) REVERT: C 655 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8806 (mt) REVERT: C 676 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7578 (ptm160) REVERT: C 863 GLN cc_start: 0.6947 (tp40) cc_final: 0.6735 (tp40) REVERT: C 885 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7822 (tptt) REVERT: C 986 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6415 (mmt180) REVERT: C 1001 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7182 (tm130) REVERT: C 1115 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8375 (mttt) REVERT: C 1185 MET cc_start: 0.7843 (mtp) cc_final: 0.7623 (mmm) REVERT: D 173 GLN cc_start: 0.0733 (OUTLIER) cc_final: 0.0336 (tp-100) REVERT: D 195 TYR cc_start: 0.2404 (OUTLIER) cc_final: 0.1903 (t80) REVERT: D 314 ILE cc_start: 0.1246 (OUTLIER) cc_final: 0.0983 (mp) REVERT: D 426 CYS cc_start: -0.0432 (OUTLIER) cc_final: -0.0951 (p) REVERT: D 465 CYS cc_start: 0.0202 (OUTLIER) cc_final: -0.0250 (p) REVERT: E 234 LYS cc_start: 0.0252 (OUTLIER) cc_final: 0.0032 (pttt) REVERT: E 273 LEU cc_start: 0.1885 (OUTLIER) cc_final: 0.1579 (tt) REVERT: E 286 ILE cc_start: -0.0046 (OUTLIER) cc_final: -0.0256 (pt) REVERT: E 371 MET cc_start: -0.0730 (OUTLIER) cc_final: -0.1337 (tmm) REVERT: E 430 LEU cc_start: 0.3937 (OUTLIER) cc_final: 0.2562 (pt) REVERT: E 440 ASP cc_start: -0.1274 (OUTLIER) cc_final: -0.1812 (t70) REVERT: E 465 CYS cc_start: 0.1135 (OUTLIER) cc_final: 0.0740 (t) outliers start: 517 outliers final: 182 residues processed: 748 average time/residue: 1.0128 time to fit residues: 977.7368 Evaluate side-chains 420 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 199 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1183 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 640 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 850 LEU 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 898 SER Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 969 PRO Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1115 LYS Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 429 PHE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 465 CYS Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 7.9990 chunk 324 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 218 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 335 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 371 ASN A 372 ASN A 410 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 561 ASN A 611 ASN A 630 GLN A 654 ASN A 863 GLN A 872 ASN A 876 HIS A 998 ASN A1001 GLN A1079 ASN A1122 ASN A1136 ASN A1180 GLN B 22 ASN B 108 ASN B 323 ASN B 413 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 840 ASN B 876 HIS B1122 ASN C 465 HIS C 630 GLN C 789 GLN C 876 HIS C 881 ASN C 938 GLN C 998 ASN C1001 GLN C1122 ASN C1136 ASN D 198 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 398 ASN D 408 GLN E 279 HIS ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 35749 Z= 0.191 Angle : 0.650 13.540 48671 Z= 0.341 Chirality : 0.047 0.457 5704 Planarity : 0.006 0.095 6140 Dihedral : 11.904 103.752 6980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 7.05 % Allowed : 16.91 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.12), residues: 4304 helix: -0.04 (0.18), residues: 793 sheet: -1.13 (0.17), residues: 937 loop : -2.67 (0.10), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 575 HIS 0.005 0.001 HIS A 201 PHE 0.025 0.001 PHE C 473 TYR 0.019 0.001 TYR A 203 ARG 0.005 0.000 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 217 time to evaluate : 3.615 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 155 MET cc_start: 0.7511 (mmm) cc_final: 0.6783 (mmm) REVERT: A 206 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7658 (mtt180) REVERT: A 371 ASN cc_start: 0.4102 (OUTLIER) cc_final: 0.3543 (p0) REVERT: A 431 LEU cc_start: 0.1167 (OUTLIER) cc_final: 0.0348 (mm) REVERT: A 437 ASN cc_start: 0.2048 (OUTLIER) cc_final: 0.0062 (OUTLIER) REVERT: A 516 CYS cc_start: -0.1413 (OUTLIER) cc_final: -0.1851 (m) REVERT: A 676 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8210 (mtm180) REVERT: A 706 PHE cc_start: 0.4839 (OUTLIER) cc_final: 0.4178 (t80) REVERT: A 788 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7800 (mt) REVERT: A 789 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7468 (mm110) REVERT: A 828 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 831 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7364 (mp0) REVERT: A 903 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7699 (mp) REVERT: A 1003 LEU cc_start: 0.8402 (mt) cc_final: 0.7888 (tt) REVERT: A 1095 ASP cc_start: 0.6827 (m-30) cc_final: 0.6339 (t0) REVERT: A 1105 ARG cc_start: 0.6914 (tpt170) cc_final: 0.6523 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6415 (tt0) cc_final: 0.6133 (tp30) REVERT: B 182 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4302 (tp) REVERT: B 213 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.5792 (t80) REVERT: B 256 TYR cc_start: 0.7910 (t80) cc_final: 0.7591 (t80) REVERT: B 800 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: B 835 PHE cc_start: 0.8023 (t80) cc_final: 0.6683 (t80) REVERT: B 862 MET cc_start: 0.7660 (mmm) cc_final: 0.7376 (mmp) REVERT: B 1010 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7509 (tttp) REVERT: B 1012 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 1210 VAL cc_start: 0.9113 (m) cc_final: 0.8889 (p) REVERT: C 140 GLN cc_start: 0.5278 (tt0) cc_final: 0.5072 (mt0) REVERT: C 204 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6965 (pt0) REVERT: C 205 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5605 (tp30) REVERT: C 361 ARG cc_start: 