Starting phenix.real_space_refine on Fri Feb 23 18:28:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9c_35266/02_2024/8i9c_35266.pdb" } resolution = 3.85 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= 0.004 sd= 0.057 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 195 5.16 5 C 25198 2.51 5 N 6420 2.21 5 O 7722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 549": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 479": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39535 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7821 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 8 Chain: "B" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7827 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "C" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7821 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.96, per 1000 atoms: 0.48 Number of scatterers: 39535 At special positions: 0 Unit cell: (183.703, 204.356, 247.836, 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 195 16.00 O 7722 8.00 N 6420 7.00 C 25198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.35 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.47 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " 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 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN F 53 " " NAG e 1 " - " ASN F 90 " " NAG f 1 " - " ASN F 103 " " NAG g 1 " - " ASN F 432 " " NAG h 1 " - " ASN F 546 " " NAG i 1 " - " ASN D 53 " " NAG j 1 " - " ASN D 90 " " NAG k 1 " - " ASN D 103 " " NAG l 1 " - " ASN D 432 " " NAG m 1 " - " ASN D 546 " " NAG n 1 " - " ASN E 53 " " NAG o 1 " - " ASN E 90 " " NAG p 1 " - " ASN E 103 " " NAG q 1 " - " ASN E 432 " " NAG r 1 " - " ASN E 546 " Time building additional restraints: 14.50 Conformation dependent library (CDL) restraints added in 6.3 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9008 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 47 sheets defined 38.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.977A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.700A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.739A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.552A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.976A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.773A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.589A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.572A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.339A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.976A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.020A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.269A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'F' and resid 22 through 53 removed outlier: 3.775A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.797A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.778A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.834A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.857A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.857A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 421 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.632A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 4.163A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.897A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 570 through 575 Processing helix chain 'F' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Proline residue: F 590 - end of helix Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.796A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.833A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.857A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.856A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.071A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.896A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.796A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.892A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.908A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 249 removed outlier: 3.832A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.858A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.858A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 331' Processing helix chain 'E' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.693A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.876A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.914A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 421 " --> pdb=" O HIS E 417 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.898A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Proline residue: E 