Starting phenix.real_space_refine on Fri Feb 23 19:00:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1z_33576/02_2024/7y1z_33576.pdb" } resolution = 3.4 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= 0.008 sd= 0.082 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 25240 2.51 5 N 6435 2.21 5 O 7713 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 "A ARG 493": "NH1" <-> "NH2" 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 "B ARG 493": "NH1" <-> "NH2" 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 "C ARG 493": "NH1" <-> "NH2" 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39583 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7843 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7837 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: 19.28, per 1000 atoms: 0.49 Number of scatterers: 39583 At special positions: 0 Unit cell: (184.79, 195.66, 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 7713 8.00 N 6435 7.00 C 25240 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=1.94 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.41 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=1.88 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.94 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=1.98 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=1.89 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.91 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=2.02 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: 15.78 Conformation dependent library (CDL) restraints added in 6.9 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: 9014 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 49 sheets defined 39.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.708A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 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: 3.803A 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 ARG 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: 4.430A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A 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: 4.757A 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: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.983A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.679A 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: 3.803A 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: 3.693A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG 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: 4.087A 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: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A 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: 3.650A 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: 4.239A 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: 3.595A 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: 4.323A 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 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.680A 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 ARG 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: 3.993A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.551A 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: 3.626A 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 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: 4.321A 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: 4.096A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 4.154A 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: 4.285A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.910A 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: 3.930A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.190A 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: 3.733A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.904A 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: 4.084A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.680A 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: 3.620A 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: 3.728A 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: 3.562A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.819A 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: 4.607A 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: 4.143A 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: 4.096A 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: 3.595A 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: 4.215A 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: 3.933A 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: 3.731A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.905A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.084A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.785A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.729A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.691A 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: 4.577A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.081A 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: 3.931A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 4.143A 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: 3.973A 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: 3.599A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 53 removed outlier: 4.096A pdb=" N LYS H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 removed outlier: 4.154A 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: 3.909A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.934A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.566A 