0.7866 (ptp-110) cc_final: 0.7564 (mtm110) REVERT: C 405 SER cc_start: 0.7662 (t) cc_final: 0.7441 (p) REVERT: C 676 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: C 1185 MET cc_start: 0.7774 (mtp) cc_final: 0.7543 (mmm) REVERT: D 187 ASP cc_start: 0.1242 (OUTLIER) cc_final: 0.0983 (m-30) REVERT: D 188 MET cc_start: 0.1168 (tpp) cc_final: -0.0852 (ptt) REVERT: D 371 MET cc_start: 0.1849 (tmm) cc_final: 0.1021 (tpp) REVERT: D 426 CYS cc_start: -0.0047 (OUTLIER) cc_final: -0.0887 (p) REVERT: D 465 CYS cc_start: 0.0352 (OUTLIER) cc_final: -0.0623 (p) REVERT: D 478 MET cc_start: 0.1121 (ttm) cc_final: -0.0054 (mtp) REVERT: E 234 LYS cc_start: 0.0172 (OUTLIER) cc_final: -0.0061 (pttt) REVERT: E 371 MET cc_start: -0.0394 (OUTLIER) cc_final: -0.0928 (tmm) REVERT: E 430 LEU cc_start: 0.3890 (OUTLIER) cc_final: 0.2724 (pp) outliers start: 270 outliers final: 132 residues processed: 460 average time/residue: 1.0870 time to fit residues: 645.3810 Evaluate side-chains 336 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 181 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU 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 972 SER Chi-restraints excluded: chain B residue 1012 LEU 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 465 CYS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 323 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 389 optimal weight: 20.0000 chunk 420 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 chunk 386 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 248 ASN C 465 HIS C 598 ASN C1136 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35749 Z= 0.243 Angle : 0.636 13.282 48671 Z= 0.330 Chirality : 0.047 0.453 5704 Planarity : 0.005 0.098 6140 Dihedral : 10.425 99.686 6806 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 6.47 % Allowed : 18.01 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4304 helix: 0.63 (0.19), residues: 791 sheet: -0.96 (0.16), residues: 946 loop : -2.47 (0.11), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 174 HIS 0.007 0.001 HIS C 562 PHE 0.021 0.002 PHE C 473 TYR 0.021 0.002 TYR B 203 ARG 0.003 0.000 ARG C 986 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 194 time to evaluate : 3.806 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 41 ASP cc_start: 0.7993 (t70) cc_final: 0.7400 (t70) REVERT: A 147 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: A 155 MET cc_start: 0.7528 (mmm) cc_final: 0.6822 (mmm) REVERT: A 206 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7749 (mtt180) REVERT: A 371 ASN cc_start: 0.4089 (OUTLIER) cc_final: 0.3634 (p0) REVERT: A 431 LEU cc_start: 0.1282 (OUTLIER) cc_final: 0.0673 (mm) REVERT: A 437 ASN cc_start: 0.2202 (OUTLIER) cc_final: 0.0252 (OUTLIER) REVERT: A 516 CYS cc_start: -0.1571 (OUTLIER) cc_final: -0.2106 (m) REVERT: A 643 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8221 (p0) REVERT: A 676 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: A 706 PHE cc_start: 0.4831 (OUTLIER) cc_final: 0.4164 (t80) REVERT: A 737 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7273 (mtt180) REVERT: A 789 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7422 (mm110) REVERT: A 828 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 831 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7385 (mp0) REVERT: A 903 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 1003 LEU cc_start: 0.8341 (mt) cc_final: 0.7901 (tt) REVERT: A 1069 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: A 1095 ASP cc_start: 0.6810 (m-30) cc_final: 0.6341 (t0) REVERT: A 1105 ARG cc_start: 0.6888 (tpt170) cc_final: 0.6415 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6447 (tt0) cc_final: 0.6117 (tp30) REVERT: B 132 ASN cc_start: 0.3425 (OUTLIER) cc_final: 0.3210 (p0) REVERT: B 149 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7114 (p) REVERT: B 182 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4282 (tp) REVERT: B 213 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.5793 (t80) REVERT: B 256 TYR cc_start: 0.7990 (t80) cc_final: 0.7764 (t80) REVERT: B 748 LEU cc_start: 0.6799 (tm) cc_final: 0.6568 (pt) REVERT: B 800 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7560 (pp20) REVERT: B 835 PHE cc_start: 0.8008 (t80) cc_final: 0.6717 (t80) REVERT: B 862 MET cc_start: 0.7745 (mmm) cc_final: 0.7522 (mmp) REVERT: B 1010 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7529 (tttp) REVERT: B 1210 VAL cc_start: 0.9117 (m) cc_final: 0.8904 (p) REVERT: C 204 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6994 (pt0) REVERT: C 361 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7518 (mtm110) REVERT: C 384 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (t0) REVERT: C 405 SER cc_start: 0.7657 (t) cc_final: 0.7453 (p) REVERT: C 655 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8825 (mt) REVERT: C 676 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7237 (ptm160) REVERT: C 1002 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7435 (mmmm) REVERT: D 188 MET cc_start: 0.1525 (tpp) cc_final: 0.1049 (tpp) REVERT: D 191 LYS cc_start: 0.2284 (OUTLIER) cc_final: 0.2053 (pttp) REVERT: D 426 CYS cc_start: -0.0127 (OUTLIER) cc_final: -0.0883 (p) REVERT: D 465 CYS cc_start: 0.0082 (OUTLIER) cc_final: -0.0802 (p) REVERT: E 234 LYS cc_start: 0.0353 (OUTLIER) cc_final: -0.0010 (pttt) REVERT: E 332 ILE cc_start: -0.0152 (OUTLIER) cc_final: -0.0878 (mt) REVERT: E 355 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3324 (mt) REVERT: E 430 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.2946 (pt) outliers start: 248 outliers final: 148 residues processed: 422 average