Starting phenix.real_space_refine on Fri May 17 15:02:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1e_38833/05_2024/8y1e_38833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1e_38833/05_2024/8y1e_38833.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/8y1e_38833/05_2024/8y1e_38833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1e_38833/05_2024/8y1e_38833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1e_38833/05_2024/8y1e_38833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y1e_38833/05_2024/8y1e_38833.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= -0.002 sd= 0.107 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 240 5.16 5 C 23835 2.51 5 N 6135 2.21 5 O 7401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 930": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 800": "OE1" <-> "OE2" Residue "C GLU 845": "OE1" <-> "OE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C ARG 932": "NH1" <-> "NH2" Residue "C GLU 1112": "OE1" <-> "OE2" 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" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F 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: 37611 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" 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: "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': 2, 'PTRANS': 50, '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: 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: "G" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 20.46, per 1000 atoms: 0.54 Number of scatterers: 37611 At special positions: 0 Unit cell: (151.093, 153.267, 242.401, 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 240 16.00 O 7401 8.00 N 6135 7.00 C 23835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=90, 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=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.02 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.02 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=2.04 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.02 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.01 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.04 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=2.02 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 Simple disulfide: pdb=" SG CYS F 172 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 241 " distance=2.04 Simple disulfide: pdb=" SG CYS F 244 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 297 " distance=2.02 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 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 G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " MAN L 3 " - " MAN L 6 " " MAN L 4 " - " MAN L 5 " " MAN Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " ALPHA1-4 " NAG G 2 " - " MAN G 3 " " NAG L 2 " - " MAN L 3 " " NAG Q 2 " - " MAN Q 3 " ALPHA1-6 " MAN G 3 " - " MAN G 4 " " MAN L 3 " - " MAN L 4 " " MAN Q 3 " - " MAN Q 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-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 G 1 " - " ASN A 132 " " NAG H 1 " - " ASN A 188 " " NAG I 1 " - " ASN A 335 " " NAG J 1 " - " ASN A 355 " " NAG K 1 " - " ASN A 664 " " NAG L 1 " - " ASN B 132 " " NAG M 1 " - " ASN B 188 " " NAG N 1 " - " ASN B 335 " " NAG O 1 " - " ASN B 355 " " NAG P 1 " - " ASN B 664 " " NAG Q 1 " - " ASN C 132 " " NAG R 1 " - " ASN C 188 " " NAG S 1 " - " ASN C 335 " " NAG T 1 " - " ASN C 355 " " NAG U 1 " - " ASN C 664 " Time building additional restraints: 15.55 Conformation dependent library (CDL) restraints added in 7.1 seconds 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 86 sheets defined 20.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.685A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 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: 3.788A 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: 3.928A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.025A 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 703 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 835 through 861 removed outlier: 3.521A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.903A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.618A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.948A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.811A 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 1113 removed outlier: 3.585A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.695A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.683A 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: 4.169A pdb=" N GLY B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.788A 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: 5.079A 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: 4.024A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.088A 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 861 Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.791A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.515A pdb=" N ASN B 941 " --> pdb=" O VAL B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.577A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.568A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.953A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.711A 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: 3.579A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.640A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.888A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.517A pdb=" N GLU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.169A pdb=" N GLY C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 381' Processing helix chain 'C' and resid 394 through 402 removed outlier: 5.080A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 4.034A 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 442 through 447 removed outlier: 3.927A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.025A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.090A pdb=" N THR C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) 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 835 through 861 Processing helix chain 'C' and resid 885 through 888 Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.850A 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 940 removed outlier: 3.719A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 971 through 975 removed outlier: 4.016A pdb=" N ALA C 975 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.538A 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: 3.740A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.781A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.708A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (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: 3.683A pdb=" N HIS D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.744A 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: 4.082A 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 helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.683A pdb=" N HIS F 307 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 411 removed outlier: 3.745A pdb=" N CYS F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 452 Processing helix chain 'F' and resid 483 through 487 Processing helix chain 'F' and resid 488 through 492 removed outlier: 4.135A pdb=" N ASP F 491 " --> pdb=" O MET F 488 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY F 492 " --> pdb=" O ARG F 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 488 through 492' Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.785A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 665 " --> pdb=" O ASP C 660 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 63 removed outlier: 4.016A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.793A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 97 removed outlier: 4.006A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 226 removed outlier: 5.096A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (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 308 removed outlier: 3.607A pdb=" N GLY A 308 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY A 675 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.330A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.679A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AB3, 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=AB4, 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=AB5, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB6, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB7, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB8, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.548A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 773 through 775 Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 5.987A pdb=" N SER A1152 " --> pdb=" O THR A 792 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE A 794 " --> pdb=" O PRO A1150 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 796 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A1148 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY A 798 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE A1146 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU A 800 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A1144 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 802 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A1142 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 804 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY A1140 " --> pdb=" O GLN A 804 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.783A 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: 4.260A 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 removed outlier: 3.544A pdb=" N ALA A1215 " --> pdb=" O CYS A1163 " (cutoff:3.500A) 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 67 removed outlier: 3.945A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.543A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.893A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD3, first strand: chain 'B' and resid 173 through 175 removed outlier: 7.626A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 307 removed outlier: 7.520A pdb=" N ARG B 676 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 5.173A 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: 