Starting phenix.real_space_refine on Fri Feb 23 18:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1y_33575/02_2024/7y1y_33575.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.087 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 25219 2.51 5 N 6426 2.21 5 O 7716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" 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 398": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" 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 398": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H ARG 245": "NH1" <-> "NH2" Residue "H ARG 273": "NH1" <-> "NH2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 357": "NH1" <-> "NH2" Residue "H GLU 375": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 435": "OE1" <-> "OE2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "H ARG 518": "NH1" <-> "NH2" Residue "H GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39556 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7834 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7828 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7828 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 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: "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: "H" 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: 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: "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: 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: "B" 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: "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: "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: "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: "H" 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: 20.36, per 1000 atoms: 0.51 Number of scatterers: 39556 At special positions: 0 Unit cell: (183.703, 202.182, 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 7716 8.00 N 6426 7.00 C 25219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.09 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.82 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=1.92 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.09 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.95 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=1.85 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.95 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 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=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=1.86 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.44 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 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 D 530 " - pdb=" SG CYS D 542 " distance=2.03 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 F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " 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 E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 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 A1409 " - " ASN A 709 " " 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 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 1 " - " ASN A 331 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 343 " " NAG H 701 " - " ASN H 322 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 709 " " 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 D 53 " " NAG e 1 " - " ASN D 90 " " NAG f 1 " - " ASN D 103 " " NAG g 1 " - " ASN D 432 " " NAG h 1 " - " ASN D 546 " " NAG i 1 " - " ASN F 53 " " NAG j 1 " - " ASN F 90 " " NAG k 1 " - " ASN F 103 " " NAG l 1 " - " ASN F 432 " " NAG m 1 " - " ASN F 546 " " NAG n 1 " - " ASN H 53 " " NAG o 1 " - " ASN H 90 " " NAG p 1 " - " ASN H 103 " " NAG q 1 " - " ASN H 432 " " NAG r 1 " - " ASN H 546 " Time building additional restraints: 15.72 Conformation dependent library (CDL) restraints added in 6.5 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: 149 helices and 48 sheets defined 39.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.509A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 4.046A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.694A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.516A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.649A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.519A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.018A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.693A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.793A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.726A pdb=" N PHE D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.189A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 