time/residue: 1.1044 time to fit residues: 596.0409 Evaluate side-chains 357 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 179 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1054 ILE 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 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1159 SER Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 465 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 390 optimal weight: 20.0000 chunk 413 optimal weight: 30.0000 chunk 204 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 111 optimal weight: 0.0570 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 440 ASN A 445 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN C 140 GLN C 465 HIS C 598 ASN C1023 ASN D 198 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5111 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35749 Z= 0.310 Angle : 0.652 11.415 48671 Z= 0.339 Chirality : 0.048 0.476 5704 Planarity : 0.005 0.099 6140 Dihedral : 9.927 94.182 6789 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 7.02 % Allowed : 18.06 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.12), residues: 4304 helix: 0.58 (0.19), residues: 810 sheet: -0.87 (0.16), residues: 958 loop : -2.40 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 174 HIS 0.008 0.001 HIS A 201 PHE 0.022 0.002 PHE C 968 TYR 0.022 0.002 TYR B 203 ARG 0.005 0.001 ARG C 986 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 189 time to evaluate : 3.765 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: symmetry clash REVERT: A 41 ASP cc_start: 0.8009 (t70) cc_final: 0.7442 (t70) REVERT: A 155 MET cc_start: 0.7420 (mmm) cc_final: 0.6713 (mmm) REVERT: A 187 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7203 (mtpm) REVERT: A 206 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: A 218 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: A 320 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7059 (mmp80) REVERT: A 371 ASN cc_start: 0.4238 (OUTLIER) cc_final: 0.3637 (p0) REVERT: A 431 LEU cc_start: 0.1263 (OUTLIER) cc_final: 0.0425 (mm) REVERT: A 516 CYS cc_start: -0.1296 (OUTLIER) cc_final: -0.1677 (m) REVERT: A 643 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8177 (p0) REVERT: A 676 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: A 706 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4238 (t80) REVERT: A 714 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: A 737 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: A 789 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7456 (mm110) REVERT: A 828 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 831 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7467 (mp0) REVERT: A 903 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 1003 LEU cc_start: 0.8341 (mt) cc_final: 0.7896 (tt) REVERT: A 1069 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: A 1095 ASP cc_start: 0.6864 (m-30) cc_final: 0.6392 (t0) REVERT: A 1105 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6456 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6561 (tt0) cc_final: 0.6232 (tp30) REVERT: B 28 TYR cc_start: 0.3914 (OUTLIER) cc_final: 0.3379 (p90) REVERT: B 140 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6462 (tp40) REVERT: B 182 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4240 (tp) REVERT: B 213 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.5672 (t80) REVERT: B 560 LEU cc_start: 0.1810 (OUTLIER) cc_final: 0.1484 (pp) REVERT: B 800 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B 835 PHE cc_start: 0.8078 (t80) cc_final: 0.6829 (t80) REVERT: B 849 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7318 (mp) REVERT: B 862 MET cc_start: 0.7888 (mmm) cc_final: 0.7675 (mmp) REVERT: B 1010 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7534 (tttp) REVERT: B 1210 VAL cc_start: 0.9153 (m) cc_final: 0.8940 (p) REVERT: C 204 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: C 361 ARG cc_start: 0.7920 (ptp-110) cc_final: 0.7563 (mtm110) REVERT: C 384 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8043 (t0) REVERT: C 405 SER cc_start: 0.7806 (t) cc_final: 0.7522 (p) REVERT: C 635 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: C 676 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7177 (ptm160) REVERT: C 885 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7633 (tptt) REVERT: D 174 ASP cc_start: 0.1225 (OUTLIER) cc_final: 0.0874 (m-30) REVERT: D 188 MET cc_start: 0.1588 (tpp) cc_final: -0.0962 (ptt) REVERT: D 207 THR cc_start: 0.1999 (OUTLIER) cc_final: 0.1656 (m) REVERT: D 371 MET cc_start: 0.2299 (tmm) cc_final: 0.1286 (tpp) REVERT: D 372 MET cc_start: 0.2010 (mmt) cc_final: 0.1726 (mmt) REVERT: D 426 CYS cc_start: -0.0324 (OUTLIER) cc_final: -0.0945 (p) REVERT: D 465 CYS cc_start: 0.0401 (OUTLIER) cc_final: -0.1086 (p) REVERT: D 478 MET cc_start: 0.1110 (OUTLIER) cc_final: -0.0369 (mmm) REVERT: E 234 LYS cc_start: 0.0514 (OUTLIER) cc_final: 0.0040 (pttt) REVERT: E 327 GLN cc_start: 0.1771 (OUTLIER) cc_final: 0.0114 (pt0) REVERT: E 371 MET cc_start: 0.0202 (OUTLIER) cc_final: -0.0445 (tmm) outliers start: 269 outliers final: 155 residues processed: 430 average time/residue: 1.0984 time to fit residues: 609.6017 Evaluate side-chains 371 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 181 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1054 ILE 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 1203 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 344 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 308 optimal weight: 0.7980 chunk 170 optimal weight: 40.0000 chunk 353 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 