3.867A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (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: 3.642A 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: 10.676A pdb=" N TYR B 762 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N THR B 727 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE B 764 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 729 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU B 736 " --> pdb=" O ILE B 744 " (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: 6.827A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.827A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.609A 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: 4.294A 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 removed outlier: 3.568A pdb=" N VAL B 879 " --> pdb=" O ILE B 882 " (cutoff:3.500A) 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: 7.897A pdb=" N GLN C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP C 281 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.572A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.792A 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: 3.564A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (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 155 through 160 removed outlier: 7.424A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 302 through 307 removed outlier: 7.430A pdb=" N ARG C 676 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG C 693 " --> pdb=" O ARG C 676 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 347 through 349 removed outlier: 6.680A pdb=" N TYR C 426 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 347 through 349 Processing sheet with id=AG3, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.639A pdb=" N THR C 602 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 459 through 463 removed outlier: 3.619A pdb=" N ASP C 578 " --> pdb=" O VAL C 460 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 576 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 467 through 468 Processing sheet with id=AG6, first strand: chain 'C' and resid 504 through 505 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 581 through 582 Processing sheet with id=AG9, first strand: chain 'C' and resid 724 through 731 removed outlier: 10.611A pdb=" N TYR C 762 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N THR C 727 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE C 764 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR C 729 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.801A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.457A 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 'C' and resid 1175 through 1180 Processing sheet with id=AH6, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.520A pdb=" N SER D 167 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AH7, 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=AH8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AH9, first strand: chain 'D' and resid 279 through 281 Processing sheet with id=AI1, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AI2, 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: 5.301A pdb=" N LEU D 455 " --> pdb=" O THR D 447 " (cutoff:3.500A) Processing sheet with id=AI3, 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=AI4, 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: 3.602A pdb=" N GLN E 198 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE E 200 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 209 through 212 Processing sheet with id=AI6, first strand: chain 'E' and resid 279 through 281 Processing sheet with id=AI7, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AI8, 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) Processing sheet with id=AI9, first strand: chain 'F' and resid 149 through 150 removed outlier: 3.520A pdb=" N SER F 167 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 196 through 200 removed outlier: 3.611A pdb=" N SER F 196 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 198 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE F 200 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 209 through 212 Processing sheet with id=AJ3, first strand: chain 'F' and resid 279 through 281 Processing sheet with id=AJ4, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AJ5, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.534A pdb=" N GLY F 457 " --> pdb=" O LEU F 445 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 447 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU F 455 " --> pdb=" O THR F 447 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 2931 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: 20.34 Time building geometry restraints manager: 16.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6028 1.30 - 1.43: 11060 1.43 - 1.57: 21129 1.57 - 1.70: 0 1.70 - 1.83: 294 Bond restraints: 38511 Sorted by residual: bond pdb=" C SER A 350 " pdb=" O SER A 350 " ideal model delta sigma weight residual 1.234 1.170 0.064 1.28e-02 6.10e+03 2.48e+01 bond pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.25e-02 6.40e+03 1.73e+01 bond pdb=" N PRO B 325 " pdb=" CD PRO B 325 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO C 325 " pdb=" CD PRO C 325 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N PRO A 325 " pdb=" CD PRO A 325 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 ... (remaining 38506 not shown) Histogram of bond angle deviations from ideal: 98.76 - 106.78: 1213 106.78 - 114.80: 22607 114.80 - 122.82: 24498 122.82 - 130.84: 3957 130.84 - 138.86: 153 Bond angle restraints: 52428 Sorted by residual: angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 113.20 106.92 6.28 9.60e-01 1.09e+00 4.29e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.36 117.80 -6.44 1.09e+00 8.42e-01 3.49e+01 angle pdb=" N ARG A 320 " pdb=" CA ARG A 320 " pdb=" C ARG A 320 " ideal model delta sigma weight residual 110.41 117.37 -6.96 1.18e+00 7.18e-01 3.48e+01 angle pdb=" N LYS F 340 " pdb=" CA LYS F 340 " pdb=" C LYS F 340 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.43e+01 angle pdb=" N LYS E 340 " pdb=" CA LYS E 340 " pdb=" C LYS E 340 " ideal model delta sigma weight residual 111.36 117.70 -6.34 1.09e+00 8.42e-01 3.38e+01 ... (remaining 52423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.76: 21459 20.76 - 41.52: 1891 41.52 - 62.27: 685 62.27 - 83.03: 67 83.03 - 103.79: 24 Dihedral angle restraints: 24126 sinusoidal: 10521 harmonic: 13605 Sorted by residual: dihedral pdb=" CA GLY A1127 " pdb=" C GLY A1127 " pdb=" N ASN A1128 " pdb=" CA ASN A1128 " ideal model delta harmonic sigma weight residual -180.00 -131.99 -48.01 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA VAL B 51 " pdb=" C VAL B 51 " pdb=" N LEU B 52 " pdb=" CA LEU B 52 " ideal model delta harmonic sigma weight residual -180.00 -135.98 -44.02 0 5.00e+00 4.00e-02 7.75e+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 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 24123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 6085 0.300 - 0.599: 7 0.599 - 0.898: 5 0.898 - 1.198: 3 1.198 - 1.497: 2 Chirality restraints: 6102 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.86e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 188 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.90 -1.50 2.00e-01 2.50e+01 5.61e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 188 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.75e+01 ... (remaining 6099 not shown) Planarity restraints: 6690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 188 " 0.167 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" CG ASN A 188 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 188 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 188 " -0.428 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 19 " -0.068 2.00e-02 2.50e+03 1.34e-01 2.24e+02 pdb=" CG ASN A 19 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 19 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A 19 " 0.239 2.00e-02 2.50e+03 pdb=" C1 NAG A2001 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 132 " -0.116 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" CG ASN C 132 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 132 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C 132 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.147 2.00e-02 2.50e+03 ... (remaining 6687 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8558 2.77 - 3.31: 31542 3.31 - 3.84: 61929 3.84 - 4.37: 70452 4.37 - 4.90: 123483 Nonbonded interactions: 295964 Sorted by model distance: nonbonded pdb=" O PHE B 354 " pdb=" OD1 ASN B 605 " model vdw 2.244 3.040 nonbonded pdb=" O SER B 886 " pdb=" OG SER B 901 " model vdw 2.251 2.440 nonbonded pdb=" O SER A 886 " pdb=" OG SER A 901 " model vdw 2.257 2.440 nonbonded pdb=" O SER E 448 " pdb=" OG SER E 448 " model vdw 2.267 2.440 nonbonded pdb=" O SER F 448 " pdb=" OG SER F 448 " model vdw 2.267 2.440 ... (remaining 295959 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' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.040 Extract box with map and model: 15.800 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 105.570 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 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 : 0.010 0.099 38511 Z= 0.652 Angle : 1.072 13.862 52428 Z= 0.595 Chirality : 0.073 1.497 6102 Planarity : 0.008 0.102 6624 Dihedral : 17.713 103.787 15138 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.28 % Favored : 88.57 % Rotamer: Outliers : 15.59 % Allowed : 12.41 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.27 % 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: -4.10 (0.10), residues: 4647 helix: -2.30 (0.15), residues: 805 sheet: -1.99 (0.15), residues: 1020 loop : -3.31 (0.09), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 515 HIS 0.011 0.003 HIS D 296 PHE 0.032 0.003 PHE B 391 TYR 0.027 0.003 TYR B 427 ARG 0.005 0.001 ARG C1081 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 643 poor density : 444 time to evaluate : 3.962 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: -0.0273 (OUTLIER) cc_final: -0.0792 (mmmm) REVERT: A 132 ASN cc_start: 0.0426 (OUTLIER) cc_final: 0.0021 (p0) REVERT: A 173 SER cc_start: 0.4641 (OUTLIER) cc_final: 0.4368 (p) REVERT: A 222 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.5277 (t80) REVERT: A 362 