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 252 removed outlier: 3.730A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.083A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.564A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.606A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) 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 531 removed outlier: 4.535A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.973A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix removed outlier: 3.599A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 53 removed outlier: 3.553A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.155A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 192 removed outlier: 3.909A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 4.189A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 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 252 removed outlier: 3.732A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.083A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.178A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.784A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.728A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.652A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.690A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) 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 531 removed outlier: 4.534A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.972A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.743A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 Proline residue: F 590 - end of helix removed outlier: 3.598A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 53 removed outlier: 3.992A pdb=" N PHE H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 4.156A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 157 through 192 removed outlier: 3.910A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix removed outlier: 4.189A pdb=" N GLU H 182 " --> pdb=" O PRO H 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 252 removed outlier: 3.731A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS H 234 " --> pdb=" O PHE H 230 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 4.084A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 252 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 267 No H-bonds generated for 'chain 'H' and resid 265 through 267' Processing helix chain 'H' and resid 275 through 281 removed outlier: 4.177A pdb=" N SER H 280 " --> pdb=" O ASN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.785A pdb=" N VAL H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE H 308 " --> pdb=" O ALA H 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.653A pdb=" N ASN H 330 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.691A pdb=" N HIS H 373 " --> pdb=" O PHE H 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.563A pdb=" N ILE H 407 " --> pdb=" O ALA H 403 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 448 through 466 removed outlier: 4.607A pdb=" N PHE H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 Processing helix chain 'H' and resid 499 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 513 through 531 removed outlier: 4.535A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 548 through 559 removed outlier: 3.972A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 572 removed outlier: 3.742A pdb=" N GLU H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 598 Proline residue: H 590 - end of helix removed outlier: 3.599A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.686A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.428A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.545A 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: 3.777A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.803A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A 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: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A 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: 5.769A 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 1125 removed outlier: 4.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.852A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.925A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.344A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.610A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.802A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.674A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.685A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.497A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.925A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.056A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.545A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.797A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.803A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.806A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AE9, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.806A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 347 through 350 1549 hydrogen bonds defined for protein. 