395 ASN B 445 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN C 465 HIS C 598 ASN C1023 ASN D 253 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5113 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35749 Z= 0.300 Angle : 0.630 9.138 48671 Z= 0.328 Chirality : 0.048 0.457 5704 Planarity : 0.005 0.095 6140 Dihedral : 9.419 91.452 6765 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 6.81 % Allowed : 18.66 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.05 % 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: -1.97 (0.12), residues: 4304 helix: 0.65 (0.19), residues: 813 sheet: -0.80 (0.16), residues: 959 loop : -2.30 (0.11), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 174 HIS 0.008 0.001 HIS A 201 PHE 0.021 0.002 PHE C 968 TYR 0.022 0.002 TYR B 203 ARG 0.008 0.001 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 186 time to evaluate : 3.585 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 41 ASP cc_start: 0.7984 (t70) cc_final: 0.7407 (t70) REVERT: A 52 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 155 MET cc_start: 0.7426 (mmm) cc_final: 0.6705 (mmm) REVERT: A 182 LEU cc_start: 0.7614 (mp) cc_final: 0.7412 (mt) REVERT: A 187 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7183 (mtpm) REVERT: A 206 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7691 (mtt180) REVERT: A 371 ASN cc_start: 0.4143 (OUTLIER) cc_final: 0.3589 (p0) REVERT: A 431 LEU cc_start: 0.1877 (OUTLIER) cc_final: 0.0626 (mm) REVERT: A 643 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 676 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: A 706 PHE cc_start: 0.4880 (OUTLIER) cc_final: 0.4221 (t80) REVERT: A 726 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7771 (mt) REVERT: A 737 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: A 789 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7454 (mm110) REVERT: A 831 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7472 (mp0) REVERT: A 903 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 1003 LEU cc_start: 0.8338 (mt) cc_final: 0.7892 (tt) REVERT: A 1069 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: A 1095 ASP cc_start: 0.6873 (m-30) cc_final: 0.6425 (t0) REVERT: A 1105 ARG cc_start: 0.6950 (tpt170) cc_final: 0.6454 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6530 (tt0) cc_final: 0.6212 (tp30) REVERT: B 28 TYR cc_start: 0.4092 (OUTLIER) cc_final: 0.3528 (p90) REVERT: B 140 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6506 (tp40) REVERT: B 182 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4272 (tp) REVERT: B 213 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.5613 (t80) REVERT: B 560 LEU cc_start: 0.1612 (OUTLIER) cc_final: 0.1173 (pp) REVERT: B 748 LEU cc_start: 0.6768 (tm) cc_final: 0.6532 (pt) REVERT: B 782 VAL cc_start: 0.7784 (t) cc_final: 0.7566 (p) REVERT: B 800 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: B 835 PHE cc_start: 0.8081 (t80) cc_final: 0.6764 (t80) REVERT: B 849 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7302 (mp) REVERT: B 862 MET cc_start: 0.7873 (mmm) cc_final: 0.7595 (mmp) REVERT: B 1010 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7528 (tttp) REVERT: B 1210 VAL cc_start: 0.9157 (m) cc_final: 0.8938 (p) REVERT: C 204 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6902 (pt0) REVERT: C 361 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7606 (mtm110) REVERT: C 375 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7864 (mttm) REVERT: C 384 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 405 SER cc_start: 0.7837 (t) cc_final: 0.7542 (p) REVERT: C 635 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6704 (tp30) REVERT: C 655 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8844 (mt) REVERT: C 676 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7255 (ptm160) REVERT: C 885 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7691 (tptp) REVERT: D 188 MET cc_start: 0.1525 (tpp) cc_final: -0.0954 (ptt) REVERT: D 207 THR cc_start: 0.1974 (OUTLIER) cc_final: 0.1688 (m) REVERT: D 320 MET cc_start: 0.2605 (mtm) cc_final: 0.0874 (ppp) REVERT: D 327 GLN cc_start: 0.1589 (OUTLIER) cc_final: 0.1070 (mp10) REVERT: D 371 MET cc_start: 0.1867 (tmm) cc_final: 0.1102 (tpp) REVERT: D 372 MET cc_start: 0.1984 (mmt) cc_final: 0.1706 (mmt) REVERT: D 426 CYS cc_start: -0.0442 (OUTLIER) cc_final: -0.1066 (p) REVERT: D 465 CYS cc_start: 0.0309 (OUTLIER) cc_final: -0.1084 (p) REVERT: D 478 MET cc_start: 0.0725 (OUTLIER) cc_final: -0.0434 (mtp) REVERT: E 188 MET cc_start: 0.2627 (mtt) cc_final: 0.1106 (ttp) REVERT: E 234 LYS cc_start: 0.0329 (OUTLIER) cc_final: -0.0239 (pttt) REVERT: E 358 ASN cc_start: 0.1419 (OUTLIER) cc_final: 0.0944 (p0) outliers start: 261 outliers final: 155 residues processed: 422 average time/residue: 1.0918 time to fit residues: 589.3970 Evaluate side-chains 365 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 177 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1054 ILE 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 1203 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 414 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 598 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5124 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35749 Z= 0.329 Angle : 0.648 9.175 48671 Z= 0.337 Chirality : 0.048 0.471 5704 Planarity : 0.005 0.097 6140 Dihedral : 9.291 98.155 6748 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.84 % Allowed : 19.05 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.05 % 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: -1.97 (0.12), residues: 4304 