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.062A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.947A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.656A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.911A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.568A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.808A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.929A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.655A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.631A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.902A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 7.146A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.656A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.920A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.242A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1561 hydrogen bonds defined for protein. 4398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.77 Time building geometry restraints manager: 15.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.48: 23459 1.48 - 1.75: 16748 1.75 - 2.02: 285 2.02 - 2.30: 0 2.30 - 2.57: 1 Bond restraints: 40493 Sorted by residual: bond pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 1.332 2.573 -1.241 1.40e-02 5.10e+03 7.85e+03 bond pdb=" CA SER B 698 " pdb=" C SER B 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.27e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.83e+01 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 40488 not shown) Histogram of bond angle deviations from ideal: 67.97 - 86.31: 1 86.31 - 104.66: 742 104.66 - 123.00: 51566 123.00 - 141.35: 2744 141.35 - 159.69: 1 Bond angle restraints: 55054 Sorted by residual: angle pdb=" O THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 122.59 67.97 54.62 1.33e+00 5.65e-01 1.69e+03 angle pdb=" C THR A 676 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta sigma weight residual 121.54 159.69 -38.15 1.91e+00 2.74e-01 3.99e+02 angle pdb=" CA THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 116.84 92.81 24.03 1.71e+00 3.42e-01 1.98e+02 angle pdb=" N PHE C 157 " pdb=" CA PHE C 157 " pdb=" C PHE C 157 " ideal model delta sigma weight residual 111.74 123.23 -11.49 1.35e+00 5.49e-01 7.24e+01 angle pdb=" N PHE A 157 " pdb=" CA PHE A 157 " pdb=" C PHE A 157 " ideal model delta sigma weight residual 111.74 123.21 -11.47 1.35e+00 5.49e-01 7.22e+01 ... (remaining 55049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21853 17.93 - 35.85: 2467 35.85 - 53.78: 783 53.78 - 71.70: 229 71.70 - 89.63: 56 Dihedral angle restraints: 25388 sinusoidal: 11404 harmonic: 13984 Sorted by residual: dihedral pdb=" CA THR A 676 " pdb=" C THR A 676 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta harmonic sigma weight residual -180.00 -111.11 -68.89 0 5.00e+00 4.00e-02 1.90e+02 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.05 71.95 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 25385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 6341 0.366 - 0.733: 5 0.733 - 1.099: 2 1.099 - 1.466: 0 1.466 - 1.832: 2 Chirality restraints: 6350 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.15e+02 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.57 -1.83 2.00e-01 2.50e+01 8.39e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.80 -1.60 2.00e-01 2.50e+01 6.37e+01 ... (remaining 6347 not shown) Planarity restraints: 7045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 676 " -0.183 2.00e-02 2.50e+03 2.67e-01 7.12e+02 pdb=" C THR A 676 " 0.424 2.00e-02 2.50e+03 pdb=" O THR A 676 " -0.266 2.00e-02 2.50e+03 pdb=" N GLN A 690 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.114 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN C 331 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.211 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " 0.097 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" CG ASN B 801 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " -0.222 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.148 2.00e-02 2.50e+03 ... (remaining 7042 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 219 2.48 - 3.08: 26947 3.08 - 3.69: 54882 3.69 - 4.29: 83558 4.29 - 4.90: 139891 Nonbonded interactions: 305497 Sorted by model distance: nonbonded pdb=" O GLY C 799 " pdb=" O PHE C 800 " model vdw 1.871 3.040 nonbonded pdb=" O ALA A 694 " pdb=" CB TYR A 695 " model vdw 2.095 3.440 nonbonded pdb=" N GLU C 748 " pdb=" OE1 GLU C 748 " model vdw 2.142 2.520 nonbonded pdb=" O GLY B 700 " pdb=" O ALA B 701 " model vdw 2.166 3.040 nonbonded pdb=" O SER B 813 " pdb=" OG SER B 813 " model vdw 2.183 2.440 ... (remaining 305492 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' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.380 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 93.790 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.760 