4335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.30 Time building geometry restraints manager: 16.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8727 1.33 - 1.45: 10831 1.45 - 1.58: 20673 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40516 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.41e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.35e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.058 1.20e-02 6.94e+03 2.30e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.88e+01 ... (remaining 40511 not shown) Histogram of bond angle deviations from ideal: 99.75 - 107.56: 1807 107.56 - 115.36: 24196 115.36 - 123.17: 26790 123.17 - 130.97: 2100 130.97 - 138.78: 185 Bond angle restraints: 55078 Sorted by residual: angle pdb=" N CYS C 291 " pdb=" CA CYS C 291 " pdb=" C CYS C 291 " ideal model delta sigma weight residual 109.71 120.49 -10.78 1.41e+00 5.03e-01 5.85e+01 angle pdb=" N PHE H 28 " pdb=" CA PHE H 28 " pdb=" C PHE H 28 " ideal model delta sigma weight residual 111.56 100.42 11.14 1.53e+00 4.27e-01 5.30e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 102.25 8.99 1.29e+00 6.01e-01 4.85e+01 angle pdb=" N SER C 530 " pdb=" CA SER C 530 " pdb=" C SER C 530 " ideal model delta sigma weight residual 108.19 116.99 -8.80 1.29e+00 6.01e-01 4.65e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.90 7.17 1.07e+00 8.73e-01 4.50e+01 ... (remaining 55073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23278 17.68 - 35.35: 1548 35.35 - 53.03: 426 53.03 - 70.70: 94 70.70 - 88.38: 71 Dihedral angle restraints: 25417 sinusoidal: 11434 harmonic: 13983 Sorted by residual: 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 5.37 87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.80 -73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.74 -69.26 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 25414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 6328 0.330 - 0.661: 12 0.661 - 0.991: 5 0.991 - 1.322: 0 1.322 - 1.652: 2 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-02 2.50e+03 4.51e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-02 2.50e+03 1.42e+03 ... (remaining 6344 not shown) Planarity restraints: 7047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.218 2.00e-02 2.50e+03 2.68e-01 8.97e+02 pdb=" CG ASN D 90 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.233 2.00e-02 2.50e+03 2.47e-01 7.60e+02 pdb=" CG ASN A 61 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.373 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.146 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" CG ASN C 165 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.359 2.00e-02 2.50e+03 pdb=" C1 NAG C1403 " -0.235 2.00e-02 2.50e+03 ... (remaining 7044 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 265 2.52 - 3.12: 30723 3.12 - 3.71: 55846 3.71 - 4.31: 81153 4.31 - 4.90: 133436 Nonbonded interactions: 301423 Sorted by model distance: nonbonded pdb=" O ILE A 332 " pdb=" OG1 THR A 333 " model vdw 1.930 2.440 nonbonded pdb=" O PRO B 527 " pdb=" NZ LYS B 528 " model vdw 2.071 2.520 nonbonded pdb=" O PHE B 497 " pdb=" CG ARG B 498 " model vdw 2.138 3.440 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 2.175 2.440 nonbonded pdb=" OG SER A 45 " pdb=" N SER A 46 " model vdw 2.201 2.520 ... (remaining 301418 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' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.600 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 99.100 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 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 : 0.007 0.104 40516 Z= 0.484 Angle : 0.920 13.780 55078 Z= 0.552 Chirality : 0.071 1.652 6347 Planarity : 0.005 0.082 6981 Dihedral : 13.433 88.377 16265 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.12 % Favored : 91.00 % Rotamer: Outliers : 2.16 % Allowed : 5.18 % Favored : 92.66 % 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: -3.28 (0.11), residues: 4720 helix: -1.68 (0.11), residues: 1635 sheet: -1.23 (0.19), residues: 674 loop : -2.88 (0.11), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 594 HIS 0.003 0.001 HIS H 378 PHE 0.016 0.001 PHE A 592 TYR 0.021 0.001 TYR A 495 ARG 0.002 