helix: 0.56 (0.19), residues: 819 sheet: -0.70 (0.17), residues: 928 loop : -2.31 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 174 HIS 0.008 0.001 HIS A 201 PHE 0.022 0.002 PHE C 473 TYR 0.022 0.002 TYR B 203 ARG 0.010 0.001 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 184 time to evaluate : 3.771 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 41 ASP cc_start: 0.7980 (t70) cc_final: 0.7391 (t70) REVERT: A 155 MET cc_start: 0.7406 (mmm) cc_final: 0.6607 (mmm) REVERT: A 187 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7239 (mtpm) REVERT: A 206 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: A 213 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7145 (p90) REVERT: A 371 ASN cc_start: 0.4405 (OUTLIER) cc_final: 0.3817 (p0) REVERT: A 431 LEU cc_start: 0.2536 (OUTLIER) cc_final: 0.2252 (pp) REVERT: A 643 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8159 (p0) REVERT: A 676 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7954 (mtt180) REVERT: A 706 PHE cc_start: 0.4820 (OUTLIER) cc_final: 0.4193 (t80) REVERT: A 726 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 737 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7208 (mtt180) REVERT: A 789 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7504 (mm110) REVERT: A 831 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 903 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7762 (mp) REVERT: A 1003 LEU cc_start: 0.8360 (mt) cc_final: 0.7914 (tt) REVERT: A 1069 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: A 1095 ASP cc_start: 0.6899 (m-30) cc_final: 0.6400 (t0) REVERT: A 1105 ARG cc_start: 0.6973 (tpt170) cc_final: 0.6457 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6539 (tt0) cc_final: 0.6219 (tp30) REVERT: B 28 TYR cc_start: 0.4129 (OUTLIER) cc_final: 0.3609 (p90) REVERT: B 140 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6528 (tp40) REVERT: B 182 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4310 (tp) REVERT: B 213 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.5606 (t80) REVERT: B 437 ASN cc_start: 0.2479 (OUTLIER) cc_final: 0.1635 (t0) REVERT: B 560 LEU cc_start: 0.1962 (OUTLIER) cc_final: 0.1564 (pp) REVERT: B 595 ASN cc_start: 0.4878 (OUTLIER) cc_final: 0.4168 (p0) REVERT: B 748 LEU cc_start: 0.6669 (tm) cc_final: 0.6379 (pt) REVERT: B 782 VAL cc_start: 0.7783 (t) cc_final: 0.7555 (p) REVERT: B 800 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: B 835 PHE cc_start: 0.8079 (t80) cc_final: 0.6820 (t80) REVERT: B 849 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (mp) REVERT: B 1010 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7534 (tttp) REVERT: B 1210 VAL cc_start: 0.9161 (m) cc_final: 0.8944 (p) REVERT: C 204 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6982 (pt0) REVERT: C 361 ARG cc_start: 0.7868 (ptp-110) cc_final: 0.7619 (mtm110) REVERT: C 375 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7890 (mttm) REVERT: C 384 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8079 (t0) REVERT: C 405 SER cc_start: 0.7861 (t) cc_final: 0.7549 (p) REVERT: C 635 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: C 676 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7223 (ptm160) REVERT: C 885 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7676 (tptp) REVERT: C 1185 MET cc_start: 0.7908 (mtp) cc_final: 0.7547 (mmm) REVERT: D 188 MET cc_start: 0.1662 (tpp) cc_final: -0.0941 (ptt) REVERT: D 320 MET cc_start: 0.2410 (mtm) cc_final: 0.0713 (ppp) REVERT: D 327 GLN cc_start: 0.1780 (OUTLIER) cc_final: 0.1065 (mp10) REVERT: D 371 MET cc_start: 0.1628 (tmm) cc_final: 0.1113 (tpp) REVERT: D 424 MET cc_start: 0.3793 (OUTLIER) cc_final: 0.3561 (ptm) REVERT: D 426 CYS cc_start: -0.0154 (OUTLIER) cc_final: -0.0708 (p) REVERT: D 465 CYS cc_start: 0.0051 (OUTLIER) cc_final: -0.1276 (p) REVERT: D 478 MET cc_start: 0.0709 (OUTLIER) cc_final: -0.0223 (mtp) REVERT: E 188 MET cc_start: 0.2651 (mtt) cc_final: 0.1036 (ttp) REVERT: E 234 LYS cc_start: 0.0656 (OUTLIER) cc_final: -0.0070 (pttt) REVERT: E 327 GLN cc_start: 0.2125 (OUTLIER) cc_final: 0.0434 (pt0) REVERT: E 358 ASN cc_start: 0.1435 (OUTLIER) cc_final: 0.1012 (p0) REVERT: E 488 MET cc_start: 0.0257 (OUTLIER) cc_final: -0.1150 (tpt) outliers start: 262 outliers final: 164 residues processed: 422 average time/residue: 1.1025 time to fit residues: 594.5011 Evaluate side-chains 382 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 182 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1170 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1054 ILE 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 1203 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1220 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 0.0370 chunk 46 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 302 optimal weight: 0.1980 chunk 234 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 412 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 438 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS B 587 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 552 ASN C 598 ASN C 799 HIS C1136 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35749 Z= 0.141 Angle : 0.546 8.427 48671 Z= 0.285 Chirality : 0.044 0.400 5704 Planarity : 0.004 0.083 6140 Dihedral : 8.482 96.981 6743 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.67 % Allowed : 21.06 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.59 (0.13), residues: 4304 helix: 1.16 (0.20), residues: 813 sheet: -0.52 (0.17), residues: 939 loop : -2.13 (0.11), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 971 HIS 0.004 0.001 HIS A 201 PHE 0.021 0.001 PHE C 473 