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 371 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.4876 (p0) REVERT: A 437 ASN cc_start: 0.6040 (OUTLIER) cc_final: 0.5321 (p0) REVERT: A 731 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 789 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: A 805 THR cc_start: 0.8193 (p) cc_final: 0.7920 (t) REVERT: A 811 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8296 (m) REVERT: A 851 ASP cc_start: 0.5929 (m-30) cc_final: 0.5410 (m-30) REVERT: A 852 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6662 (mp) REVERT: A 1028 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7474 (ttpp) REVERT: A 1076 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7350 (mtm-85) REVERT: A 1135 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (tp40) REVERT: A 1219 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5633 (p90) REVERT: B 30 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5484 (ptpt) REVERT: B 52 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 120 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5753 (mm-30) REVERT: B 147 GLU cc_start: 0.7555 (tt0) cc_final: 0.6821 (tm-30) REVERT: B 182 LEU cc_start: 0.7805 (mt) cc_final: 0.7435 (tt) REVERT: B 227 TYR cc_start: 0.8450 (t80) cc_final: 0.8213 (t80) REVERT: B 241 THR cc_start: 0.8123 (m) cc_final: 0.7683 (p) REVERT: B 296 SER cc_start: 0.7533 (t) cc_final: 0.7175 (p) REVERT: B 319 ARG cc_start: 0.6258 (tpt-90) cc_final: 0.5596 (mpt90) REVERT: B 516 CYS cc_start: -0.0006 (OUTLIER) cc_final: -0.0355 (p) REVERT: B 696 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7946 (mmpt) REVERT: B 735 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: B 748 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6085 (tp) REVERT: B 831 GLU cc_start: 0.8060 (pt0) cc_final: 0.7820 (pt0) REVERT: B 863 GLN cc_start: 0.6374 (tp40) cc_final: 0.5440 (tp40) REVERT: B 872 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7479 (m-40) REVERT: B 900 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: B 952 GLU cc_start: 0.6894 (tp30) cc_final: 0.6633 (tp30) REVERT: B 1010 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7682 (ttpt) REVERT: B 1028 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7579 (mmmt) REVERT: B 1045 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7663 (mm110) REVERT: B 1068 PRO cc_start: 0.7815 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: B 1182 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: C 405 SER cc_start: 0.0343 (OUTLIER) cc_final: -0.0005 (m) REVERT: C 621 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7074 (m-40) REVERT: C 711 PHE cc_start: 0.6139 (m-80) cc_final: 0.5793 (m-10) REVERT: C 735 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7656 (p0) REVERT: C 738 MET cc_start: 0.8125 (mmm) cc_final: 0.7795 (mmt) REVERT: C 845 GLU cc_start: 0.7187 (tt0) cc_final: 0.6803 (pt0) REVERT: C 863 GLN cc_start: 0.7214 (tp40) cc_final: 0.6985 (tp40) REVERT: C 952 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5678 (mm-30) REVERT: C 994 MET cc_start: 0.7835 (tpp) cc_final: 0.7582 (tpt) REVERT: C 1002 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5940 (mptp) REVERT: C 1010 LYS cc_start: 0.7121 (ttmm) cc_final: 0.6240 (mppt) REVERT: C 1030 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: D 229 ASP cc_start: 0.0016 (OUTLIER) cc_final: -0.0423 (t70) REVERT: D 234 LYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3101 (ttmm) REVERT: D 251 SER cc_start: 0.1933 (OUTLIER) cc_final: 0.1458 (m) REVERT: D 256 ILE cc_start: -0.0763 (OUTLIER) cc_final: -0.1062 (mm) REVERT: D 273 LEU cc_start: 0.2205 (OUTLIER) cc_final: 0.1755 (pp) REVERT: D 320 MET cc_start: -0.2321 (mtm) cc_final: -0.3592 (pp-130) REVERT: D 345 ASP cc_start: 0.3807 (t0) cc_final: 0.3538 (m-30) REVERT: D 392 LYS cc_start: 0.3204 (OUTLIER) cc_final: 0.2848 (mppt) REVERT: D 430 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.4826 (mp) REVERT: E 171 VAL cc_start: 0.0560 (t) cc_final: 0.0229 (t) REVERT: E 211 LYS cc_start: 0.0341 (mmtt) cc_final: 0.0053 (mttt) REVERT: E 285 ILE cc_start: 0.1695 (OUTLIER) cc_final: 0.1374 (mm) REVERT: E 286 ILE cc_start: 0.1176 (OUTLIER) cc_final: 0.0964 (pt) REVERT: E 303 ASN cc_start: 0.4309 (OUTLIER) cc_final: 0.3686 (t0) REVERT: E 327 GLN cc_start: 0.3039 (OUTLIER) cc_final: 0.2557 (mp10) REVERT: E 346 ILE cc_start: 0.2733 (OUTLIER) cc_final: 0.2412 (tt) REVERT: E 392 LYS cc_start: 0.1407 (OUTLIER) cc_final: 0.1085 (tppt) REVERT: E 429 PHE cc_start: 0.1144 (OUTLIER) cc_final: 0.0668 (m-80) REVERT: E 477 VAL cc_start: 0.1696 (OUTLIER) cc_final: 0.1403 (p) REVERT: F 173 GLN cc_start: 0.0039 (OUTLIER) cc_final: -0.1465 (tt0) REVERT: F 198 GLN cc_start: 0.3937 (OUTLIER) cc_final: 0.3266 (mm110) REVERT: F 320 MET cc_start: 0.1116 (mtm) cc_final: 0.0175 (ptp) REVERT: F 327 GLN cc_start: 0.3866 (OUTLIER) cc_final: 0.3248 (mp10) REVERT: F 396 VAL cc_start: 0.1525 (OUTLIER) cc_final: 0.1291 (m) REVERT: F 418 ASN cc_start: 0.2196 (m-40) cc_final: 0.1657 (t0) REVERT: F 438 GLN cc_start: 0.0642 (OUTLIER) cc_final: -0.0028 (pt0) outliers start: 643 outliers final: 179 residues processed: 1005 average time/residue: 1.0725 time to fit residues: 1398.8652 Evaluate side-chains 493 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 264 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 828 LEU 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 872 ASN Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 900 ARG Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1089 VAL 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 1115 LYS Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1182 ASP Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR 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 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 102 ILE 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 168 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 621 ASN Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 877 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1189 SER 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 207 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 429 PHE Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 429 PHE Chi-restraints excluded: chain F residue 438 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 362 optimal weight: 40.0000 chunk 140 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 419 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 234 HIS A 323 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 583 ASN A 630 GLN A 876 HIS A 881 ASN A1086 ASN A1091 GLN A1122 ASN A1136 ASN B 73 ASN B 152 GLN B 204 GLN B 371 ASN B 413 ASN B 424 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 630 GLN B 840 ASN B 876 HIS B1001 GLN B1023 ASN B1045 GLN B1079 ASN B1091 GLN B1122 ASN B1136 ASN B1201 ASN C 140 GLN C 413 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 559 GLN ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 GLN C 854 GLN C 876 HIS ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN C1038 GLN C1079 ASN C1086 ASN C1091 GLN C1136 ASN ** D 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 398 ASN D 431 GLN E 164 GLN E 173 GLN E 253 GLN ** E 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 GLN E 327 GLN F 198 GLN F 227 HIS F 327 GLN F 398 ASN F 408 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38511 Z= 0.216 Angle : 0.715 13.360 52428 Z= 0.373 Chirality : 0.049 0.556 6102 Planarity : 0.006 0.083 6624 Dihedral : 12.233 96.376 7364 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.24 % Favored : 91.72 % Rotamer: Outliers : 7.88 % Allowed : 19.39 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.16 (0.11), residues: 4647 helix: -0.71 (0.18), residues: 831 sheet: -1.53 (0.15), residues: 1100 loop : -2.93 (0.10), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 168 HIS 0.009 0.001 HIS A 465 PHE 0.019 0.001 PHE F 429 TYR 0.027 0.002 TYR B 609 ARG 0.013 0.001 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 322 time to evaluate : 4.087 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.4387 (OUTLIER) cc_final: 0.4128 (mmtt) REVERT: A 34 ARG cc_start: 0.3521 (OUTLIER) cc_final: 0.3289 (ppt-90) REVERT: A 80 LYS cc_start: -0.0572 (OUTLIER) cc_final: -0.1310 (tttm) REVERT: A 132 ASN cc_start: 0.0441 (OUTLIER) cc_final: 0.0152 (p0) REVERT: A 362 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7268 (mt) REVERT: A 371 ASN cc_start: 0.5353 (OUTLIER) cc_final: 0.4853 (p0) REVERT: A 374 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5646 (m-30) REVERT: A 398 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6352 (tpt-90) REVERT: A 511 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.3208 (p90) REVERT: A 789 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7811 (mm-40) REVERT: A 805 THR cc_start: 0.8190 (p) cc_final: 0.7945 (t) REVERT: A 811 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8120 (m) REVERT: A 845 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: A 851 ASP cc_start: 0.5726 (m-30) cc_final: 0.5261 (m-30) REVERT: A 1028 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7289 (ttpt) REVERT: A 1038 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6540 (mp10) REVERT: A 1219 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5560 (p90) REVERT: B 30 LYS cc_start: 0.5903 (OUTLIER) cc_final: 0.4670 (mtmm) REVERT: B 52 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 120 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5821 (mm-30) REVERT: B 147 GLU cc_start: 0.7211 (tt0) cc_final: 0.6516 (mp0) REVERT: B 227 TYR cc_start: 0.8401 (t80) cc_final: 0.8180 (t80) REVERT: B 296 SER cc_start: 0.7404 (t) cc_final: 0.7076 (p) REVERT: B 319 ARG cc_start: 0.6101 (tpt-90) cc_final: 0.5533 (mpt180) REVERT: B 516 CYS cc_start: 0.0448 (OUTLIER) cc_final: -0.0246 (p) REVERT: B 696 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7742 (mmmt) REVERT: B 735 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: B 748 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6025 (tp) REVERT: B 787 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: B 863 GLN cc_start: 0.6155 (tp40) cc_final: 0.5260 (tp40) REVERT: B 872 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: B 1028 LYS cc_start: 0.7482 (mttp) cc_final: 0.7253 (mtmt) REVERT: C 213 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7378 (p90) REVERT: C 487 LYS cc_start: 