0.000 ARG A 457 *********************** 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 852 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 761 time to evaluate : 4.310 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: A 615 VAL cc_start: 0.6549 (t) cc_final: 0.6347 (t) REVERT: A 1052 PHE cc_start: 0.6531 (m-80) cc_final: 0.5930 (m-80) REVERT: B 28 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: C 371 PHE cc_start: 0.2437 (OUTLIER) cc_final: 0.1970 (t80) REVERT: F 29 LEU cc_start: 0.2126 (OUTLIER) cc_final: 0.1468 (tp) REVERT: F 190 MET cc_start: 0.1298 (tmm) cc_final: 0.1081 (ttp) REVERT: F 383 MET cc_start: 0.0212 (mtp) cc_final: -0.1229 (tmm) REVERT: H 474 MET cc_start: -0.3008 (mmp) cc_final: -0.3278 (tpp) outliers start: 91 outliers final: 23 residues processed: 837 average time/residue: 0.5107 time to fit residues: 691.8802 Evaluate side-chains 395 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 369 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 35 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 50.0000 chunk 359 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 371 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 430 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 417 ASN A 477 ASN A 690 GLN A 901 GLN B 321 GLN B 417 ASN B 450 ASN B 477 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 901 GLN B 914 ASN B1119 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 417 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 101 GLN D 137 ASN D 442 GLN D 472 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 101 GLN F 137 ASN F 442 GLN F 472 GLN F 599 ASN H 60 GLN H 101 GLN H 137 ASN H 277 ASN H 325 GLN H 417 HIS H 442 GLN H 472 GLN H 572 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 40516 Z= 0.373 Angle : 0.867 16.693 55078 Z= 0.427 Chirality : 0.054 0.454 6347 Planarity : 0.006 0.113 6981 Dihedral : 7.957 73.973 7360 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.40 % Favored : 93.22 % Rotamer: Outliers : 3.14 % Allowed : 11.02 % Favored : 85.84 % 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: -2.46 (0.11), residues: 4720 helix: -0.62 (0.12), residues: 1707 sheet: -1.34 (0.18), residues: 638 loop : -2.54 (0.11), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 64 HIS 0.009 0.002 HIS H 34 PHE 0.043 0.003 PHE A 497 TYR 0.050 0.002 TYR A1067 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 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 487 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 355 time to evaluate : 4.532 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: A 523 THR cc_start: 0.4366 (OUTLIER) cc_final: 0.3809 (m) REVERT: B 329 PHE cc_start: 0.5264 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: C 153 MET cc_start: 0.1495 (ppp) cc_final: 0.1285 (ppp) REVERT: C 1129 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7093 (t) REVERT: D 249 MET cc_start: 0.4545 (mtt) cc_final: 0.3819 (tpp) REVERT: F 29 LEU cc_start: 0.0017 (OUTLIER) cc_final: -0.0378 (tt) REVERT: F 323 MET cc_start: -0.0752 (OUTLIER) cc_final: -0.2327 (tpp) REVERT: F 383 MET cc_start: 0.0529 (mtp) cc_final: -0.1283 (tmm) REVERT: H 228 HIS cc_start: 0.1565 (OUTLIER) cc_final: -0.1021 (t70) REVERT: H 474 MET cc_start: -0.3144 (mmp) cc_final: -0.3357 (tpp) outliers start: 132 outliers final: 53 residues processed: 465 average time/residue: 0.4758 time to fit residues: 376.4131 Evaluate side-chains 311 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 252 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 358 optimal weight: 50.0000 chunk 293 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 431 optimal weight: 30.0000 chunk 465 optimal weight: 40.0000 chunk 384 optimal weight: 40.0000 chunk 427 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 477 ASN A 965 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 658 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 101 GLN D 330 ASN D 505 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN H 330 ASN H 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 40516 Z= 0.376 Angle : 0.749 11.190 55078 Z= 0.374 Chirality : 0.050 0.539 6347 Planarity : 0.005 0.093 6981 Dihedral : 6.988 69.773 7328 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.46 % Favored : 93.18 % Rotamer: Outliers : 3.28 % Allowed : 13.75 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.11), residues: 4720 helix: -0.10 (0.13), residues: 1713 sheet: -1.04 (0.18), residues: 695 loop : -2.41 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 165 HIS 0.012 0.001 HIS B 49 PHE 0.026 0.002 PHE B 898 TYR 0.029 0.002 TYR A 796 ARG 0.009 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 