TYR 0.023 0.001 TYR A 609 ARG 0.012 0.000 ARG C1064 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 194 time to evaluate : 3.788 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 37 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 41 ASP cc_start: 0.7839 (t70) cc_final: 0.7247 (t70) REVERT: A 155 MET cc_start: 0.7545 (mmm) cc_final: 0.6829 (mmm) REVERT: A 318 TYR cc_start: 0.7361 (t80) cc_final: 0.7040 (t80) REVERT: A 371 ASN cc_start: 0.4452 (OUTLIER) cc_final: 0.3809 (p0) REVERT: A 431 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.1246 (mm) REVERT: A 643 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8020 (p0) REVERT: A 676 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: A 706 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4144 (t80) REVERT: A 726 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7526 (mt) REVERT: A 788 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 789 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7400 (mm110) REVERT: A 831 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7233 (mp0) REVERT: A 1003 LEU cc_start: 0.8389 (mt) cc_final: 0.7886 (tt) REVERT: A 1069 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: A 1095 ASP cc_start: 0.6703 (m-30) cc_final: 0.6341 (t0) REVERT: A 1105 ARG cc_start: 0.6875 (tpt170) cc_final: 0.6386 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6519 (tt0) cc_final: 0.6253 (tp30) REVERT: B 28 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.3555 (p90) REVERT: B 182 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4235 (tp) REVERT: B 213 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5764 (t80) REVERT: B 560 LEU cc_start: 0.1926 (OUTLIER) cc_final: 0.1565 (pp) REVERT: B 595 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4061 (p0) REVERT: B 748 LEU cc_start: 0.6619 (tm) cc_final: 0.6394 (pt) REVERT: B 800 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: B 835 PHE cc_start: 0.7970 (t80) cc_final: 0.6697 (t80) REVERT: B 862 MET cc_start: 0.7664 (mmm) cc_final: 0.7443 (mmp) REVERT: B 1010 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7546 (tttp) REVERT: C 264 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6072 (ptm160) REVERT: C 635 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6736 (tp30) REVERT: C 655 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8866 (mt) REVERT: D 188 MET cc_start: 0.0936 (tpp) cc_final: -0.1049 (ptt) REVERT: D 320 MET cc_start: 0.0917 (mtm) cc_final: 0.0418 (ppp) REVERT: D 327 GLN cc_start: 0.2141 (OUTLIER) cc_final: 0.1382 (mp10) REVERT: D 372 MET cc_start: 0.1693 (mmt) cc_final: 0.1485 (mmt) REVERT: D 426 CYS cc_start: -0.0235 (OUTLIER) cc_final: -0.0793 (p) REVERT: D 465 CYS cc_start: -0.0366 (OUTLIER) cc_final: -0.1813 (p) REVERT: D 478 MET cc_start: 0.0664 (OUTLIER) cc_final: -0.0442 (mmm) REVERT: E 188 MET cc_start: 0.2576 (mtt) cc_final: 0.0979 (ttp) REVERT: E 234 LYS cc_start: 0.0478 (OUTLIER) cc_final: -0.0179 (pttt) REVERT: E 327 GLN cc_start: 0.1563 (OUTLIER) cc_final: 0.0012 (pm20) REVERT: E 332 ILE cc_start: -0.0512 (OUTLIER) cc_final: -0.1195 (mt) REVERT: E 488 MET cc_start: 0.0070 (OUTLIER) cc_final: -0.1158 (tpt) outliers start: 179 outliers final: 97 residues processed: 354 average time/residue: 1.1360 time to fit residues: 512.7191 Evaluate side-chains 311 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 188 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN 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 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 20.0000 chunk 164 optimal weight: 0.0980 chunk 246 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 0.0770 chunk 262 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 598 ASN C 863 GLN C 938 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35749 Z= 0.142 Angle : 0.537 8.467 48671 Z= 0.279 Chirality : 0.044 0.392 5704 Planarity : 0.004 0.072 6140 Dihedral : 7.837 97.252 6712 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.20 % Allowed : 21.32 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -1.42 (0.13), residues: 4304 helix: 1.49 (0.20), residues: 795 sheet: -0.46 (0.17), residues: 928 loop : -2.04 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 454 HIS 0.005 0.001 HIS A 201 PHE 0.020 0.001 PHE C 473 TYR 0.021 0.001 TYR B 712 ARG 0.014 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 193 time to evaluate : 3.921 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 41 ASP cc_start: 0.7824 (t70) cc_final: 0.7239 (t70) REVERT: A 155 MET cc_start: 0.7568 (mmm) cc_final: 0.6949 (mmm) REVERT: A 318 TYR cc_start: 0.7133 (t80) cc_final: 0.6902 (t80) REVERT: A 371 ASN cc_start: 0.4397 (OUTLIER) cc_final: 0.3699 (p0) REVERT: A 431 LEU cc_start: 0.2672 (OUTLIER) cc_final: 0.1234 (mm) REVERT: A 789 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: A 831 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7197 (mp0) REVERT: A 1003 LEU cc_start: 0.8314 (mt) cc_final: 0.7881 (tt) REVERT: A 1069 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: A 1095 ASP cc_start: 0.6663 (m-30) cc_final: 0.6340 (t0) REVERT: A 1105 ARG cc_start: 0.6830 (tpt170) cc_final: 0.6354 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6523 (tt0) cc_final: 0.6192 (tp30) REVERT: B 182 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4064 (tt) REVERT: B 213 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.5814 (t80) REVERT: B 560 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.2119 (pp) REVERT: B 595 ASN cc_start: 0.4848 (OUTLIER) cc_final: 0.4065 (p0) REVERT: B 748 LEU cc_start: 0.6585 (tm) cc_final: 0.6358 (OUTLIER) REVERT: B 788 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7590 (pt) REVERT: B 800 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: B 835 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6742 (t80) REVERT: B 862 MET cc_start: 0.7695 (mmm) cc_final: 0.7393 (mmp) REVERT: B 1010 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7548 (tttp) REVERT: C 205 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5693 (tp30) REVERT: C 635 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6693 (tp30) REVERT: C 655 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8857 (mt) REVERT: C 863 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: C 1001 GLN cc_start: 0.7452 (tt0) cc_final: 0.6988 (tm-30) REVERT: D 188 MET cc_start: 0.0846 (tpp) cc_final: -0.0940 (OUTLIER) REVERT: D 320 MET cc_start: 0.1290 (mtm) cc_final: 0.0632 (ppp) REVERT: D 327 GLN cc_start: 0.2132 (OUTLIER) cc_final: 0.1311 (mp10) REVERT: D 332 ILE cc_start: -0.0459 (OUTLIER) cc_final: -0.0694 (mp) REVERT: D 372 MET cc_start: 0.1300 (mmt) cc_final: -0.0854 (tpt) REVERT: D 426 CYS cc_start: -0.0239 (OUTLIER) cc_final: -0.0860 (p) REVERT: D 478 MET cc_start: 0.0528 (OUTLIER) cc_final: -0.0556 (mmm) REVERT: E 188 MET cc_start: 0.2678 (mtt) cc_final: 0.1043 (ttp) REVERT: E 327 GLN cc_start: 0.1078 (OUTLIER) cc_final: -0.0189 (pm20) REVERT: E 332 ILE cc_start: -0.0471 (OUTLIER) cc_final: -0.1144 (mt) REVERT: E 396 VAL cc_start: 0.1931 (OUTLIER) cc_final: 0.1516 (m) REVERT: E 488 MET cc_start: 0.0007 (OUTLIER) cc_final: -0.1169 (tpt) outliers start: 161 outliers final: 101 residues processed: 328 average time/residue: 1.1420 time to fit residues: 478.2134 Evaluate side-chains 299 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 177 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 375 optimal weight: 20.0000 chunk 395 optimal weight: 8.9990 chunk 360 optimal weight: 0.0980 chunk 384 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 363 optimal weight: 0.7980 chunk 383 optimal weight: 9.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 709 GLN B 789 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 465 HIS C 598 ASN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5083 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35749 Z= 0.195 Angle : 0.565 8.913 48671 Z= 0.294 Chirality : 0.045 0.421 5704 Planarity : 0.005 0.088 6140 Dihedral : 7.658 97.715 6683 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.12 % Allowed : 21.56 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.45 (0.13), residues: 4304 helix: 1.36 (0.20), residues: 798 sheet: -0.52 (0.17), residues: 928 loop : -2.00 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 267 HIS 0.006 0.001 HIS A 201 PHE 0.019 0.001 PHE C 473 TYR 0.018 0.001 TYR B1148 ARG 0.019 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 182 time to evaluate : 3.705 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 41 ASP cc_start: 0.7904 (t70) cc_final: 0.7337 (t70) REVERT: A 155 MET cc_start: 0.7579 (mmm) cc_final: 0.6881 (mmm) REVERT: A 187 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7214 (mtpm) REVERT: A 326 ASP cc_start: 0.3770 (OUTLIER) cc_final: 0.3263 (t0) REVERT: A 371 ASN cc_start: 0.4278 (OUTLIER) cc_final: 0.3744 (p0) REVERT: A 726 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7702 (mt) REVERT: A 789 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7578 (mm110) REVERT: A 831 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7220 (mp0) REVERT: A 1003 LEU cc_start: 0.8312 (mt) cc_final: 0.7878 (tt) REVERT: A 1069 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: A 1095 ASP cc_start: 0.6722 (m-30) cc_final: 0.6341 (t0) REVERT: A 1105 ARG cc_start: 0.6903 (tpt170) cc_final: 0.6381 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6541 (tt0) cc_final: 0.6219 (tp30) REVERT: B 182 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3945 (tt) REVERT: B 213 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5845 (t80) REVERT: B 437 ASN cc_start: 0.2183 (OUTLIER) cc_final: 0.1292 (t0) REVERT: B 560 LEU cc_start: 0.2298 (OUTLIER) cc_final: 0.2036 (pp) REVERT: B 595 ASN cc_start: 0.4875 (OUTLIER) cc_final: 0.4124 (p0) REVERT: B 748 LEU cc_start: 0.6580 (tm) cc_final: 0.6356 (pt) REVERT: B 788 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7541 (pt) REVERT: B 789 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7899 (mm110) REVERT: B 800 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: B 835 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.6761 (t80) REVERT: B 862 MET cc_start: 0.7702 (mmm) cc_final: 0.7488 (mmp) REVERT: B 1010 LYS cc_start: 0.7872 (ttmm) cc_final: 0.7561 (tttp) REVERT: C 405 SER cc_start: 0.7773 (t) cc_final: 0.7545 (p) REVERT: C 635 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: C 655 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8857 (mt) REVERT: C 1001 GLN cc_start: 0.7458 (tt0) cc_final: 0.7027 (tm-30) REVERT: D 188 MET cc_start: 0.0717 (tpp) cc_final: -0.1034 (OUTLIER) REVERT: D 320 MET cc_start: 0.1229 (mtm) cc_final: 0.0584 (ppp) REVERT: D 327 GLN cc_start: 0.2254 (OUTLIER) cc_final: 0.1559 (mp10) REVERT: D 332 ILE cc_start: -0.0212 (OUTLIER) cc_final: -0.0465 (mp) REVERT: D 372 MET cc_start: 0.1084 (mmt) cc_final: -0.0866 (tpt) REVERT: D 426 CYS cc_start: -0.0186 (OUTLIER) cc_final: -0.0815 (p) REVERT: D 478 MET cc_start: 0.0509 (OUTLIER) cc_final: -0.0402 (mmm) REVERT: E 188 MET cc_start: 0.2676 (mtt) cc_final: 0.1047 (ttp) REVERT: E 327 GLN cc_start: 0.1106 (OUTLIER) cc_final: -0.0259 (pm20) REVERT: E 332 ILE cc_start: -0.0471 (OUTLIER) cc_final: -0.1139 (mt) REVERT: E 488 MET cc_start: -0.0037 (OUTLIER) cc_final: -0.1138 (tpt) outliers start: 158 outliers