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.241 40493 Z= 0.623 Angle : 0.939 54.624 55054 Z= 0.548 Chirality : 0.067 1.832 6350 Planarity : 0.007 0.267 6979 Dihedral : 17.289 89.631 16254 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 1.53 % Allowed : 8.14 % Favored : 90.34 % Rotamer: Outliers : 9.03 % Allowed : 16.77 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.10), residues: 4720 helix: -1.39 (0.12), residues: 1643 sheet: -2.05 (0.17), residues: 747 loop : -3.35 (0.10), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 104 HIS 0.009 0.001 HIS B1048 PHE 0.025 0.002 PHE B 898 TYR 0.027 0.002 TYR C1067 ARG 0.007 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 530 time to evaluate : 4.330 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: 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 216 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1920 (mp) REVERT: A 324 GLU cc_start: 0.3722 (OUTLIER) cc_final: 0.3166 (tm-30) REVERT: A 395 VAL cc_start: 0.4229 (OUTLIER) cc_final: 0.3605 (p) REVERT: A 480 CYS cc_start: 0.2270 (OUTLIER) cc_final: -0.0651 (m) REVERT: A 929 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7489 (m) REVERT: B 692 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7101 (mm) REVERT: B 722 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6882 (m) REVERT: B 973 ILE cc_start: 0.4641 (OUTLIER) cc_final: 0.4409 (pt) REVERT: C 289 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7233 (t) REVERT: F 270 MET cc_start: 0.0161 (tpp) cc_final: -0.0407 (mmm) REVERT: E 256 ILE cc_start: -0.2311 (OUTLIER) cc_final: -0.2682 (mt) REVERT: E 401 HIS cc_start: 0.0477 (OUTLIER) cc_final: 0.0081 (p90) outliers start: 380 outliers final: 58 residues processed: 855 average time/residue: 0.4809 time to fit residues: 681.1888 Evaluate side-chains 322 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 253 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 40.0000 chunk 359 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 371 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 225 optimal weight: 0.2980 chunk 276 optimal weight: 2.9990 chunk 430 optimal weight: 40.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 196 ASN A 314 GLN A 317 ASN A 460 ASN A 540 ASN A 542 ASN A 544 ASN A 613 GLN A 644 GLN A 675 GLN A 703 ASN A 751 ASN A 784 GLN A 901 GLN A 914 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1071 GLN A1101 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 188 ASN B 354 ASN B 460 ASN B 542 ASN B 644 GLN B 658 ASN B 762 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 919 ASN B 954 HIS B 992 GLN B1058 HIS B1101 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN C 239 GLN C 354 ASN C 460 ASN C 542 ASN C 644 GLN C 658 ASN C 703 ASN C 901 GLN C 914 ASN C 919 ASN C 920 GLN C 926 GLN C 992 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN F 58 ASN F 96 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 239 HIS F 277 ASN F 378 HIS F 472 GLN F 493 HIS F 505 HIS F 522 GLN F 599 ASN D 58 ASN D 96 GLN D 239 HIS D 378 HIS D 493 HIS D 505 HIS D 522 GLN D 578 ASN D 599 ASN E 42 GLN E 51 ASN E 58 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS E 378 HIS E 472 GLN E 493 HIS E 505 HIS E 522 GLN E 599 ASN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 40493 Z= 0.265 Angle : 0.749 11.751 55054 Z= 0.373 Chirality : 0.048 0.757 6350 Planarity : 0.005 0.089 6979 Dihedral : 9.268 73.628 7436 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 4.85 % Allowed : 21.02 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 4722 helix: 0.03 (0.13), residues: 1671 sheet: -1.38 (0.17), residues: 751 loop : -2.76 (0.11), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.011 0.001 HIS A 954 PHE 0.028 0.002 PHE F 504 TYR 0.025 0.002 TYR B1067 ARG 0.005 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 271 time to evaluate : 4.521 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: B 48 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7737 (pp) REVERT: B 117 LEU cc_start: 0.6019 (tp) cc_final: 0.5797 (tt) REVERT: B 692 ILE cc_start: 0.7863 (mm) cc_final: 0.7635 (mm) REVERT: C 97 LYS cc_start: 0.2926 (OUTLIER) cc_final: 0.2389 (tppt) REVERT: F 270 MET cc_start: 0.0146 (tpp) cc_final: -0.0242 (tpp) REVERT: D 82 MET cc_start: 0.3372 (tmm) cc_final: 0.3055 (ppp) REVERT: E 401 HIS cc_start: 0.0434 (OUTLIER) cc_final: -0.0035 (p-80) REVERT: E 557 MET cc_start: 0.2451 (ppp) cc_final: 0.2231 (ppp) outliers start: 204 outliers final: 96 residues processed: 455 average time/residue: 0.4489 time to fit residues: 353.2452 Evaluate side-chains 304 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 205 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 40.0000 chunk 133 optimal weight: 30.0000 chunk 358 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 431 optimal weight: 50.0000 chunk 465 optimal weight: 50.0000 chunk 384 optimal weight: 40.0000 chunk 427 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 345 optimal weight: 50.