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 425 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 287 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.4273 (OUTLIER) cc_final: 0.3812 (m) REVERT: B 48 LEU cc_start: 0.8486 (mp) cc_final: 0.8267 (mt) REVERT: B 785 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7630 (m) REVERT: C 153 MET cc_start: 0.1770 (ppp) cc_final: 0.0924 (ppp) REVERT: C 872 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: C 995 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7291 (ptm160) REVERT: D 249 MET cc_start: 0.4045 (mtt) cc_final: 0.3008 (tpp) REVERT: D 265 HIS cc_start: 0.1171 (p-80) cc_final: 0.0833 (p90) REVERT: D 579 MET cc_start: -0.0376 (mtp) cc_final: -0.0577 (mtp) REVERT: F 29 LEU cc_start: 0.0244 (OUTLIER) cc_final: -0.0271 (tt) REVERT: F 323 MET cc_start: -0.0913 (OUTLIER) cc_final: -0.2363 (tpp) REVERT: F 376 MET cc_start: 0.4994 (ttm) cc_final: 0.4713 (ttm) REVERT: F 383 MET cc_start: 0.1061 (mtp) cc_final: -0.1245 (tmm) REVERT: F 455 MET cc_start: 0.2754 (OUTLIER) cc_final: 0.2537 (ppp) REVERT: H 474 MET cc_start: -0.2972 (mmp) cc_final: -0.3424 (tpp) outliers start: 138 outliers final: 71 residues processed: 413 average time/residue: 0.4635 time to fit residues: 328.6215 Evaluate side-chains 301 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1057 PRO Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 8.9990 chunk 324 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 432 optimal weight: 4.9990 chunk 458 optimal weight: 4.9990 chunk 226 optimal weight: 0.0670 chunk 410 optimal weight: 50.0000 chunk 123 optimal weight: 20.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN B 394 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 417 HIS F 417 HIS H 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 40516 Z= 0.269 Angle : 0.659 12.575 55078 Z= 0.325 Chirality : 0.047 0.849 6347 Planarity : 0.004 0.074 6981 Dihedral : 6.488 59.500 7325 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.74 % Favored : 93.96 % Rotamer: Outliers : 2.66 % Allowed : 15.18 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4720 helix: 0.27 (0.13), residues: 1707 sheet: -0.90 (0.18), residues: 698 loop : -2.21 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.010 0.001 HIS B 49 PHE 0.021 0.002 PHE B 238 TYR 0.024 0.001 TYR A1067 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 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 349 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 237 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.4280 (OUTLIER) cc_final: 0.3817 (m) REVERT: B 48 LEU cc_start: 0.8596 (mp) cc_final: 0.8378 (mt) REVERT: C 654 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: C 872 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: D 249 MET cc_start: 0.4118 (mtt) cc_final: 0.3156 (tpp) REVERT: D 297 MET cc_start: -0.1925 (mtm) cc_final: -0.2294 (mtp) REVERT: D 579 MET cc_start: -0.0350 (mtp) cc_final: -0.0582 (mtp) REVERT: F 176 LEU cc_start: -0.4533 (OUTLIER) cc_final: -0.4887 (mm) REVERT: F 383 MET cc_start: 0.1108 (mtp) cc_final: -0.1193 (tmm) REVERT: H 323 MET cc_start: 0.2291 (ptp) cc_final: 0.1331 (ppp) REVERT: H 366 MET cc_start: 0.0297 (tpt) cc_final: -0.0071 (mmm) REVERT: H 474 MET cc_start: -0.3018 (mmp) cc_final: -0.3425 (tpp) outliers start: 112 outliers final: 78 residues processed: 337 average time/residue: 0.4554 time to fit residues: 268.6931 Evaluate side-chains 298 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 216 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 572 ASN Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 chunk 189 optimal weight: 0.6980 chunk 390 optimal weight: 20.0000 chunk 316 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 411 optimal weight: 20.0000 chunk 115 optimal weight: 0.0980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN B 487 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 599 ASN F 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40516 Z= 0.230 Angle : 0.618 11.855 55078 Z= 0.302 Chirality : 0.046 0.755 6347 Planarity : 0.004 0.062 6981 Dihedral : 6.133 59.947 7323 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.51 % Favored : 94.19 % Rotamer: Outliers : 2.68 % Allowed : 15.65 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4720 helix: 0.64 (0.13), residues: 1687 sheet: -0.69 (0.18), residues: 714 loop : -2.06 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.009 0.001 HIS B 49 PHE 0.028 0.002 PHE A 855 TYR 0.022 0.001 TYR A1067 ARG 0.009 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 5 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 347 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 