final: 112 residues processed: 319 average time/residue: 1.0849 time to fit residues: 447.1825 Evaluate side-chains 317 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 182 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1066 ASP 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 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 0.0000 chunk 406 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 426 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 339 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 598 ASN C 789 GLN D 438 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35749 Z= 0.214 Angle : 0.575 10.061 48671 Z= 0.299 Chirality : 0.045 0.413 5704 Planarity : 0.005 0.075 6140 Dihedral : 7.657 97.191 6679 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.84 % Allowed : 21.89 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -1.46 (0.13), residues: 4304 helix: 1.29 (0.20), residues: 798 sheet: -0.51 (0.17), residues: 935 loop : -2.00 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 267 HIS 0.006 0.001 HIS A 201 PHE 0.019 0.001 PHE C 473 TYR 0.020 0.001 TYR B 712 ARG 0.017 0.001 ARG C 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 186 time to evaluate : 3.699 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 41 ASP cc_start: 0.7929 (t70) cc_final: 0.7340 (t70) REVERT: A 155 MET cc_start: 0.7576 (mmm) cc_final: 0.6872 (mmm) REVERT: A 187 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7225 (mtpm) REVERT: A 326 ASP cc_start: 0.3765 (OUTLIER) cc_final: 0.3260 (t0) REVERT: A 371 ASN cc_start: 0.3887 (OUTLIER) cc_final: 0.3290 (p0) REVERT: A 431 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1185 (mm) REVERT: A 726 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7721 (mt) REVERT: A 789 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7579 (mm110) REVERT: A 831 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7206 (mp0) REVERT: A 1003 LEU cc_start: 0.8319 (mt) cc_final: 0.7887 (tt) REVERT: A 1069 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: A 1095 ASP cc_start: 0.6729 (m-30) cc_final: 0.6350 (t0) REVERT: A 1105 ARG cc_start: 0.6936 (tpt170) cc_final: 0.6421 (tpp-160) REVERT: A 1108 GLU cc_start: 0.6416 (tt0) cc_final: 0.6085 (tp30) REVERT: B 182 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3923 (tt) REVERT: B 213 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.5843 (t80) REVERT: B 437 ASN cc_start: 0.2324 (OUTLIER) cc_final: 0.1444 (t0) REVERT: B 560 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.2012 (pp) REVERT: B 595 ASN cc_start: 0.4854 (OUTLIER) cc_final: 0.4123 (p0) REVERT: B 748 LEU cc_start: 0.6579 (tm) cc_final: 0.6359 (pt) REVERT: B 800 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: B 835 PHE cc_start: 0.8055 (t80) cc_final: 0.6791 (t80) REVERT: B 862 MET cc_start: 0.7944 (mmm) cc_final: 0.7724 (mmp) REVERT: B 1010 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7562 (tttp) REVERT: C 205 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5891 (tp30) REVERT: C 405 SER cc_start: 0.7802 (t) cc_final: 0.7563 (p) REVERT: C 635 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: C 655 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8864 (mt) REVERT: C 1001 GLN cc_start: 0.7423 (tt0) cc_final: 0.6975 (tm-30) REVERT: D 188 MET cc_start: 0.0724 (tpp) cc_final: -0.1029 (OUTLIER) REVERT: D 320 MET cc_start: 0.1241 (mtm) cc_final: 0.0578 (ppp) REVERT: D 332 ILE cc_start: -0.0265 (OUTLIER) cc_final: -0.0516 (mp) REVERT: D 371 MET cc_start: 0.2740 (tpp) cc_final: 0.1729 (ttm) REVERT: D 372 MET cc_start: 0.1312 (mmt) cc_final: -0.0703 (tpt) REVERT: D 426 CYS cc_start: -0.0290 (OUTLIER) cc_final: -0.0839 (p) REVERT: D 478 MET cc_start: 0.0548 (OUTLIER) cc_final: -0.0384 (mmm) REVERT: E 188 MET cc_start: 0.2669 (mtt) cc_final: 0.1051 (ttp) REVERT: E 327 GLN cc_start: 0.0876 (OUTLIER) cc_final: -0.0374 (pm20) REVERT: E 332 ILE cc_start: -0.0467 (OUTLIER) cc_final: -0.1130 (mt) REVERT: E 488 MET cc_start: -0.0029 (OUTLIER) cc_final: -0.1135 (tpt) outliers start: 147 outliers final: 114 residues processed: 313 average time/residue: 1.0869 time to fit residues: 441.1735 Evaluate side-chains 317 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 182 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 29 ASN 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 64 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1066 ASP 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 1178 ILE Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 269 optimal weight: 2.9990 chunk 361 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 349 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 HIS ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS C 465 HIS C 598 ASN D 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151410 restraints weight = 51820.312| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.76 r_work: 0.3358 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35749 Z= 0.177 Angle : 0.562 9.966 48671 Z= 0.291 Chirality : 0.045 0.403 5704 Planarity : 0.005 0.076 6140 Dihedral : 7.541 96.209 6679 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.73 % Allowed : 22.16 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -1.40 (0.13), residues: 4304 helix: 1.33 (0.20), residues: 804 sheet: -0.46 (0.17), residues: 932 loop : -1.97 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 971 HIS 0.006 0.001 HIS A 201 PHE 0.019 0.001 PHE C 473 TYR 0.018 0.001 TYR B1148 ARG 0.018 0.000 ARG C 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12120.16 seconds wall clock time: 218 minutes 31.34 seconds (13111.34 seconds total)