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: 4.590A pdb=" N GLU H 232 " --> pdb=" O HIS H 228 " (cutoff:3.500A) removed outlier: 3.904A 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: 4.083A 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: 4.296A 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: 4.179A 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: 3.728A pdb=" N ILE H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.813A pdb=" N GLY H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.652A 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: 3.980A 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: 3.564A 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: 4.081A 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: 4.606A 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: 4.534A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.973A 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: 3.743A 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 28 through 30 removed outlier: 3.685A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.508A 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: 4.410A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A 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: 5.091A 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: 5.352A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.765A 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: 5.059A 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 319 removed outlier: 5.333A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.613A 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: 3.811A 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: 6.076A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.665A 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: 6.729A 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: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.542A 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: 6.729A 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: 6.300A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A 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: 4.484A 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: 5.770A 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: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 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: 7.497A 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: 4.410A 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: 6.630A 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: 6.608A 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: 3.765A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.665A 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 319 removed outlier: 5.329A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (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: 5.612A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.796A 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: 3.811A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.530A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.473A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A 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: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A 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: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A 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=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A 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: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A 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: 6.995A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.114A 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=AD2, 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=AD3, 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=AD4, 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: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.499A 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=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A 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: 6.628A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A 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: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A 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=AD7, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.740A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.049A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.560A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.796A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.811A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A 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=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A 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: 6.827A 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: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A 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: 6.827A 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: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, 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=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF3, 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=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 347 through 350 1564 hydrogen bonds defined for protein. 