234 time to evaluate : 4.400 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: B 48 LEU cc_start: 0.8591 (mp) cc_final: 0.8359 (mp) REVERT: C 153 MET cc_start: 0.2281 (ppp) cc_final: 0.1631 (ppp) REVERT: C 654 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: D 249 MET cc_start: 0.4029 (mtt) cc_final: 0.3082 (tpp) REVERT: D 297 MET cc_start: -0.1647 (mtm) cc_final: -0.2165 (mtp) REVERT: D 579 MET cc_start: -0.0405 (mtp) cc_final: -0.0623 (mtp) REVERT: F 176 LEU cc_start: -0.4564 (OUTLIER) cc_final: -0.4939 (mm) REVERT: F 287 GLN cc_start: 0.0329 (OUTLIER) cc_final: 0.0023 (tp40) REVERT: F 327 PHE cc_start: -0.1704 (OUTLIER) cc_final: -0.1933 (t80) REVERT: F 376 MET cc_start: 0.4482 (ttm) cc_final: 0.4236 (ttm) REVERT: F 383 MET cc_start: 0.1316 (mtp) cc_final: -0.1055 (tmm) REVERT: F 474 MET cc_start: -0.1248 (mmm) cc_final: -0.1729 (mmm) REVERT: H 366 MET cc_start: -0.0173 (tpt) cc_final: -0.0871 (mmm) REVERT: H 474 MET cc_start: -0.3051 (mmp) cc_final: -0.3486 (mmp) outliers start: 113 outliers final: 77 residues processed: 328 average time/residue: 0.4553 time to fit residues: 261.8812 Evaluate side-chains 296 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 215 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 572 ASN Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 3.9990 chunk 412 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 458 optimal weight: 8.9990 chunk 380 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 321 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 644 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN F 98 GLN F 505 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40516 Z= 0.271 Angle : 0.628 11.510 55078 Z= 0.307 Chirality : 0.045 0.540 6347 Planarity : 0.004 0.065 6981 Dihedral : 6.055 59.877 7323 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.71 % Rotamer: Outliers : 3.49 % Allowed : 15.20 % Favored : 81.31 % 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: -1.13 (0.12), residues: 4720 helix: 0.70 (0.13), residues: 1694 sheet: -0.57 (0.19), residues: 701 loop : -1.97 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.008 0.001 HIS B 49 PHE 0.033 0.002 PHE B 238 TYR 0.026 0.001 TYR A1067 ARG 0.007 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 6 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 376 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 229 time to evaluate : 5.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.5081 (m) REVERT: B 48 LEU cc_start: 0.8597 (mp) cc_final: 0.8344 (mp) REVERT: B 816 SER cc_start: 0.7848 (p) cc_final: 0.7584 (p) REVERT: B 878 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7864 (mt) REVERT: C 153 MET cc_start: 0.2192 (ppp) cc_final: 0.1317 (ppp) REVERT: C 654 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: D 249 MET cc_start: 0.3995 (mtt) cc_final: 0.3065 (tpp) REVERT: D 297 MET cc_start: -0.1438 (mtm) cc_final: -0.2012 (mtp) REVERT: F 82 MET cc_start: 0.3155 (ptt) cc_final: 0.2334 (ptt) REVERT: F 176 LEU cc_start: -0.4584 (OUTLIER) cc_final: -0.4955 (mm) REVERT: F 287 GLN cc_start: 0.0137 (OUTLIER) cc_final: -0.0204 (tp40) REVERT: F 376 MET cc_start: 0.4418 (ttm) cc_final: 0.4138 (ttm) REVERT: F 383 MET cc_start: 0.1494 (mtp) cc_final: -0.0861 (tmm) REVERT: F 474 MET cc_start: -0.1299 (mmm) cc_final: -0.1843 (mmm) REVERT: H 462 MET cc_start: 0.1985 (ptm) cc_final: 0.1694 (mmp) REVERT: H 474 MET cc_start: -0.2904 (mmp) cc_final: -0.3161 (mmp) outliers start: 147 outliers final: 102 residues processed: 356 average time/residue: 0.4464 time to fit residues: 279.2609 Evaluate side-chains 319 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 212 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 530 CYS Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 334 optimal weight: 40.0000 chunk 259 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 456 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 278 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40516 Z= 0.171 Angle : 0.591 10.813 55078 Z= 0.288 Chirality : 0.044 0.431 6347 Planarity : 0.004 0.065 6981 Dihedral : 5.808 59.983 7323 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.08 % Favored : 94.60 % Rotamer: Outliers : 2.47 % Allowed : 16.32 % Favored : 81.21 % 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: -0.90 (0.12), residues: 4720 helix: 0.91 (0.13), residues: 1695 sheet: -0.44 (0.19), residues: 709 loop : -1.87 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.008 0.001 HIS B 49 PHE 0.033 0.001 PHE F 327 TYR 0.019 0.001 TYR C1067 ARG 0.009 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 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 325 