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 196 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 992 GLN A1071 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1108 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 613 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1088 HIS B1108 ASN B1135 ASN C 317 ASN C 675 GLN C 690 GLN C 751 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN F 63 ASN F 117 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 437 ASN D 63 ASN D 277 ASN D 437 ASN D 578 ASN E 42 GLN E 63 ASN E 89 GLN E 117 ASN E 437 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.159 40493 Z= 0.565 Angle : 1.009 18.205 55054 Z= 0.505 Chirality : 0.055 0.701 6350 Planarity : 0.007 0.069 6979 Dihedral : 8.738 59.543 7361 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.22 % Favored : 91.59 % Rotamer: Outliers : 7.17 % Allowed : 20.24 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.11), residues: 4722 helix: -0.04 (0.12), residues: 1662 sheet: -1.33 (0.18), residues: 708 loop : -2.65 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 886 HIS 0.010 0.002 HIS C1064 PHE 0.048 0.003 PHE B1062 TYR 0.059 0.003 TYR A1067 ARG 0.011 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 179 time to evaluate : 4.420 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 422 ASN cc_start: 0.1406 (OUTLIER) cc_final: -0.0298 (t0) REVERT: A 480 CYS cc_start: 0.2910 (OUTLIER) cc_final: 0.0122 (m) REVERT: A 921 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6616 (pttp) REVERT: B 48 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8034 (pp) REVERT: B 227 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.6215 (t) REVERT: F 338 ASN cc_start: 0.5508 (p0) cc_final: 0.5303 (p0) REVERT: E 233 ILE cc_start: -0.2467 (OUTLIER) cc_final: -0.2846 (mt) REVERT: E 557 MET cc_start: 0.2636 (ppp) cc_final: 0.2409 (ppp) outliers start: 302 outliers final: 164 residues processed: 469 average time/residue: 0.4406 time to fit residues: 361.0801 Evaluate side-chains 327 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 157 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 295 PRO Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 50.0000 chunk 324 optimal weight: 40.0000 chunk 223 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 205 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 432 optimal weight: 30.0000 chunk 458 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 410 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 542 ASN A 804 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 901 GLN C 935 GLN C1002 GLN C1010 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN E 401 HIS E 493 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 40493 Z= 0.266 Angle : 0.711 14.132 55054 Z= 0.346 Chirality : 0.048 0.821 6350 Planarity : 0.004 0.054 6979 Dihedral : 7.574 59.021 7343 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 4.32 % Allowed : 22.97 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 4722 helix: 0.55 (0.13), residues: 1671 sheet: -1.08 (0.18), residues: 731 loop : -2.42 (0.11), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1102 HIS 0.010 0.001 HIS B 954 PHE 0.021 0.002 PHE C 371 TYR 0.027 0.001 TYR A1067 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 173 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4669 (OUTLIER) cc_final: 0.4240 (p-80) REVERT: A 153 MET cc_start: 0.2512 (tpp) cc_final: 0.1164 (tmm) REVERT: A 731 MET cc_start: 0.7869 (ppp) cc_final: 0.7452 (ppp) REVERT: A 935 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: B 48 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8035 (pp) REVERT: C 97 LYS cc_start: 0.2233 (OUTLIER) cc_final: 0.1980 (tppt) REVERT: C 310 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5059 (tptp) REVERT: C 523 THR cc_start: 0.5461 (OUTLIER) cc_final: 0.5065 (t) REVERT: C 865 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7655 (mp) REVERT: D 82 MET cc_start: 0.3054 (tmm) cc_final: 0.2245 (ppp) REVERT: D 249 MET cc_start: 0.2315 (mmm) cc_final: 0.1102 (ptt) REVERT: D 318 VAL cc_start: -0.2021 (OUTLIER) cc_final: -0.2308 (m) REVERT: E 152 MET cc_start: -0.2651 (mmt) cc_final: -0.5073 (ptt) REVERT: E 233 ILE cc_start: -0.2647 (OUTLIER) cc_final: -0.2883 (mt) REVERT: E 332 MET cc_start: 0.0460 (ppp) cc_final: 0.0249 (ppp) REVERT: E 366 MET cc_start: 0.2861 (tpp) cc_final: 0.2624 (tpp) outliers start: 182 outliers final: 117 residues processed: 342 average time/residue: 0.4634 time to fit residues: 278.4166 Evaluate side-chains 275 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 149 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 189 optimal weight: 0.8980 chunk 390 optimal weight: 50.0000 chunk 316 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 411 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 8.