4386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.14 Time building geometry restraints manager: 16.98 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: 8630 1.33 - 1.45: 10902 1.45 - 1.58: 20726 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40543 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+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 2.34e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.33e+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 1.92e+01 ... (remaining 40538 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.50: 1760 107.50 - 115.25: 24168 115.25 - 123.01: 26260 123.01 - 130.76: 2743 130.76 - 138.52: 183 Bond angle restraints: 55114 Sorted by residual: angle pdb=" N PHE H 28 " pdb=" CA PHE H 28 " pdb=" C PHE H 28 " ideal model delta sigma weight residual 111.24 101.82 9.42 1.29e+00 6.01e-01 5.34e+01 angle pdb=" N PHE F 28 " pdb=" CA PHE F 28 " pdb=" C PHE F 28 " ideal model delta sigma weight residual 111.24 101.84 9.40 1.29e+00 6.01e-01 5.31e+01 angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 111.24 101.85 9.39 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N LEU F 45 " pdb=" CA LEU F 45 " pdb=" C LEU F 45 " ideal model delta sigma weight residual 111.07 103.93 7.14 1.07e+00 8.73e-01 4.46e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 111.07 103.95 7.12 1.07e+00 8.73e-01 4.43e+01 ... (remaining 55109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 23376 17.88 - 35.77: 1516 35.77 - 53.65: 397 53.65 - 71.54: 87 71.54 - 89.42: 65 Dihedral angle restraints: 25441 sinusoidal: 11452 harmonic: 13989 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 3.42 -89.42 1 1.00e+01 1.00e-02 9.50e+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 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 25.65 67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 25438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 6339 0.331 - 0.661: 7 0.661 - 0.992: 5 0.992 - 1.323: 0 1.323 - 1.653: 2 Chirality restraints: 6353 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.04e+02 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 -1.95 -0.45 2.00e-02 2.50e+03 5.02e+02 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 -1.95 -0.45 2.00e-02 2.50e+03 5.00e+02 ... (remaining 6350 not shown) Planarity restraints: 7050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.239 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" CG ASN B 331 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.563 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.418 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.142 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" CG ASN A 801 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.271 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.105 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" CG ASN A 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.196 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.140 2.00e-02 2.50e+03 ... (remaining 7047 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 30471 3.12 - 3.71: 55966 3.71 - 4.31: 81226 4.31 - 4.90: 133628 Nonbonded interactions: 301524 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.926 3.340 nonbonded pdb=" O ASP B 40 " pdb=" O LYS B 41 " model vdw 1.995 3.040 nonbonded pdb=" O VAL C 445 " pdb=" OG SER C 446 " model vdw 2.034 2.440 nonbonded pdb=" O VAL B 445 " pdb=" OG SER B 446 " model vdw 2.035 2.440 nonbonded pdb=" O VAL A 445 " pdb=" OG SER A 446 " model vdw 2.035 2.440 ... (remaining 301519 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.300 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 102.220 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.890 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 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 0.103 40543 Z= 0.475 Angle : 0.892 13.515 55114 Z= 0.536 Chirality : 0.069 1.653 6353 Planarity : 0.005 0.106 6984 Dihedral : 13.261 88.438 16283 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 1.65 % Allowed : 6.76 % Favored : 91.59 % Rotamer: Outliers : 1.54 % Allowed : 4.72 % Favored : 93.73 % Cbeta Deviations : 0.02 % 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: -3.20 (0.11), residues: 4720 helix: -1.64 (0.11), residues: 1645 sheet: -1.15 (0.19), residues: 649 loop : -2.81 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 594 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE C 456 TYR 0.014 0.001 TYR C 369 ARG 0.002 0.000 ARG F 161 *********************** 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 842 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 777 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.5924 (m-80) cc_final: 0.5620 (m-80) REVERT: A 332 ILE cc_start: 0.3760 (OUTLIER) cc_final: 0.3329 (tt) REVERT: A 371 PHE cc_start: 0.0628 (OUTLIER) cc_final: 0.0054 (t80) REVERT: A 800 PHE cc_start: 0.6115 (m-80) cc_final: 0.5050 (m-80) REVERT: B 231 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5195 (mm) REVERT: B 909 ILE cc_start: 0.7729 (pt) cc_final: 0.7195 (pt) REVERT: B 1143 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: C 1031 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6994 (tt0) REVERT: D 85 LEU cc_start: -0.1612 (tp) cc_final: -0.1825 (pt) REVERT: D 189 GLU cc_start: 0.4969 (mt-10) cc_final: 0.4570 (mm-30) REVERT: F 31 LYS cc_start: 0.0371 (OUTLIER) cc_final: 0.0157 (tptt) REVERT: F 474 MET cc_start: -0.2123 (mmp) cc_final: -0.2793 (ttt) REVERT: H 39 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4673 (mt) REVERT: H 270 MET cc_start: 0.2103 (tpt) cc_final: 0.1050 (tpp) outliers start: 65 outliers final: 16 residues processed: 831 average time/residue: 0.5086 time to fit residues: 684.6532 Evaluate side-chains 379 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 358 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 39 LEU 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: 10.0000 chunk 199 optimal weight: 0.0000 chunk 122 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 371 optimal weight: 40.0000 chunk 143 optimal weight: 20.0000 chunk 225 optimal weight: 40.0000 chunk 276 optimal weight: 0.9980 chunk 430 optimal weight: 50.