0.2002 (OUTLIER) cc_final: 0.1672 (tmtp) REVERT: C 643 ASN cc_start: 0.7603 (p0) cc_final: 0.7272 (p0) REVERT: C 711 PHE cc_start: 0.6062 (m-80) cc_final: 0.5697 (m-10) REVERT: C 735 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 738 MET cc_start: 0.8180 (mmm) cc_final: 0.7832 (mmt) REVERT: C 863 GLN cc_start: 0.7104 (tp40) cc_final: 0.6856 (tp40) REVERT: C 888 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7134 (mp) REVERT: C 952 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5426 (mm-30) REVERT: C 1002 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5831 (mptp) REVERT: C 1010 LYS cc_start: 0.7004 (ttmm) cc_final: 0.6143 (mppt) REVERT: D 223 LYS cc_start: 0.4002 (mmtt) cc_final: 0.3227 (tppt) REVERT: D 229 ASP cc_start: 0.0255 (OUTLIER) cc_final: -0.0173 (t70) REVERT: D 234 LYS cc_start: 0.4082 (OUTLIER) cc_final: 0.3087 (ttmm) REVERT: D 301 PRO cc_start: 0.1051 (Cg_endo) cc_final: 0.0773 (Cg_exo) REVERT: D 425 ILE cc_start: 0.2020 (OUTLIER) cc_final: 0.1638 (pp) REVERT: D 430 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4389 (mp) REVERT: D 459 THR cc_start: 0.3162 (OUTLIER) cc_final: 0.2840 (m) REVERT: D 480 PHE cc_start: 0.2144 (OUTLIER) cc_final: 0.0563 (m-80) REVERT: E 188 MET cc_start: 0.4153 (ptp) cc_final: 0.3452 (ptp) REVERT: E 285 ILE cc_start: 0.1771 (OUTLIER) cc_final: 0.1341 (OUTLIER) REVERT: E 303 ASN cc_start: 0.4157 (OUTLIER) cc_final: 0.3722 (t0) REVERT: E 320 MET cc_start: -0.0446 (mtm) cc_final: -0.0769 (mmt) REVERT: E 346 ILE cc_start: 0.2846 (OUTLIER) cc_final: 0.2476 (tt) REVERT: E 362 LYS cc_start: 0.3709 (mtmm) cc_final: 0.2982 (tppt) REVERT: E 371 MET cc_start: 0.2113 (tmm) cc_final: 0.1547 (tmm) REVERT: E 392 LYS cc_start: 0.1261 (OUTLIER) cc_final: 0.1007 (tppt) REVERT: E 477 VAL cc_start: 0.1566 (OUTLIER) cc_final: 0.1294 (p) REVERT: F 210 MET cc_start: -0.0869 (OUTLIER) cc_final: -0.1072 (mmt) REVERT: F 315 LEU cc_start: 0.2272 (OUTLIER) cc_final: 0.1975 (mp) REVERT: F 320 MET cc_start: 0.0168 (mtm) cc_final: -0.0164 (ptp) REVERT: F 355 LEU cc_start: 0.2215 (OUTLIER) cc_final: 0.1090 (tp) REVERT: F 413 ARG cc_start: 0.3998 (OUTLIER) cc_final: 0.2346 (mtm180) REVERT: F 418 ASN cc_start: 0.2592 (m-40) cc_final: 0.2143 (t0) REVERT: F 438 GLN cc_start: 0.0869 (OUTLIER) cc_final: 0.0307 (pt0) outliers start: 325 outliers final: 147 residues processed: 613 average time/residue: 1.0643 time to fit residues: 856.2827 Evaluate side-chains 443 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 252 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 515 TRP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS 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 253 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 828 LEU 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 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1042 SER Chi-restraints excluded: chain B residue 1089 VAL 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 1165 SER Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR 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 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 944 LYS Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1090 SER Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 438 GLN Chi-restraints excluded: chain F residue 459 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 349 optimal weight: 0.6980 chunk 285 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 420 optimal weight: 30.0000 chunk 454 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 416 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 337 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A1091 GLN A1135 GLN B 371 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN B1136 ASN C 440 ASN C 445 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 ASN C 605 ASN C 709 GLN C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN C1030 GLN C1079 ASN C1122 ASN ** D 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 HIS E 343 ASN E 368 ASN ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38511 Z= 0.281 Angle : 0.696 10.611 52428 Z= 0.361 Chirality : 0.049 0.527 6102 Planarity : 0.005 0.078 6624 Dihedral : 10.893 103.808 7196 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 7.78 % Allowed : 20.29 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.78 (0.11), residues: 4647 helix: -0.22 (0.18), residues: 833 sheet: -1.32 (0.15), residues: 1086 loop : -2.74 (0.10), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 454 HIS 0.007 0.001 HIS B1129 PHE 0.024 0.002 PHE F 429 TYR 0.025 0.002 TYR A 462 ARG 0.008 0.001 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 274 time to evaluate : 4.267 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8717 (p) cc_final: 0.8337 (t) REVERT: A 80 LYS cc_start: -0.1127 (OUTLIER) cc_final: -0.1463 (mtpt) REVERT: A 222 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.5279 (t80) REVERT: A 362 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7354 (mt) REVERT: A 371 ASN cc_start: 0.5745 (OUTLIER) cc_final: 0.5103 (p0) REVERT: A 374 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5575 (m-30) REVERT: A 511 TYR cc_start: 0.4302 (OUTLIER) cc_final: 0.3027 (p90) REVERT: A 758 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5758 (tp) REVERT: A 772 VAL cc_start: 0.6182 (OUTLIER) cc_final: 0.5864 (m) REVERT: A 789 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7998 (mm-40) REVERT: A 805 THR cc_start: 0.8214 (p) cc_final: 0.7951 (t) REVERT: A 811 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (m) REVERT: A 851 ASP cc_start: 0.5816 (m-30) cc_final: 0.5313 (m-30) REVERT: A 994 MET cc_start: 0.7264 (mmt) cc_final: 0.6940 (mmt) REVERT: A 1010 LYS cc_start: 0.7562 (ttmm) cc_final: 0.6900 (mppt) REVERT: A 1028 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7314 (ttpp) REVERT: A 1038 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6606 (mp10) REVERT: A 1099 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7109 (mp) REVERT: A 1219 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5599 (p90) REVERT: B 30 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.4615 (mtmm) REVERT: B 107 LYS cc_start: 0.8368 (tmtm) cc_final: 0.7872 (tmmt) REVERT: B 120 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5952 (mm-30) REVERT: B 147 GLU cc_start: 0.7289 (tt0) cc_final: 0.6633 (mp0) REVERT: B 227 TYR cc_start: 0.8467 (t80) cc_final: 0.8231 (t80) REVERT: B 296 SER cc_start: 0.7570 (t) cc_final: 0.7200 (p) REVERT: B 319 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5415 (mpt180) REVERT: B 516 CYS cc_start: 0.0535 (OUTLIER) cc_final: -0.0017 (p) REVERT: B 735 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: B 737 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8244 (mpp-170) REVERT: B 748 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5972 (tp) REVERT: B 787 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: B 863 GLN cc_start: 0.6101 (tp40) cc_final: 0.5883 (mm110) REVERT: B 872 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7484 (m-40) REVERT: B 1028 LYS cc_start: 0.7557 (mttp) cc_final: 0.7255 (mtmt) REVERT: B 1185 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.5928 (mtp) REVERT: C 213 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7414 (p90) REVERT: C 484 SER cc_start: 0.4968 (OUTLIER) cc_final: 0.4614 (p) REVERT: C 487 LYS cc_start: 0.2033 (OUTLIER) cc_final: 0.1672 (tmtp) REVERT: C 643 ASN cc_start: 0.7525 (p0) cc_final: 0.7227 (p0) REVERT: C 711 PHE cc_start: 0.6062 (m-80) cc_final: 0.5710 (m-10) REVERT: C 735 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7596 (p0) REVERT: C 738 MET cc_start: 0.8168 (mmm) cc_final: 0.7871 (mmt) REVERT: C 952 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5473 (mm-30) REVERT: C 1002 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6182 (mptp) REVERT: C 1038 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6619 (mp-120) REVERT: D 234 LYS cc_start: 0.4114 (OUTLIER) cc_final: 0.2904 (ttmm) REVERT: D 349 MET cc_start: 0.4122 (tmm) cc_final: 0.3001 (ttt) REVERT: D 425 ILE cc_start: 0.1953 (OUTLIER) cc_final: 0.1682 (pp) REVERT: D 430 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4552 (mt) REVERT: D 459 THR cc_start: 0.4052 (OUTLIER) cc_final: 0.3380 (m) REVERT: E 253 GLN cc_start: 0.0678 (OUTLIER) cc_final: 0.0297 (pt0) REVERT: E 285 ILE cc_start: 0.1688 (OUTLIER) cc_final: 0.1289 (mt) REVERT: E 303 ASN cc_start: 0.3936 (p0) cc_final: 0.3428 (t0) REVERT: E 346 ILE cc_start: 0.2454 (OUTLIER) cc_final: 0.1944 (tt) REVERT: E 362 LYS cc_start: 0.3813 (mtmm) cc_final: 0.3147 (tppt) REVERT: E 392 LYS cc_start: 0.1487 (OUTLIER) cc_final: 0.1186 (tppt) REVERT: E 459 THR cc_start: 0.0510 (OUTLIER) cc_final: 0.0287 (m) REVERT: F 322 TYR cc_start: 0.2767 (OUTLIER) cc_final: 0.2382 (m-80) REVERT: F 352 GLN cc_start: 0.4339 (OUTLIER) cc_final: 0.4130 (pt0) REVERT: F 413 ARG cc_start: 0.3872 (OUTLIER) cc_final: 0.2088 (mtm180) REVERT: F 418 ASN cc_start: 0.2568 (m-40) cc_final: 0.2223 (t0) REVERT: F 419 LEU cc_start: 0.2499 (OUTLIER) cc_final: 0.1856 (tp) REVERT: F 445 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4713 (tp) outliers start: 321 outliers final: 164 residues processed: 551 average time/residue: 0.9960 time to fit residues: 729.8738 Evaluate side-chains 448 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 239 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS 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 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1023 ASN Chi-restraints excluded: chain B residue 1089 VAL 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 1165 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR 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 48 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 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 248 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 322 TYR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 398 ASN Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 20.0000 chunk 316 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 421 optimal weight: 3.9990 chunk 446 optimal weight: 20.0000 chunk 220 optimal weight: 0.7980 chunk 399 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A 863 GLN A1046 GLN A1091 GLN A1135 GLN B 371 ASN B 440 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN C 654 ASN C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38511 