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 334 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 955 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 117 ASN E 277 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 40493 Z= 0.431 Angle : 0.824 16.540 55054 Z= 0.405 Chirality : 0.050 1.046 6350 Planarity : 0.005 0.063 6979 Dihedral : 7.624 59.432 7343 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.37 % Favored : 91.53 % Rotamer: Outliers : 6.18 % Allowed : 22.19 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.11), residues: 4722 helix: 0.50 (0.13), residues: 1643 sheet: -1.18 (0.19), residues: 683 loop : -2.34 (0.11), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.008 0.001 HIS B 66 PHE 0.035 0.003 PHE C 329 TYR 0.042 0.002 TYR A1067 ARG 0.008 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 156 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3186 (tpp) cc_final: 0.1694 (tmm) REVERT: A 480 CYS cc_start: 0.2382 (OUTLIER) cc_final: 0.0138 (m) REVERT: A 731 MET cc_start: 0.8019 (ppp) cc_final: 0.7608 (ppp) REVERT: A 1029 MET cc_start: 0.7757 (tpp) cc_final: 0.7260 (ttm) REVERT: B 48 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8113 (pp) REVERT: B 697 MET cc_start: 0.6835 (mtp) cc_final: 0.6608 (mtm) REVERT: C 270 LEU cc_start: 0.5989 (mp) cc_final: 0.5682 (mp) REVERT: C 865 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7811 (mp) REVERT: F 408 MET cc_start: 0.4770 (ptp) cc_final: 0.4438 (ptp) REVERT: D 249 MET cc_start: 0.1947 (mmm) cc_final: 0.1048 (ptt) REVERT: D 318 VAL cc_start: -0.1849 (OUTLIER) cc_final: -0.2108 (m) REVERT: E 233 ILE cc_start: -0.2273 (OUTLIER) cc_final: -0.2600 (mt) REVERT: E 256 ILE cc_start: -0.1830 (OUTLIER) cc_final: -0.2165 (mt) REVERT: E 366 MET cc_start: 0.3386 (tpp) cc_final: 0.3105 (tpp) REVERT: E 531 GLN cc_start: 0.4926 (OUTLIER) cc_final: 0.3368 (mp10) outliers start: 260 outliers final: 168 residues processed: 401 average time/residue: 0.4456 time to fit residues: 315.5488 Evaluate side-chains 320 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 145 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 481 LYS Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 2.9990 chunk 412 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 458 optimal weight: 30.0000 chunk 380 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 151 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1005 GLN C1106 GLN F 63 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 40493 Z= 0.246 Angle : 0.691 15.862 55054 Z= 0.333 Chirality : 0.047 0.799 6350 Planarity : 0.004 0.054 6979 Dihedral : 7.178 59.484 7338 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.56 % Rotamer: Outliers : 4.77 % Allowed : 24.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4722 helix: 0.91 (0.13), residues: 1632 sheet: -1.12 (0.18), residues: 702 loop : -2.16 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.009 0.001 HIS B 954 PHE 0.026 0.002 PHE C 133 TYR 0.028 0.001 TYR A1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 152 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.7916 (ppp) cc_final: 0.7555 (ppp) REVERT: C 865 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (mp) REVERT: F 408 MET cc_start: 0.4396 (ptp) cc_final: 0.3912 (ptt) REVERT: F 579 MET cc_start: 0.1511 (tpp) cc_final: 0.1290 (tpt) REVERT: D 82 MET cc_start: 0.2725 (tmm) cc_final: 0.1650 (ppp) REVERT: D 249 MET cc_start: 0.1627 (mmm) cc_final: 0.1047 (ptt) REVERT: D 318 VAL cc_start: -0.1859 (OUTLIER) cc_final: -0.2127 (m) REVERT: D 332 MET cc_start: -0.0275 (ttt) cc_final: -0.0567 (ttt) REVERT: E 136 ASP cc_start: 0.2026 (OUTLIER) cc_final: 0.0538 (m-30) REVERT: E 152 MET cc_start: -0.3143 (mmt) cc_final: -0.4618 (ptt) REVERT: E 233 ILE cc_start: -0.2292 (OUTLIER) cc_final: -0.2661 (mt) REVERT: E 256 ILE cc_start: -0.1753 (OUTLIER) cc_final: -0.2112 (mt) REVERT: E 366 MET cc_start: 0.3424 (tpp) cc_final: 0.3027 (tpt) REVERT: E 531 GLN cc_start: 0.4908 (OUTLIER) cc_final: 0.3361 (mp10) outliers start: 201 outliers final: 149 residues processed: 343 average time/residue: 0.4276 time to fit residues: 259.6635 Evaluate side-chains 303 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 148 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 386 optimal weight: 50.0000 chunk 256 optimal weight: 3.9990 chunk 456 optimal weight: 30.0000 chunk 285 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN F 51 ASN F 139 GLN D 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 40493 Z= 0.221 Angle : 0.674 15.771 55054 Z= 0.323 Chirality : 0.046 0.722 6350 Planarity : 0.004 0.050 6979 Dihedral : 6.874 59.650 7337 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 4.54 % Allowed : 24.13 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4722 helix: 1.13 (0.13), residues: 1635 sheet: -1.04 (0.18), residues: 691 loop : -2.05 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 104 HIS 0.014 0.001 HIS B 954 PHE 0.027 0.001 PHE C 133 TYR 0.023 0.001 TYR A1067 ARG 0.005 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 160 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4335 (OUTLIER) cc_final: 0.3906 (p-80) REVERT: A 153 MET cc_start: 0.2683 (tpt) cc_final: 0.2113 (tpt) REVERT: A 731 MET cc_start: 0.7885 (ppp) cc_final: 0.7534 (ppp) REVERT: A 921 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6746 (pttp) REVERT: C 865 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7633 (mp) REVERT: F 270 MET cc_start: -0.1342 (tpp) cc_final: -0.1615 (tpp) REVERT: F 383 MET cc_start: 0.7707 (ppp) cc_final: 0.6894 (ppp) REVERT: D 82 MET cc_start: 0.2859 (tmm) cc_final: 0.1696 (ppp) REVERT: D 249 MET cc_start: 0.1499 (mmm) cc_final: 0.1207 (ptt) REVERT: D 318 VAL cc_start: -0.1700 (OUTLIER) cc_final: -0.1936 (m) REVERT: E 136 ASP cc_start: 0.2484 (OUTLIER) cc_final: 0.0398 (m-30) REVERT: E 233 ILE cc_start: -0.2309 (OUTLIER) cc_final: -0.2673 (mt) REVERT: E 256 ILE cc_start: -0.1550 (OUTLIER) cc_final: -0.1907 (mt) REVERT: E 332 MET cc_start: 0.1422 (ppp) cc_final: 0.1128 (ppp) REVERT: E 366 MET cc_start: 0.3407 (tpp) cc_final: 0.3018 (tpt) REVERT: E 531 GLN cc_start: 0.4784 (OUTLIER) cc_final: 0.3500 (mp10) outliers start: 191 outliers final: 140 residues processed: 336 average time/residue: 0.4302 time to fit residues: 257.4827 Evaluate side-chains 300 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 152 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 272 optimal weight: 0.0770 chunk 137 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 311 optimal weight: 50.0000 chunk 225 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 359 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 196 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 40493 Z= 0.197 Angle : 0.660 15.424 55054 Z= 0.315 Chirality : 0.046 0.616 6350 Planarity : 0.004 0.049 6979 Dihedral : 6.642 59.740 7332 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 4.11 % Allowed : 24.63 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4722 helix: 1.21 (0.13), residues: 1653 sheet: -0.92 (0.18), residues: 695 loop : -1.95 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A 104 HIS 0.004 0.001 HIS B 66 PHE 0.030 0.001 PHE C 133 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 158 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.4226 (OUTLIER) cc_final: 0.3894 (p-80) REVERT: A 153 MET cc_start: 0.2060 (tpt) cc_final: 0.1682 (tpt) REVERT: A 731 MET cc_start: 0.7947 (ppp) cc_final: 0.7586 (ppp) REVERT: B 773 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: C 865 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7618 (mp) REVERT: F 383 MET cc_start: 0.7641 (ppp) cc_final: 0.6851 (ppp) REVERT: F 408 MET cc_start: 0.3948 (ptp) cc_final: 0.3331 (ptt) REVERT: F 579 MET cc_start: 0.0287 (tpt) cc_final: -0.0935 (tpp) REVERT: D 82 MET cc_start: 0.3092 (tmm) cc_final: 0.1954 (ppp) REVERT: D 318 VAL cc_start: -0.1676 (OUTLIER) cc_final: -0.1923 (m) REVERT: D 332 MET cc_start: -0.0538 (ttt) cc_final: -0.0822 (ttt) REVERT: E 233 ILE cc_start: -0.2306 (OUTLIER) cc_final: -0.2665 (mt) REVERT: E 256 ILE cc_start: -0.1568 (OUTLIER) cc_final: -0.1923 (mt) REVERT: E 366 MET cc_start: 0.3465 (tpp) cc_final: 0.3048 (tpt) REVERT: E 531 GLN cc_start: 0.5028 (OUTLIER) cc_final: 0.3788 (mp10) outliers start: 173 outliers final: 136 residues processed: 319 average time/residue: 0.4489 time to fit residues: 252.9162 Evaluate side-chains 296 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 153 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 40.0000 chunk 437 optimal weight: 50.0000 chunk 399 optimal weight: 50.0000 chunk 425 optimal weight: 50.0000 chunk 256 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 334 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 402 optimal weight: 50.0000 chunk 424 optimal weight: 10.0000 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 40493 Z= 0.381 Angle : 0.772 16.536 55054 Z= 0.374 Chirality : 0.049 0.992 6350 Planarity : 0.005 0.059 6979 Dihedral : 7.020 59.752 7330 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 4.37 % Allowed : 24.42 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4722 helix: 0.90 (0.13), residues: 1654 sheet: -1.08 (0.19), residues: 680 loop : -1.98 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.007 0.001 HIS B 66 PHE 0.032 0.002 PHE C 133 TYR 0.041 0.002 TYR A1067 ARG 0.008 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 147 time to evaluate : 4.