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 221 time to evaluate : 4.726 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: B 48 LEU cc_start: 0.8464 (mp) cc_final: 0.8217 (mp) REVERT: B 816 SER cc_start: 0.7746 (p) cc_final: 0.7478 (p) REVERT: B 1128 VAL cc_start: 0.7955 (m) cc_final: 0.7703 (p) REVERT: C 153 MET cc_start: 0.2016 (ppp) cc_final: 0.1157 (ppp) REVERT: C 273 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7673 (mmt-90) REVERT: D 249 MET cc_start: 0.3987 (mtt) cc_final: 0.3069 (tpp) REVERT: D 297 MET cc_start: -0.1617 (mtm) cc_final: -0.2032 (mtp) REVERT: F 82 MET cc_start: 0.2737 (ptt) cc_final: 0.2532 (ptt) REVERT: F 176 LEU cc_start: -0.4609 (OUTLIER) cc_final: -0.4970 (mm) REVERT: F 287 GLN cc_start: 0.0527 (OUTLIER) cc_final: 0.0266 (tp40) REVERT: F 376 MET cc_start: 0.4392 (ttm) cc_final: 0.4079 (ttm) REVERT: F 383 MET cc_start: 0.1535 (mtp) cc_final: -0.0902 (tmm) REVERT: F 474 MET cc_start: -0.0812 (mmm) cc_final: -0.1395 (mmm) REVERT: H 462 MET cc_start: 0.2124 (ptm) cc_final: 0.1568 (mmp) REVERT: H 474 MET cc_start: -0.3017 (mmp) cc_final: -0.3243 (mmp) outliers start: 104 outliers final: 81 residues processed: 305 average time/residue: 0.4580 time to fit residues: 245.2115 Evaluate side-chains 295 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 211 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 311 optimal weight: 40.0000 chunk 225 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 359 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN F 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40516 Z= 0.191 Angle : 0.586 10.070 55078 Z= 0.285 Chirality : 0.044 0.399 6347 Planarity : 0.004 0.066 6981 Dihedral : 5.585 59.745 7321 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.23 % Favored : 94.47 % Rotamer: Outliers : 2.54 % Allowed : 16.20 % Favored : 81.26 % 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: -0.74 (0.12), residues: 4720 helix: 1.06 (0.13), residues: 1686 sheet: -0.33 (0.19), residues: 680 loop : -1.76 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.007 0.001 HIS B 49 PHE 0.036 0.001 PHE B 238 TYR 0.021 0.001 TYR A1067 ARG 0.009 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 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 325 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 218 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.5267 (OUTLIER) cc_final: 0.4955 (m) REVERT: B 48 LEU cc_start: 0.8477 (mp) cc_final: 0.8218 (mp) REVERT: B 816 SER cc_start: 0.7781 (p) cc_final: 0.7511 (p) REVERT: C 153 MET cc_start: 0.2114 (ppp) cc_final: 0.1135 (ppp) REVERT: C 273 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7686 (mmt-90) REVERT: D 249 MET cc_start: 0.3899 (mtt) cc_final: 0.3006 (tpp) REVERT: D 297 MET cc_start: -0.1536 (mtm) cc_final: -0.1919 (mtp) REVERT: F 176 LEU cc_start: -0.4589 (OUTLIER) cc_final: -0.4980 (mm) REVERT: F 376 MET cc_start: 0.4504 (ttm) cc_final: 0.4137 (ttm) REVERT: F 474 MET cc_start: -0.0803 (mmm) cc_final: -0.1376 (mmm) REVERT: H 462 MET cc_start: 0.2207 (ptm) cc_final: 0.1771 (mmp) REVERT: H 474 MET cc_start: -0.2942 (mmp) cc_final: -0.3448 (tpp) outliers start: 107 outliers final: 89 residues processed: 309 average time/residue: 0.4807 time to fit residues: 258.8467 Evaluate side-chains 300 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 208 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 4.9990 chunk 437 optimal weight: 50.0000 chunk 399 optimal weight: 8.9990 chunk 425 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 334 optimal weight: 50.0000 chunk 130 optimal weight: 30.0000 chunk 384 optimal weight: 7.9990 chunk 402 optimal weight: 20.0000 chunk 424 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1106 GLN B 30 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 30 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 98 GLN H 89 GLN H 290 ASN H 340 GLN H 493 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 40516 Z= 0.514 Angle : 0.767 10.376 55078 Z= 0.381 Chirality : 0.050 0.347 6347 Planarity : 0.005 0.084 6981 Dihedral : 6.572 59.954 7321 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.91 % Favored : 92.80 % Rotamer: Outliers : 2.80 % Allowed : 16.22 % Favored : 80.97 % 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: -1.17 (0.12), residues: 4720 helix: 0.63 (0.13), residues: 1699 sheet: -0.71 (0.20), residues: 632 loop : -1.89 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 886 HIS 0.012 0.002 HIS B1058 PHE 0.036 0.003 PHE F 327 TYR 0.044 0.002 TYR A1067 ARG 0.011 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 9 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 339 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 221 