Z= 0.251 Angle : 0.662 14.071 52428 Z= 0.341 Chirality : 0.048 0.510 6102 Planarity : 0.005 0.076 6624 Dihedral : 10.176 97.531 7159 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 7.59 % Allowed : 21.14 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.52 (0.12), residues: 4647 helix: 0.07 (0.19), residues: 828 sheet: -1.11 (0.16), residues: 1057 loop : -2.60 (0.10), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 454 HIS 0.006 0.001 HIS B1129 PHE 0.023 0.002 PHE B 884 TYR 0.026 0.002 TYR C 622 ARG 0.006 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 260 time to evaluate : 4.149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: -0.1217 (OUTLIER) cc_final: -0.1594 (ttpp) REVERT: A 124 ILE cc_start: 0.4174 (OUTLIER) cc_final: 0.3873 (tp) REVERT: A 222 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.5266 (t80) REVERT: A 348 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 371 ASN cc_start: 0.5690 (OUTLIER) cc_final: 0.5072 (p0) REVERT: A 374 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5624 (m-30) REVERT: A 511 TYR cc_start: 0.4393 (OUTLIER) cc_final: 0.3121 (p90) REVERT: A 737 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6613 (mtp180) REVERT: A 758 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5759 (tp) REVERT: A 772 VAL cc_start: 0.6159 (OUTLIER) cc_final: 0.5879 (m) REVERT: A 789 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: A 805 THR cc_start: 0.8235 (p) cc_final: 0.7953 (t) REVERT: A 811 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 851 ASP cc_start: 0.5836 (m-30) cc_final: 0.5350 (m-30) REVERT: A 994 MET cc_start: 0.7306 (mmt) cc_final: 0.7034 (mmt) REVERT: A 1010 LYS cc_start: 0.7547 (ttmm) cc_final: 0.6874 (mppt) REVERT: A 1022 THR cc_start: 0.7991 (m) cc_final: 0.7726 (p) REVERT: A 1028 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7319 (ttpp) REVERT: A 1038 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: A 1219 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.5538 (p90) REVERT: B 30 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.4794 (mtmm) REVERT: B 107 LYS cc_start: 0.8385 (tmtm) cc_final: 0.7863 (tmmt) REVERT: B 147 GLU cc_start: 0.7234 (tt0) cc_final: 0.6539 (mp0) REVERT: B 227 TYR cc_start: 0.8499 (t80) cc_final: 0.8254 (t80) REVERT: B 296 SER cc_start: 0.7558 (t) cc_final: 0.7190 (p) REVERT: B 735 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: B 748 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5929 (tp) REVERT: B 787 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: B 863 GLN cc_start: 0.6163 (tp40) cc_final: 0.5903 (mm110) REVERT: B 872 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7394 (m-40) REVERT: B 1028 LYS cc_start: 0.7539 (mttp) cc_final: 0.7241 (mtmt) REVERT: B 1185 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.5835 (mtp) REVERT: C 34 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4713 (mtp180) REVERT: C 213 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7340 (p90) REVERT: C 487 LYS cc_start: 0.1940 (OUTLIER) cc_final: 0.0998 (mmpt) REVERT: C 545 HIS cc_start: 0.2790 (OUTLIER) cc_final: 0.1336 (m-70) REVERT: C 643 ASN cc_start: 0.7474 (p0) cc_final: 0.7214 (p0) REVERT: C 687 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.8009 (t) REVERT: C 711 PHE cc_start: 0.6061 (m-80) cc_final: 0.5709 (m-10) REVERT: C 735 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7584 (p0) REVERT: C 738 MET cc_start: 0.8210 (mmm) cc_final: 0.7936 (mmt) REVERT: C 888 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7373 (mp) REVERT: C 952 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5290 (mm-30) REVERT: C 1002 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6189 (mptp) REVERT: C 1038 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6669 (mp-120) REVERT: C 1091 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: D 234 LYS cc_start: 0.4232 (OUTLIER) cc_final: 0.2875 (ttmm) REVERT: D 308 TRP cc_start: 0.1327 (m100) cc_final: 0.0682 (m-90) REVERT: D 320 MET cc_start: -0.2154 (mtm) cc_final: -0.3476 (tmm) REVERT: D 349 MET cc_start: 0.4034 (tmm) cc_final: 0.2989 (ttt) REVERT: D 371 MET cc_start: 0.1973 (ttm) cc_final: -0.2168 (tpt) REVERT: D 430 LEU cc_start: 0.4857 (OUTLIER) cc_final: 0.4544 (mt) REVERT: D 480 PHE cc_start: 0.2782 (OUTLIER) cc_final: 0.1161 (m-80) REVERT: E 226 TYR cc_start: -0.0278 (p90) cc_final: -0.1617 (p90) REVERT: E 303 ASN cc_start: 0.3767 (p0) cc_final: 0.3331 (t0) REVERT: E 346 ILE cc_start: 0.2240 (OUTLIER) cc_final: 0.2004 (tt) REVERT: E 362 LYS cc_start: 0.3896 (mtmm) cc_final: 0.3214 (tppt) REVERT: E 392 LYS cc_start: 0.1402 (OUTLIER) cc_final: 0.1152 (tppt) REVERT: E 459 THR cc_start: 0.0559 (OUTLIER) cc_final: 0.0349 (m) REVERT: F 188 MET cc_start: 0.3324 (OUTLIER) cc_final: 0.2848 (ptt) REVERT: F 322 TYR cc_start: 0.2679 (OUTLIER) cc_final: 0.2363 (m-80) REVERT: F 371 MET cc_start: 0.0179 (ttt) cc_final: -0.0837 (mmp) REVERT: F 413 ARG cc_start: 0.3722 (OUTLIER) cc_final: 0.2018 (mtm180) REVERT: F 418 ASN cc_start: 0.2269 (m-40) cc_final: 0.1950 (t0) REVERT: F 419 LEU cc_start: 0.2648 (OUTLIER) cc_final: 0.1983 (tp) outliers start: 313 outliers final: 178 residues processed: 532 average time/residue: 1.0283 time to fit residues: 723.3155 Evaluate side-chains 456 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 236 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 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 242 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 322 TYR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 465 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.0270 chunk 253 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 332 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 400 optimal weight: 50.0000 chunk 112 optimal weight: 0.7980 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 372 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A1091 GLN A1135 GLN B 152 GLN B 371 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 438 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38511 Z= 0.186 Angle : 0.626 15.484 52428 Z= 0.319 Chirality : 0.048 0.873 6102 Planarity : 0.004 0.074 6624 Dihedral : 9.484 102.410 7135 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.90 % Favored : 92.06 % Rotamer: Outliers : 6.91 % Allowed : 21.75 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.26 (0.12), residues: 4647 helix: 0.33 (0.19), residues: 847 sheet: -0.88 (0.16), residues: 1054 loop : -2.48 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 269 HIS 0.005 0.001 HIS B1129 PHE 0.028 0.001 PHE B 884 TYR 0.022 0.001 TYR A 462 ARG 0.005 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 280 time to evaluate : 4.283 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8648 (p) cc_final: 0.8213 (t) REVERT: A 222 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.5191 (t80) REVERT: A 371 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5140 (p0) REVERT: A 374 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5707 (m-30) REVERT: A 511 TYR cc_start: 0.4355 (OUTLIER) cc_final: 0.3128 (p90) REVERT: A 758 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5778 (tp) REVERT: A 789 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: A 805 THR cc_start: 0.8189 (p) cc_final: 0.7947 (t) REVERT: A 811 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 845 GLU cc_start: 0.7228 (tt0) cc_final: 0.6884 (pt0) REVERT: A 851 ASP cc_start: 0.5702 (m-30) cc_final: 0.5249 (m-30) REVERT: A 994 MET cc_start: 0.7311 (mmt) cc_final: 0.7047 (mmt) REVERT: A 1010 LYS cc_start: 0.7533 (ttmm) cc_final: 0.6827 (mppt) REVERT: A 1022 THR cc_start: 0.7935 (m) cc_final: 0.7640 (p) REVERT: A 1028 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7296 (ttpp) REVERT: A 1038 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: A 1219 TYR cc_start: 0.6003 (OUTLIER) cc_final: 0.5469 (p90) REVERT: B 30 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.4586 (mtmm) REVERT: B 107 LYS cc_start: 0.8398 (tmtm) cc_final: 0.7886 (tmmt) REVERT: B 147 GLU cc_start: 0.7162 (tt0) cc_final: 0.6451 (mp0) REVERT: B 227 TYR cc_start: 0.8489 (t80) cc_final: 0.8238 (t80) REVERT: B 296 SER cc_start: 0.7555 (t) cc_final: 0.7189 (p) REVERT: B 735 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7035 (m-30) REVERT: B 748 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5886 (tp) REVERT: B 787 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: B 863 GLN cc_start: 0.6060 (tp40) cc_final: 0.5743 (mm-40) REVERT: B 872 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: B 994 MET cc_start: 0.7309 (tpp) cc_final: 0.7027 (tpt) REVERT: B 1028 LYS cc_start: 0.7512 (mttp) cc_final: 0.7232 (mtmt) REVERT: B 1154 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7660 (ttpp) REVERT: C 34 ARG cc_start: 0.5356 (OUTLIER) cc_final: 0.4746 (mtp180) REVERT: C 38 ASP cc_start: 0.5418 (OUTLIER) cc_final: 0.5196 (m-30) REVERT: C 213 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7349 (p90) REVERT: C 487 LYS cc_start: 0.2235 (OUTLIER) cc_final: 0.1031 (mmpt) REVERT: C 545 HIS cc_start: 0.2276 (OUTLIER) cc_final: 0.0828 (m-70) REVERT: C 643 ASN cc_start: 0.7410 (p0) cc_final: 0.7208 (p0) REVERT: C 711 PHE cc_start: 0.6096 (m-80) cc_final: 0.5727 (m-10) REVERT: C 735 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7576 (p0) REVERT: C 738 MET cc_start: 0.8233 (mmm) cc_final: 0.7948 (mmt) REVERT: C 888 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (mp) REVERT: C 952 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5274 (mm-30) REVERT: C 1002 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6151 (mptp) REVERT: C 1014 SER cc_start: 0.7551 (m) cc_final: 0.7325 (p) REVERT: C 1038 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6658 (mp-120) REVERT: C 1091 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: D 234 LYS cc_start: 0.4167 (OUTLIER) cc_final: 0.2780 (ttmm) REVERT: D 308 TRP cc_start: 0.1299 (m100) cc_final: 0.0998 (m-90) REVERT: D 320 MET cc_start: -0.2002 (mtm) cc_final: -0.3399 (tmm) REVERT: D 349 MET cc_start: 0.4226 (tmm) cc_final: 0.3282 (ttt) REVERT: D 420 ILE cc_start: 0.3408 (OUTLIER) cc_final: 0.2815 (tt) REVERT: D 430 LEU cc_start: 0.4853 (OUTLIER) cc_final: 0.4544 (mt) REVERT: D 480 PHE cc_start: 0.2875 (OUTLIER) cc_final: 0.1176 (m-80) REVERT: E 176 TRP cc_start: 0.1590 (OUTLIER) cc_final: 0.0928 (m-10) REVERT: E 303 ASN cc_start: 0.3783 (p0) cc_final: 0.3391 (t0) REVERT: E 362 LYS