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2599 (tpt) cc_final: 0.2157 (tpt) REVERT: A 731 MET cc_start: 0.7977 (ppp) cc_final: 0.7615 (ppp) REVERT: A 1029 MET cc_start: 0.7789 (tpp) cc_final: 0.7063 (ttm) REVERT: B 773 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: C 233 ILE cc_start: 0.4857 (OUTLIER) cc_final: 0.4496 (tt) REVERT: C 865 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7677 (mp) REVERT: F 579 MET cc_start: 0.0607 (tpt) cc_final: -0.0681 (tpp) REVERT: D 82 MET cc_start: 0.3352 (tmm) cc_final: 0.2197 (ppp) REVERT: D 318 VAL cc_start: -0.1540 (OUTLIER) cc_final: -0.1777 (m) REVERT: E 233 ILE cc_start: -0.2148 (OUTLIER) cc_final: -0.2517 (mt) REVERT: E 256 ILE cc_start: -0.1344 (OUTLIER) cc_final: -0.1725 (mt) REVERT: E 366 MET cc_start: 0.3533 (tpp) cc_final: 0.3109 (tpt) REVERT: E 531 GLN cc_start: 0.5072 (OUTLIER) cc_final: 0.3781 (mp10) outliers start: 184 outliers final: 157 residues processed: 317 average time/residue: 0.4487 time to fit residues: 254.3660 Evaluate side-chains 309 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 145 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.8980 chunk 450 optimal weight: 50.0000 chunk 274 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 312 optimal weight: 30.0000 chunk 472 optimal weight: 50.0000 chunk 434 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 39 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40493 Z= 0.219 Angle : 0.681 16.219 55054 Z= 0.324 Chirality : 0.046 0.780 6350 Planarity : 0.004 0.052 6979 Dihedral : 6.759 59.854 7330 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.56 % Rotamer: Outliers : 3.66 % Allowed : 25.11 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4722 helix: 1.12 (0.13), residues: 1654 sheet: -0.97 (0.19), residues: 683 loop : -1.86 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 478 HIS 0.005 0.001 HIS B 66 PHE 0.030 0.001 PHE C 133 TYR 0.025 0.001 TYR A1067 ARG 0.006 0.000 ARG F 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9444 Ramachandran restraints generated. 4722 Oldfield, 0 Emsley, 4722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 150 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.7888 (ppp) cc_final: 0.7539 (ppp) REVERT: C 865 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7639 (mp) REVERT: F 383 MET cc_start: 0.7703 (ppp) cc_final: 0.7158 (ppp) REVERT: F 408 MET cc_start: 0.3776 (ptp) cc_final: 0.3413 (ptp) REVERT: F 579 MET cc_start: 0.0940 (tpt) cc_final: -0.0286 (tpp) REVERT: D 82 MET cc_start: 0.3257 (tmm) cc_final: 0.2131 (ppp) REVERT: D 249 MET cc_start: 0.2841 (ptt) cc_final: 0.2306 (mmt) REVERT: D 318 VAL cc_start: -0.1665 (OUTLIER) cc_final: -0.1910 (m) REVERT: D 579 MET cc_start: -0.3077 (mtt) cc_final: -0.3613 (mmm) REVERT: E 233 ILE cc_start: -0.2378 (OUTLIER) cc_final: -0.2629 (mt) REVERT: E 256 ILE cc_start: -0.1580 (OUTLIER) cc_final: -0.1968 (mt) REVERT: E 366 MET cc_start: 0.3361 (tpp) cc_final: 0.2918 (tpt) REVERT: E 531 GLN cc_start: 0.4992 (OUTLIER) cc_final: 0.3703 (mp10) outliers start: 154 outliers final: 138 residues processed: 291 average time/residue: 0.4551 time to fit residues: 236.5725 Evaluate side-chains 290 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 147 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 40.0000 chunk 400 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 chunk 346 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 376 optimal weight: 50.0000 chunk 157 optimal weight: 0.0770 chunk 386 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.101473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.067732 restraints weight = 268664.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.067890 restraints weight = 146448.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067909 restraints weight = 102285.550| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 40493 Z= 0.252 Angle : 0.692 15.895 55054 Z= 0.329 Chirality : 0.047 0.835 6350 Planarity : 0.004 0.053 6979 Dihedral : 6.706 59.980 7330 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 3.66 % Allowed : 25.08 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4722 helix: 1.14 (0.13), residues: 1653 sheet: -1.01 (0.19), residues: 664 loop : -1.83 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 478 HIS 0.005 0.001 HIS B 66 PHE 0.030 0.002 PHE C 133 TYR 0.026 0.001 TYR A1067 ARG 0.007 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7499.66 seconds wall clock time: 139 minutes 56.07 seconds (8396.07 seconds total)