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.5351 (OUTLIER) cc_final: 0.5138 (m) REVERT: B 878 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7887 (mt) REVERT: B 990 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6584 (tp30) REVERT: C 654 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: D 249 MET cc_start: 0.3930 (mtt) cc_final: 0.2738 (tpp) REVERT: D 297 MET cc_start: -0.1611 (mtm) cc_final: -0.1936 (mtp) REVERT: F 176 LEU cc_start: -0.4617 (OUTLIER) cc_final: -0.5005 (mm) REVERT: F 376 MET cc_start: 0.4368 (ttm) cc_final: 0.4098 (ttm) REVERT: F 474 MET cc_start: -0.0744 (mmm) cc_final: -0.1360 (mmm) REVERT: F 557 MET cc_start: 0.2314 (ttt) cc_final: 0.1603 (ttt) REVERT: H 462 MET cc_start: 0.2155 (ptm) cc_final: 0.1544 (mmp) REVERT: H 474 MET cc_start: -0.2779 (mmp) cc_final: -0.3002 (tpp) outliers start: 118 outliers final: 91 residues processed: 324 average time/residue: 0.4881 time to fit residues: 279.1097 Evaluate side-chains 294 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 198 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 572 ASN Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.6980 chunk 450 optimal weight: 50.0000 chunk 274 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 312 optimal weight: 30.0000 chunk 472 optimal weight: 5.9990 chunk 434 optimal weight: 40.0000 chunk 376 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40516 Z= 0.288 Angle : 0.651 16.018 55078 Z= 0.320 Chirality : 0.046 0.316 6347 Planarity : 0.004 0.066 6981 Dihedral : 6.159 59.786 7320 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.30 % Favored : 94.43 % Rotamer: Outliers : 2.21 % Allowed : 17.05 % Favored : 80.74 % 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: -1.00 (0.12), residues: 4720 helix: 0.76 (0.13), residues: 1706 sheet: -0.67 (0.19), residues: 668 loop : -1.79 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 886 HIS 0.007 0.001 HIS B 49 PHE 0.034 0.002 PHE B 238 TYR 0.027 0.001 TYR A1067 ARG 0.010 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 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 303 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 210 time to evaluate : 6.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.5357 (OUTLIER) cc_final: 0.5128 (m) REVERT: B 878 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7890 (mt) REVERT: B 990 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6452 (tp30) REVERT: D 249 MET cc_start: 0.4021 (mtt) cc_final: 0.2842 (tpp) REVERT: D 265 HIS cc_start: 0.1524 (p-80) cc_final: 0.1158 (p90) REVERT: D 297 MET cc_start: -0.1668 (mtm) cc_final: -0.1969 (mtp) REVERT: F 176 LEU cc_start: -0.4640 (OUTLIER) cc_final: -0.5035 (mm) REVERT: F 376 MET cc_start: 0.4442 (ttm) cc_final: 0.4139 (ttm) REVERT: F 474 MET cc_start: -0.0825 (mmm) cc_final: -0.1426 (mmm) REVERT: F 557 MET cc_start: 0.2401 (ttt) cc_final: 0.1977 (ttt) REVERT: H 462 MET cc_start: 0.2365 (ptm) cc_final: 0.1936 (mmp) REVERT: H 474 MET cc_start: -0.2816 (mmp) cc_final: -0.3018 (tpp) outliers start: 93 outliers final: 86 residues processed: 289 average time/residue: 0.4784 time to fit residues: 242.5333 Evaluate side-chains 286 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 196 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 203 TRP Chi-restraints excluded: chain H residue 228 HIS Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 400 PHE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 607 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 20.0000 chunk 400 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 376 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 386 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 207 HIS ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.209791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.169459 restraints weight = 90068.068| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 4.59 r_work: 0.3485 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 40516 Z= 0.448 Angle : 0.722 14.788 55078 Z= 0.357 Chirality : 0.048 0.315 6347 Planarity : 0.005 0.068 6981 Dihedral : 6.482 59.911 7318 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.18 % Favored : 92.52 % Rotamer: Outliers : 2.35 % Allowed : 17.05 % Favored : 80.59 % 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: -1.14 (0.12), residues: 4720 helix: 0.65 (0.13), residues: 1711 sheet: -0.85 (0.19), residues: 667 loop : -1.84 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 886 HIS 0.009 0.001 HIS B 49 PHE 0.033 0.002 PHE B 238 TYR 0.035 0.002 TYR A1067 ARG 0.015 0.001 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8182.85 seconds wall clock time: 151 minutes 53.87 seconds (9113.87 seconds total)