cc_start: 0.3619 (mtmm) cc_final: 0.3138 (mptt) REVERT: E 392 LYS cc_start: 0.1381 (OUTLIER) cc_final: 0.1150 (tppt) REVERT: E 406 GLU cc_start: 0.4285 (OUTLIER) cc_final: 0.3995 (tm-30) REVERT: F 371 MET cc_start: 0.0281 (ttt) cc_final: -0.0839 (mmp) REVERT: F 413 ARG cc_start: 0.3757 (OUTLIER) cc_final: 0.1852 (mtm180) REVERT: F 418 ASN cc_start: 0.2495 (m-40) cc_final: 0.2145 (t0) REVERT: F 419 LEU cc_start: 0.2559 (OUTLIER) cc_final: 0.2096 (tp) outliers start: 285 outliers final: 158 residues processed: 527 average time/residue: 1.0253 time to fit residues: 715.2542 Evaluate side-chains 435 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 241 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS 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 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1154 LYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1202 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 242 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 465 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 447 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN A 545 HIS A 583 ASN A 630 GLN A 863 GLN A1023 ASN A1046 GLN A1091 GLN A1135 GLN B 248 ASN B 483 ASN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 395 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS C 854 GLN C 874 ASN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 38511 Z= 0.518 Angle : 0.830 21.409 52428 Z= 0.421 Chirality : 0.055 0.767 6102 Planarity : 0.006 0.075 6624 Dihedral : 10.076 106.925 7106 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.81 % Favored : 90.10 % Rotamer: Outliers : 7.78 % Allowed : 21.87 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.70 (0.11), residues: 4647 helix: -0.65 (0.17), residues: 866 sheet: -0.98 (0.16), residues: 987 loop : -2.62 (0.10), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 308 HIS 0.010 0.002 HIS B1129 PHE 0.032 0.003 PHE B 884 TYR 0.027 0.003 TYR C 622 ARG 0.006 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 247 time to evaluate : 4.482 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: symmetry clash REVERT: A 42 VAL cc_start: 0.8769 (p) cc_final: 0.8331 (t) REVERT: A 197 TRP cc_start: 0.4341 (OUTLIER) cc_final: 0.3908 (m-90) REVERT: A 222 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5270 (t80) REVERT: A 371 ASN cc_start: 0.5994 (OUTLIER) cc_final: 0.5493 (t0) REVERT: A 511 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.3136 (p90) REVERT: A 737 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6749 (mtp180) REVERT: A 772 VAL cc_start: 0.6149 (OUTLIER) cc_final: 0.5856 (m) REVERT: A 789 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: A 845 GLU cc_start: 0.7337 (tt0) cc_final: 0.6925 (pt0) REVERT: A 851 ASP cc_start: 0.5826 (m-30) cc_final: 0.5386 (m-30) REVERT: A 994 MET cc_start: 0.7427 (mmt) cc_final: 0.7150 (mmt) REVERT: A 1010 LYS cc_start: 0.7554 (ttmm) cc_final: 0.6901 (mppt) REVERT: A 1022 THR cc_start: 0.7976 (m) cc_final: 0.7722 (p) REVERT: A 1028 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7383 (ttpp) REVERT: A 1038 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6624 (mp10) REVERT: A 1099 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7258 (mt) REVERT: A 1135 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7059 (tp40) REVERT: A 1219 TYR cc_start: 0.6153 (OUTLIER) cc_final: 0.5551 (p90) REVERT: B 30 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.4849 (mtmm) REVERT: B 107 LYS cc_start: 0.8398 (tmtm) cc_final: 0.7949 (tmmt) REVERT: B 147 GLU cc_start: 0.7380 (tt0) cc_final: 0.6588 (mp0) REVERT: B 177 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.5505 (m-30) REVERT: B 227 TYR cc_start: 0.8585 (t80) cc_final: 0.8325 (t80) REVERT: B 296 SER cc_start: 0.7586 (t) cc_final: 0.7120 (p) REVERT: B 506 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2348 (pp) REVERT: B 735 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: B 748 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.5995 (tp) REVERT: B 863 GLN cc_start: 0.6179 (tp40) cc_final: 0.5948 (mm-40) REVERT: B 872 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7462 (m-40) REVERT: B 1028 LYS cc_start: 0.7550 (mttp) cc_final: 0.7271 (mtmt) REVERT: B 1095 ASP cc_start: 0.6682 (m-30) cc_final: 0.6306 (m-30) REVERT: B 1149 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6895 (ttpp) REVERT: B 1185 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6008 (mtp) REVERT: B 1219 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.5630 (p90) REVERT: C 34 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.5151 (mtp180) REVERT: C 38 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.5130 (m-30) REVERT: C 213 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7479 (p90) REVERT: C 487 LYS cc_start: 0.1902 (OUTLIER) cc_final: 0.1127 (mmpt) REVERT: C 687 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (t) REVERT: C 711 PHE cc_start: 0.6131 (m-80) cc_final: 0.5757 (m-10) REVERT: C 735 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7387 (p0) REVERT: C 738 MET cc_start: 0.8192 (mmm) cc_final: 0.7980 (mmt) REVERT: C 952 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5461 (mm-30) REVERT: C 1002 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6275 (mptp) REVERT: C 1091 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: D 229 ASP cc_start: 0.0483 (OUTLIER) cc_final: 0.0152 (t70) REVERT: D 234 LYS cc_start: 0.4132 (OUTLIER) cc_final: 0.2663 (ttmm) REVERT: D 320 MET cc_start: -0.1765 (mtm) cc_final: -0.3338 (tmm) REVERT: D 359 ASP cc_start: 0.1542 (OUTLIER) cc_final: 0.0920 (m-30) REVERT: D 420 ILE cc_start: 0.2882 (OUTLIER) cc_final: 0.2220 (tt) REVERT: D 424 MET cc_start: 0.2122 (tpt) cc_final: 0.1753 (tpt) REVERT: D 480 PHE cc_start: 0.3128 (OUTLIER) cc_final: 0.1236 (m-80) REVERT: E 176 TRP cc_start: 0.1727 (OUTLIER) cc_final: 0.1475 (m100) REVERT: E 242 ILE cc_start: 0.1136 (tp) cc_final: 0.0476 (tp) REVERT: E 320 MET cc_start: -0.0785 (mtm) cc_final: -0.1353 (ttm) REVERT: E 362 LYS cc_start: 0.3759 (mtmm) cc_final: 0.3187 (tppt) REVERT: E 363 PRO cc_start: 0.3781 (Cg_endo) cc_final: 0.3551 (Cg_exo) REVERT: E 377 GLN cc_start: 0.5060 (OUTLIER) cc_final: 0.4755 (tp40) REVERT: E 392 LYS cc_start: 0.1406 (OUTLIER) cc_final: 0.0942 (mmtm) REVERT: E 406 GLU cc_start: 0.4346 (OUTLIER) cc_final: 0.4071 (tm-30) REVERT: E 483 TRP cc_start: 0.3663 (t60) cc_final: 0.2585 (t60) REVERT: F 355 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2129 (pp) REVERT: F 371 MET cc_start: 0.0118 (ttt) cc_final: -0.0968 (mmp) REVERT: F 413 ARG cc_start: 0.3939 (OUTLIER) cc_final: 0.1946 (mtm180) REVERT: F 418 ASN cc_start: 0.2316 (m-40) cc_final: 0.1910 (t0) outliers start: 321 outliers final: 196 residues processed: 525 average time/residue: 1.0420 time to fit residues: 722.3203 Evaluate side-chains 458 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 221 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 831 GLU 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 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 213 TYR 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 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1064 ARG Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 398 ASN Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 376 optimal weight: 50.0000 chunk 249 optimal weight: 3.9990 chunk 445 optimal weight: 0.3980 chunk 278 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 583 ASN A 630 GLN A1023 ASN A1046 GLN A1079 ASN A1091 GLN A1135 GLN B 152 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN D 307 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38511 Z= 0.173 Angle : 0.639 16.611 52428 Z= 0.325 Chirality : 0.047 0.668 6102 Planarity : 0.004 0.075 6624 Dihedral : 9.169 105.467 7096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 5.99 % Allowed : 23.61 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4647 helix: 0.19 (0.19), residues: 858 sheet: -0.71 (0.16), residues: 1009 loop : -2.44 (0.10), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 454 HIS 0.013 0.001 HIS E 334 PHE 0.026 0.001 PHE B 884 TYR 0.021 0.001 TYR A 462 ARG 0.012 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 264 time to evaluate : 4.066 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 176 ILE cc_start: 0.1086 (OUTLIER) cc_final: 0.0755 (mt) REVERT: A 197 TRP cc_start: 0.4265 (OUTLIER) cc_final: 0.3891 (m-90) REVERT: A 222 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.5173 (t80) REVERT: A 356 LEU cc_start: 0.7804 (mp) cc_final: 0.7331 (mt) REVERT: A 371 ASN cc_start: 0.5853 (OUTLIER) cc_final: 0.5224 (p0) REVERT: A 511 TYR cc_start: 0.4298 (OUTLIER) cc_final: 0.3070 (p90) REVERT: A 737 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6637 (mtp180) REVERT: A 758 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5822 (tp) REVERT: A 789 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8130 (mm-40) REVERT: A 805 THR cc_start: 0.8145 (p) cc_final: 0.7871 (t) REVERT: A 845 GLU cc_start: 0.7153 (tt0) cc_final: 0.6760 (pt0) REVERT: A 851 ASP cc_start: 0.5661 (m-30) cc_final: 0.5218 (m-30) REVERT: A 994 MET cc_start: 0.7316 (mmt) cc_final: 0.7095 (mmt) REVERT: A 1022 THR cc_start: 0.7973 (m) cc_final: 0.7648 (p) REVERT: A 1028 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7286 (ttpp) REVERT: A 1038 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: A 1219 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5481 (p90) REVERT: B 30 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.4766 (mtmm) REVERT: B 147 GLU cc_start: 0.7126 (tt0) cc_final: 0.6398 (mp0) REVERT: B 227 TYR cc_start: 0.8472 (t80) cc_final: 0.8232 (t80) REVERT: B 296 SER cc_start: 0.7553 (t) cc_final: 0.7174 (p) REVERT: B 506 LEU cc_start: 0.2485 (OUTLIER) cc_final: 0.2277 (pp) REVERT: B 735 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: B 748 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5876 (tp) REVERT: B 863 GLN cc_start: 0.6156 (tp40) cc_final: 0.5910 (mm-40) REVERT: B 872 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7440 (m-40) REVERT: B 994 MET cc_start: 0.7291 (tpp) cc_final: 0.7010 (tpt) REVERT: B 1028 LYS cc_start: 0.7503 (mttp) cc_final: 0.7229 (mtmt) REVERT: B 1095 ASP cc_start: 0.6549 (m-30) cc_final: 0.6175 (m-30) REVERT: B 1219 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5867 (p90) REVERT: C 213 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7409 (p90) REVERT: C 487 LYS cc_start: 0.1794 (OUTLIER) cc_final: 0.1080 (mmpt) REVERT: C 545 HIS cc_start: 0.2806 (OUTLIER) cc_final: 0.1406 (m-70) REVERT: C 711 PHE cc_start: 0.6072 (m-80) cc_final: 0.5754 (m-10) REVERT: C 735 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (p0) REVERT: C 738 MET cc_start: 0.8245 (mmm) cc_final: 0.8029 (mmt) REVERT: C 952 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5346 (mm-30) REVERT: C 1002 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6191 (mptp) REVERT: C 1014 SER cc_start: 0.7502 (m) cc_final: 0.7277 (p) REVERT: C 1038 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6674 (mp-120) REVERT: C 1091 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: D 234 LYS cc_start: 0.4385 (OUTLIER) cc_final: 0.2988 (ttmm) REVERT: D 301 PRO cc_start: 0.0525 (Cg_endo) cc_final: 0.0166 (Cg_exo) REVERT: D 320 MET cc_start: -0.2051 (mtm) cc_final: -0.3098 (tmm) REVERT: D 420 ILE cc_start: 0.2974 (OUTLIER) cc_final: 0.2354 (tt) REVERT: D 470 ARG cc_start: 0.1551 (mtm180) cc_final: 0.1108 (mtm180) REVERT: D 478 MET cc_start: 0.2295 (tpp) cc_final: 0.1878 (tpp) REVERT: D 480 PHE cc_start: 0.2984 (OUTLIER) cc_final: 0.0944 (m-80) REVERT: E 242 ILE cc_start: 0.0864 (tp) cc_final: 0.0249 (tp) REVERT: E 320 MET cc_start: -0.0885 (mtm) cc_final: -0.1478 (ttm) REVERT: E 362 LYS cc_start: 0.3766 (mtmm) cc_final: 0.3260 (mptt) REVERT: E 363 PRO cc_start: 0.3645 (Cg_endo) cc_final: 0.3374 (Cg_exo) REVERT: E 377 GLN cc_start: 0.5137 (OUTLIER) cc_final: 0.4824 (tp40) REVERT: E 392 LYS cc_start: 0.1679 (OUTLIER) cc_final: 0.1343 (tppt) REVERT: E 406 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3978 (tm-30) REVERT: E 483 TRP cc_start: 0.3462 (t60) cc_final: 0.2623 (t60) REVERT: F 371 MET cc_start: 0.0071 (ttt) cc_final: -0.0896 (mmp) REVERT: F 413 ARG cc_start: 0.3733 (OUTLIER) cc_final: 0.1228 (mtm180) REVERT: F 418 ASN cc_start: 0.2514 (m-40) cc_final: 0.2171 (t0) outliers start: 247 outliers final: 148 residues processed: 476 average time/residue: 1.1422 time to fit residues: 700.2449 Evaluate side-chains 426 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 246 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL 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 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 480 PHE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 283 optimal weight: 30.0000 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 350 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 583 ASN A 630 GLN A1023 ASN A1091 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 38511 Z= 0.321 Angle : 0.712 15.739 52428 Z= 0.360 Chirality : 0.050 0.612 6102 Planarity : 0.005 0.074 6624 Dihedral : 9.360 104.614 7090 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.94 % Rotamer: Outliers : 6.13 % Allowed : 23.56 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 4647 helix: -0.09 (0.18), residues: 864 sheet: -0.70 (0.16), residues: 1023 loop : -2.45 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 454 HIS 0.030 0.002 HIS C 545 PHE 0.027 0.002 PHE B 884 TYR 0.029 0.002 TYR C 622 ARG 0.006 0.001 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 256 time to evaluate : 4.242 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 176 ILE cc_start: 0.1085 (OUTLIER) cc_final: 0.0781 (mt) REVERT: A 197 TRP cc_start: 0.4337 (OUTLIER) cc_final: 0.3932 (m-90) REVERT: A 222 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.5160 (t80) REVERT: A 348 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 356 LEU cc_start: 0.7942 (mp) cc_final: 0.7450 (mt) REVERT: A 371 ASN cc_start: 0.5895 (OUTLIER) cc_final: 0.5328 (t0) REVERT: A 511 TYR cc_start: 0.4235 (OUTLIER) cc_final: 0.2972 (p90) REVERT: A 737 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6690 (mtp180) REVERT: A 758 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5760 (tp) REVERT: A 772 VAL cc_start: 0.6068 (OUTLIER) cc_final: 0.5786 (m) REVERT: A 789 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: A 805 THR cc_start: 0.8195 (p) cc_final: 0.7878 (t) REVERT: A 845 GLU cc_start: 0.7276 (tt0) cc_final: 0.6893 (pt0) REVERT: A 851 ASP cc_start: 0.5860 (m-30) cc_final: 0.5350 (m-30) REVERT: A 994 MET cc_start: 0.7390 (mmt) cc_final: 0.7094 (mmt) REVERT: A 1010 LYS cc_start: 0.7606 (ttmm) cc_final: 0.6915 (mppt) REVERT: A 1022 THR cc_start: 0.7913 (m) cc_final: 0.7621 (p) REVERT: A 1028 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7340 (ttpp) REVERT: A 1038 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: A 1099 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7136 (mp) REVERT: A 1219 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5483 (p90) REVERT: B 30 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5200 (mtmm) REVERT: B 107 LYS cc_start: 0.8399 (tmtm) cc_final: 0.7959 (tmmt) REVERT: B 147 GLU cc_start: 0.7205 (tt0) cc_final: 0.6449 (mp0) REVERT: B 227 TYR cc_start: 0.8529 (t80) cc_final: 0.8284 (t80) REVERT: B 296 SER cc_start: 0.7591 (t) cc_final: 0.7130 (p) REVERT: B 506 LEU cc_start: 0.2323 (OUTLIER) cc_final: 0.2102 (pp) REVERT: B 735 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: B 748 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5877 (tp) REVERT: B 863 GLN cc_start: 0.6192 (tp40) cc_final: 0.5961 (mm-40) REVERT: B 872 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7435 (m-40) REVERT: B 1028 LYS cc_start: 0.7540 (mttp) cc_final: 0.7258 (mtmt) REVERT: B 1185 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.5993 (mtp) REVERT: B 1219 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5791 (p90) REVERT: C 213 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7455 (p90) REVERT: C 487 LYS cc_start: 0.1803 (OUTLIER) cc_final: 0.1052 (mmpt) REVERT: C 545 HIS cc_start: 0.3413 (OUTLIER) cc_final: 0.2626 (m-70) REVERT: C 687 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.8036 (t) REVERT: C 711 PHE cc_start: 0.6066 (m-80) cc_final: 0.5707 (m-10) REVERT: C 735 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7410 (p0) REVERT: C 738 MET cc_start: 0.8185 (mmm) cc_final: 0.7954 (mmt) REVERT: C 952 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5418 (mm-30) REVERT: C 1002 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6171 (mptp) REVERT: C 1014 SER cc_start: 0.7770 (m) cc_final: 0.7492 (p) REVERT: C 1038 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6610 (mp-120) REVERT: C 1091 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: D 234 LYS cc_start: 0.4461 (OUTLIER) cc_final: 0.3010 (ttmm) REVERT: D 301 PRO cc_start: 0.0655 (Cg_endo) cc_final: 0.0313 (Cg_exo) REVERT: D 320 MET cc_start: -0.2140 (mtm) cc_final: -0.3140 (tmm) REVERT: D 349 MET cc_start: 0.3805 (tmm) cc_final: 0.2488 (ttt) REVERT: D 356 THR cc_start: 0.2934 (p) cc_final: 0.2679 (t) REVERT: D 470 ARG cc_start: 0.1617 (mtm180) cc_final: 0.1279 (mtm180) REVERT: E 242 ILE cc_start: 0.0939 (tp) cc_final: 0.0313 (tp) REVERT: E 320 MET cc_start: -0.0750 (mtm) cc_final: -0.1356 (ttm) REVERT: E 362 LYS cc_start: 0.3696 (mtmm) cc_final: 0.3153 (mptt) REVERT: E 377 GLN cc_start: 0.5096 (OUTLIER) cc_final: 0.4748 (tp40) REVERT: E 392 LYS cc_start: 0.1636 (OUTLIER) cc_final: 0.1132 (mmtm) REVERT: E 406 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.4246 (tm-30) REVERT: E 483 TRP cc_start: 0.3625 (t60) cc_final: 0.2629 (t-100) REVERT: F 355 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.2342 (pp) REVERT: F 371 MET cc_start: 0.0109 (ttt) cc_final: -0.0841 (mmp) REVERT: F 413 ARG cc_start: 0.3742 (OUTLIER) cc_final: 0.1822 (mtm180) REVERT: F 418 ASN cc_start: 0.2462 (m-40) cc_final: 0.2133 (t0) outliers start: 253 outliers final: 176 residues processed: 476 average time/residue: 1.1099 time to fit residues: 685.0829 Evaluate side-chains 450 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 238 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL 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 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 944 LYS Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 429 PHE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 9.9990 chunk 426 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 414 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 374 optimal weight: 0.7980 chunk 392 optimal weight: 30.0000 chunk 413 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A1023 ASN A1046 GLN A1091 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN E 179 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38511 Z= 0.335 Angle : 0.721 15.915 52428 Z= 0.364 Chirality : 0.050 0.584 6102 Planarity : 0.005 0.075 6624 Dihedral : 9.407 103.317 7087 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.06 % Favored : 90.88 % Rotamer: Outliers : 5.77 % Allowed : 24.22 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.34 (0.12), residues: 4647 helix: -0.20 (0.18), residues: 867 sheet: -0.72 (0.16), residues: 1026 loop : -2.47 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 461 HIS 0.022 0.002 HIS C 545 PHE 0.028 0.002 PHE B 884 TYR 0.024 0.002 TYR A 462 ARG 0.008 0.001 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 248 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8779 (p) cc_final: 0.8276 (t) REVERT: A 197 TRP cc_start: 0.4298 (OUTLIER) cc_final: 0.3872 (m-90) REVERT: A 222 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.5107 (t80) REVERT: A 348 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 371 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5411 (t0) REVERT: A 511 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.2993 (p90) REVERT: A 737 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6690 (mtp180) REVERT: A 758 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5818 (tp) REVERT: A 772 VAL cc_start: 0.6085 (OUTLIER) cc_final: 0.5801 (m) REVERT: A 789 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8060 (mm-40) REVERT: A 805 THR cc_start: 0.8166 (p) cc_final: 0.7863 (t) REVERT: A 851 ASP cc_start: 0.5857 (m-30) cc_final: 0.5352 (m-30) REVERT: A 994 MET cc_start: 0.7379 (mmt) cc_final: 0.7104 (mmt) REVERT: A 1022 THR cc_start: 0.7915 (m) cc_final: 0.7614 (p) REVERT: A 1028 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7347 (ttpp) REVERT: A 1038 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6609 (mp10) REVERT: A 1099 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7103 (mp) REVERT: A 1219 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5483 (p90) REVERT: B 30 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.5239 (mtmm) REVERT: B 107 LYS cc_start: 0.8405 (tmtm) cc_final: 0.7961 (tmmt) REVERT: B 147 GLU cc_start: 0.7195 (tt0) cc_final: 0.6443 (mp0) REVERT: B 227 TYR cc_start: 0.8521 (t80) cc_final: 0.8281 (t80) REVERT: B 296 SER cc_start: 0.7584 (t) cc_final: 0.7121 (p) REVERT: B 735 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 748 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5885 (tp) REVERT: B 863 GLN cc_start: 0.6159 (tp40) cc_final: 0.5329 (tp40) REVERT: B 872 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7440 (m-40) REVERT: B 1028 LYS cc_start: 0.7549 (mttp) cc_final: 0.7266 (mtmt) REVERT: B 1185 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6001 (mtp) REVERT: B 1219 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5936 (p90) REVERT: C 213 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7438 (p90) REVERT: C 487 LYS cc_start: 0.1805 (OUTLIER) cc_final: 0.1104 (mmpt) REVERT: C 687 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8076 (t) REVERT: C 711 PHE cc_start: 0.6090 (m-80) cc_final: 0.5755 (m-10) REVERT: C 735 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7389 (p0) REVERT: C 738 MET cc_start: 0.8200 (mmm) cc_final: 0.7972 (mmt) REVERT: C 952 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5545 (mm-30) REVERT: C 1002 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6172 (mptp) REVERT: C 1014 SER cc_start: 0.7780 (m) cc_final: 0.7498 (p) REVERT: C 1038 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6721 (mp-120) REVERT: C 1091 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: D 210 MET cc_start: 0.0284 (ttt) cc_final: -0.0220 (ttp) REVERT: D 234 LYS cc_start: 0.4387 (OUTLIER) cc_final: 0.2959 (ttmm) REVERT: D 301 PRO cc_start: 0.0641 (Cg_endo) cc_final: 0.0303 (Cg_exo) REVERT: D 320 MET cc_start: -0.2574 (mtm) cc_final: -0.3414 (tmm) REVERT: D 349 MET cc_start: 0.3784 (tmm) cc_final: 0.2551 (ttt) REVERT: D 424 MET cc_start: 0.1979 (tpt) cc_final: 0.1521 (tpt) REVERT: D 470 ARG cc_start: 0.1574 (mtm180) cc_final: 0.1293 (mtm180) REVERT: E 242 ILE cc_start: 0.1004 (tp) cc_final: 0.0336 (tp) REVERT: E 362 LYS cc_start: 0.3698 (mtmm) cc_final: 0.3201 (mptt) REVERT: E 372 MET cc_start: 0.4689 (mmm) cc_final: 0.3500 (mpp) REVERT: E 377 GLN cc_start: 0.5115 (OUTLIER) cc_final: 0.4914 (tp40) REVERT: E 392 LYS cc_start: 0.1694 (OUTLIER) cc_final: 0.1169 (mmtm) REVERT: E 406 GLU cc_start: 0.4537 (OUTLIER) cc_final: 0.4252 (tm-30) REVERT: E 424 MET cc_start: 0.1193 (mmm) cc_final: 0.0205 (mtt) REVERT: E 483 TRP cc_start: 0.3648 (t60) cc_final: 0.2623 (t-100) REVERT: F 371 MET cc_start: 0.0083 (OUTLIER) cc_final: -0.0843 (mmp) REVERT: F 413 ARG cc_start: 0.3950 (OUTLIER) cc_final: 0.1911 (mtm180) REVERT: F 418 ASN cc_start: 0.2189 (m-40) cc_final: 0.1890 (t0) outliers start: 238 outliers final: 175 residues processed: 457 average time/residue: 1.1508 time to fit residues: 680.2992 Evaluate side-chains 430 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 222 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL 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 852 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 413 ARG Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 0.5980 chunk 438 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 460 optimal weight: 20.0000 chunk 423 optimal weight: 30.0000 chunk 366 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A1023 ASN A1046 GLN A1091 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN E 164 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38511 Z= 0.209 Angle : 0.657 14.787 52428 Z= 0.332 Chirality : 0.048 0.547 6102 Planarity : 0.004 0.076 6624 Dihedral : 9.099 103.614 7087 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.92 % Favored : 92.04 % Rotamer: Outliers : 5.12 % Allowed : 24.97 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.08 (0.12), residues: 4647 helix: 0.26 (0.19), residues: 851 sheet: -0.59 (0.16), residues: 1045 loop : -2.37 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 461 HIS 0.007 0.001 HIS E 334 PHE 0.025 0.001 PHE B 884 TYR 0.030 0.001 TYR C 622 ARG 0.008 0.000 ARG D 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 248 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8748 (p) cc_final: 0.8256 (t) REVERT: A 191 TYR cc_start: 0.6508 (p90) cc_final: 0.5211 (p90) REVERT: A 197 TRP cc_start: 0.4338 (OUTLIER) cc_final: 0.3927 (m-90) REVERT: A 222 PHE cc_start: 0.5538 (OUTLIER) cc_final: 0.5169 (t80) REVERT: A 356 LEU cc_start: 0.7813 (mp) cc_final: 0.7284 (mt) REVERT: A 371 ASN cc_start: 0.5799 (OUTLIER) cc_final: 0.5246 (t0) REVERT: A 511 TYR cc_start: 0.4237 (OUTLIER) cc_final: 0.3008 (p90) REVERT: A 737 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6543 (mtp180) REVERT: A 758 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5742 (tp) REVERT: A 789 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: A 805 THR cc_start: 0.8181 (p) cc_final: 0.7901 (t) REVERT: A 851 ASP cc_start: 0.5703 (m-30) cc_final: 0.5250 (m-30) REVERT: A 994 MET cc_start: 0.7327 (mmt) cc_final: 0.7069 (mmt) REVERT: A 1022 THR cc_start: 0.7849 (m) cc_final: 0.7533 (p) REVERT: A 1028 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7322 (ttpp) REVERT: A 1038 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: A 1099 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6997 (mp) REVERT: A 1219 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.5439 (p90) REVERT: B 30 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5272 (mtmm) REVERT: B 147 GLU cc_start: 0.7149 (tt0) cc_final: 0.6407 (mp0) REVERT: B 227 TYR cc_start: 0.8505 (t80) cc_final: 0.8278 (t80) REVERT: B 296 SER cc_start: 0.7566 (t) cc_final: 0.7177 (p) REVERT: B 735 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: B 748 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5857 (tp) REVERT: B 863 GLN cc_start: 0.6107 (tp40) cc_final: 0.5328 (tp40) REVERT: B 872 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: B 994 MET cc_start: 0.7346 (tpp) cc_final: 0.7068 (tpt) REVERT: B 1028 LYS cc_start: 0.7498 (mttp) cc_final: 0.7228 (mtmt) REVERT: B 1219 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5911 (p90) REVERT: C 213 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7400 (p90) REVERT: C 487 LYS cc_start: 0.1760 (OUTLIER) cc_final: 0.1075 (mmpt) REVERT: C 545 HIS cc_start: 0.3346 (OUTLIER) cc_final: 0.2255 (m-70) REVERT: C 711 PHE cc_start: 0.6094 (m-80) cc_final: 0.5778 (m-10) REVERT: C 735 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7509 (p0) REVERT: C 738 MET cc_start: 0.8215 (mmm) cc_final: 0.7983 (mmt) REVERT: C 952 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5263 (mm-30) REVERT: C 1002 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6198 (mptp) REVERT: C 1014 SER cc_start: 0.7573 (m) cc_final: 0.7326 (p) REVERT: C 1038 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6581 (mp-120) REVERT: C 1091 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: D 210 MET cc_start: 0.0531 (ttt) cc_final: 0.0046 (ttp) REVERT: D 229 ASP cc_start: 0.1086 (OUTLIER) cc_final: 0.0290 (t70) REVERT: D 234 LYS cc_start: 0.4461 (OUTLIER) cc_final: 0.3007 (ttmm) REVERT: D 301 PRO cc_start: 0.0574 (Cg_endo) cc_final: 0.0241 (Cg_exo) REVERT: D 320 MET cc_start: -0.2894 (mtm) cc_final: -0.3616 (tmm) REVERT: D 349 MET cc_start: 0.3825 (tmm) cc_final: 0.2716 (tpt) REVERT: D 424 MET cc_start: 0.2168 (tpt) cc_final: 0.1379 (tpt) REVERT: D 478 MET cc_start: 0.5016 (mpt) cc_final: 0.2253 (tpt) REVERT: E 164 GLN cc_start: 0.3678 (OUTLIER) cc_final: 0.3350 (pm20) REVERT: E 242 ILE cc_start: 0.1333 (tp) cc_final: 0.0640 (tp) REVERT: E 362 LYS cc_start: 0.3536 (mtmm) cc_final: 0.3113 (mptt) REVERT: E 377 GLN cc_start: 0.5085 (OUTLIER) cc_final: 0.4731 (tp40) REVERT: E 388 GLU cc_start: 0.2225 (OUTLIER) cc_final: 0.0722 (tt0) REVERT: E 392 LYS cc_start: 0.1658 (OUTLIER) cc_final: 0.1140 (mmtm) REVERT: E 483 TRP cc_start: 0.3606 (t60) cc_final: 0.2649 (t-100) REVERT: F 371 MET cc_start: -0.0146 (OUTLIER) cc_final: -0.0911 (mmp) REVERT: F 404 LEU cc_start: 0.1263 (tt) cc_final: 0.1019 (tt) REVERT: F 418 ASN cc_start: 0.2075 (m-40) cc_final: 0.1848 (t0) outliers start: 211 outliers final: 166 residues processed: 431 average time/residue: 1.0894 time to fit residues: 615.0657 Evaluate side-chains 424 residues out of total 4125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 227 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 VAL 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 852 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1208 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 735 ASP Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1120 ARG Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1208 CYS Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain B residue 1212 PHE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1219 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 630 GLN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 735 ASP Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1149 LYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1210 VAL Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 164 GLN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 377 GLN Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 337 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 630 GLN A1023 ASN A1091 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 HIS ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.228580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157164 restraints weight = 55336.845| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.94 r_work: 0.3581 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38511 Z= 0.221 Angle : 0.665 20.190 52428 Z= 0.334 Chirality : 0.048 0.518 6102 Planarity : 0.004 0.075 6624 Dihedral : 9.097 107.695 7087 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 5.24 % Allowed : 25.04 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.03 (0.12), residues: 4647 helix: 0.29 (0.19), residues: 861 sheet: -0.54 (0.16), residues: 1034 loop : -2.34 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 269 HIS 0.007 0.001 HIS E 334 PHE 0.022 0.001 PHE B 884 TYR 0.021 0.001 TYR A 462 ARG 0.011 0.000 ARG E 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15299.94 seconds wall clock time: 274 minutes 34.34 seconds (16474.34 seconds total)