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 370 ASN A 417 ASN A 955 ASN A1135 ASN B 30 ASN B 271 GLN B 370 ASN B 417 ASN B 450 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 914 ASN B1005 GLN C 121 ASN C 370 ASN C 417 ASN C 755 GLN C 762 GLN C1002 GLN C1005 GLN D 24 GLN D 101 GLN D 137 ASN D 210 ASN D 472 GLN D 599 ASN F 24 GLN F 96 GLN F 101 GLN F 137 ASN F 277 ASN F 374 HIS F 417 HIS F 472 GLN F 508 ASN F 599 ASN H 24 GLN H 101 GLN H 137 ASN H 277 ASN ** H 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 HIS H 417 HIS H 472 GLN H 531 GLN ** H 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 40543 Z= 0.406 Angle : 0.870 13.520 55114 Z= 0.433 Chirality : 0.053 0.373 6353 Planarity : 0.006 0.085 6984 Dihedral : 7.899 59.868 7375 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.89 % Favored : 93.73 % Rotamer: Outliers : 2.68 % Allowed : 11.39 % Favored : 85.92 % 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: -2.47 (0.11), residues: 4720 helix: -0.61 (0.12), residues: 1659 sheet: -1.32 (0.18), residues: 686 loop : -2.55 (0.11), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 461 HIS 0.014 0.002 HIS A1064 PHE 0.042 0.003 PHE A 456 TYR 0.041 0.002 TYR B 501 ARG 0.012 0.001 ARG A 493 *********************** 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 495 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 382 time to evaluate : 4.365 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 55 PHE cc_start: 0.6627 (m-80) cc_final: 0.6350 (m-80) REVERT: A 205 SER cc_start: 0.7881 (p) cc_final: 0.7680 (p) REVERT: A 313 TYR cc_start: 0.8032 (m-80) cc_final: 0.7820 (m-80) REVERT: A 523 THR cc_start: 0.1771 (OUTLIER) cc_final: 0.1548 (m) REVERT: A 767 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 329 PHE cc_start: 0.6668 (m-80) cc_final: 0.6456 (m-80) REVERT: B 445 VAL cc_start: -0.0775 (OUTLIER) cc_final: -0.0999 (t) REVERT: B 523 THR cc_start: 0.4827 (OUTLIER) cc_final: 0.4552 (m) REVERT: B 568 ASP cc_start: 0.6513 (p0) cc_final: 0.6281 (p0) REVERT: B 990 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6532 (tm-30) REVERT: D 32 PHE cc_start: 0.0252 (t80) cc_final: -0.0497 (t80) REVERT: D 189 GLU cc_start: 0.4710 (mt-10) cc_final: 0.4498 (mm-30) REVERT: D 190 MET cc_start: -0.0174 (tmm) cc_final: -0.1501 (ttp) REVERT: D 213 ASP cc_start: 0.2339 (t0) cc_final: 0.1803 (m-30) REVERT: D 314 PHE cc_start: 0.3565 (t80) cc_final: 0.3232 (m-10) REVERT: D 438 PHE cc_start: 0.2091 (t80) cc_final: -0.0392 (m-10) REVERT: D 557 MET cc_start: 0.0537 (OUTLIER) cc_final: 0.0254 (ppp) REVERT: H 39 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.4110 (mt) REVERT: H 82 MET cc_start: 0.3173 (mtp) cc_final: 0.2570 (mpp) REVERT: H 383 MET cc_start: 0.2065 (mtp) cc_final: 0.0490 (tmm) outliers start: 113 outliers final: 53 residues processed: 479 average time/residue: 0.4788 time to fit residues: 394.3538 Evaluate side-chains 337 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 278 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 542 CYS Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 271 TRP Chi-restraints excluded: chain H residue 563 SER Chi-restraints excluded: chain H residue 579 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 40.0000 chunk 133 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 293 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 431 optimal weight: 40.0000 chunk 465 optimal weight: 40.0000 chunk 384 optimal weight: 40.0000 chunk 427 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN A 450 ASN A 536 ASN A 644 GLN B 30 ASN B 87 ASN B 207 HIS B 314 GLN B 414 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 762 GLN C 774 GLN C1088 HIS D 34 HIS D 374 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS F 378 HIS F 429 GLN F 442 GLN H 101 GLN ** H 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 HIS H 531 GLN ** H 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 40543 Z= 0.375 Angle : 0.725 10.482 55114 Z= 0.362 Chirality : 0.049 0.303 6353 Planarity : 0.005 0.062 6984 Dihedral : 6.969 59.601 7336 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.14 % Favored : 93.56 % Rotamer: Outliers : 3.23 % Allowed : 13.48 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.11), residues: 4720 helix: -0.07 (0.13), residues: 1666 sheet: -1.12 (0.18), residues: 699 loop : -2.39 (0.11), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 459 HIS 0.009 0.001 HIS B1058 PHE 0.041 0.002 PHE A 275 TYR 0.022 0.002 TYR C1067 ARG 0.010 0.000 ARG D 357 *********************** 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 440 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 304 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 THR cc_start: 0.2109 (OUTLIER) cc_final: 0.1902 (m) REVERT: A 756 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6097 (t80) REVERT: A 896 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 1010 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6077 (tt0) REVERT: B 568 ASP cc_start: 0.6664 (p0) cc_final: 0.6327 (p0) REVERT: C 398 ASP cc_start: 0.2987 (OUTLIER) cc_final: 0.1186 (t0) REVERT: D 190 MET cc_start: -0.0186 (tmm) cc_final: -0.1209 (ttp) REVERT: D 213 ASP cc_start: 0.2084 (t0) cc_final: 0.1629 (m-30) REVERT: D 438 PHE cc_start: 0.2113 (t80) cc_final: -0.0222 (m-80) REVERT: F 190 MET cc_start: -0.0713 (ppp) cc_final: -0.0988 (ppp) REVERT: F 323 MET cc_start: -0.2933 (mmt) cc_final: -0.3524 (ppp) REVERT: F 579 MET cc_start: 0.0052 (pmm) cc_final: -0.0834 (ttp) REVERT: H 82 MET cc_start: 0.3248 (mtp) cc_final: 0.2812 (mpp) REVERT: H 141 CYS cc_start: 0.0048 (OUTLIER) cc_final: -0.0242 (p) REVERT: H 383 MET cc_start: 0.1902 (mtp) cc_final: 0.0700 (tmm) outliers start: 136 outliers final: 63 residues processed: 414 average time/residue: 0.4664 time to fit residues: 330.0474 Evaluate side-chains 314 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 245 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 493 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 0.9980 chunk 324 optimal weight: 40.0000 chunk 223 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 289 optimal weight: 0.8980 chunk 432 optimal weight: 50.0000 chunk 458 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 410 optimal weight: 50.0000 chunk 123 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 30 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 121 ASN C 450 ASN D 417 HIS H 101 GLN H 325 GLN H 580 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40543 Z= 0.281 Angle : 0.655 10.340 55114 Z= 0.325 Chirality : 0.047 0.570 6353 Planarity : 0.004 0.061 6984 Dihedral : 6.720 59.283 7330 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 2.90 % Allowed : 14.46 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4720 helix: 0.27 (0.13), residues: 1672 sheet: -1.02 (0.18), residues: 736 loop : -2.28 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 271 HIS 0.007 0.001 HIS A 505 PHE 0.044 0.002 PHE D 314 TYR 0.021 0.001 TYR C1067 ARG 0.011 0.000 ARG B 983 *********************** 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 401 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 279 time to evaluate : 4.578 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 281 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: A 523 THR cc_start: 0.2051 (OUTLIER) cc_final: 0.1842 (m) REVERT: A 767 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 967 SER cc_start: 0.6667 (m) cc_final: 0.6451 (t) REVERT: A 1010 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.5724 (tp40) REVERT: B 523 THR cc_start: 0.5022 (OUTLIER) cc_final: 0.4822 (m) REVERT: B 568 ASP cc_start: 0.6583 (p0) cc_final: 0.6304 (p0) REVERT: C 398 ASP cc_start: 0.2869 (OUTLIER) cc_final: 0.1044 (t0) REVERT: D 190 MET cc_start: -0.0069 (tmm) cc_final: -0.1049 (ttp) REVERT: D 213 ASP cc_start: 0.1968 (t0) cc_final: 0.1632 (m-30) REVERT: D 438 PHE cc_start: 0.2078 (t80) cc_final: -0.0227 (m-80) REVERT: D 557 MET cc_start: 0.0522 (OUTLIER) cc_final: 0.0299 (ppp) REVERT: F 351 LEU cc_start: 0.0406 (OUTLIER) cc_final: 0.0047 (mp) REVERT: F 459 TRP cc_start: 0.0287 (t60) cc_final: -0.0306 (t60) REVERT: F 579 MET cc_start: -0.0034 (pmm) cc_final: -0.0866 (ttp) REVERT: H 123 MET cc_start: -0.1056 (OUTLIER) cc_final: -0.1306 (ptp) REVERT: H 383 MET cc_start: 0.1839 (mtp) cc_final: 0.0642 (tmm) outliers start: 122 outliers final: 70 residues processed: 377 average time/residue: 0.4661 time to fit residues: 307.2131 Evaluate side-chains 326 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 247 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 510 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 chunk 189 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 316 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 411 optimal weight: 40.0000 chunk 115 optimal weight: 10.0000 overall best weight: 6.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 115 GLN A 207 HIS A 804 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1083 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 675 GLN C 935 GLN C1005 GLN F 96 GLN F 330 ASN F 505 HIS H 101 GLN ** H 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 40543 Z= 0.669 Angle : 0.877 16.648 55114 Z= 0.438 Chirality : 0.056 0.983 6353 Planarity : 0.006 0.093 6984 Dihedral : 7.382 59.805 7324 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.39 % Favored : 92.31 % Rotamer: Outliers : 4.13 % Allowed : 14.95 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.11), residues: 4720 helix: -0.07 (0.13), residues: 1674 sheet: -1.36 (0.18), residues: 703 loop : -2.35 (0.11), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1102 HIS 0.011 0.002 HIS B1058 PHE 0.050 0.003 PHE A 275 TYR 0.030 0.002 TYR B 707 ARG 0.008 0.001 ARG C 905 *********************** 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 453 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 279 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: A 379 CYS cc_start: 0.2996 (OUTLIER) cc_final: 0.2515 (p) REVERT: A 767 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 950 ASP cc_start: 0.8298 (m-30) cc_final: 0.7880 (m-30) REVERT: A 967 SER cc_start: 0.7312 (m) cc_final: 0.7040 (t) REVERT: A 1010 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6001 (tp40) REVERT: A 1111 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7755 (pp20) REVERT: B 568 ASP cc_start: 0.6794 (p0) cc_final: 0.6554 (p0) REVERT: B 900 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (mtp) REVERT: B 1014 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: C 266 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: C 398 ASP cc_start: 0.3413 (OUTLIER) cc_final: 0.0939 (t0) REVERT: C 895 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: C 917 TYR cc_start: 0.8583 (m-80) cc_final: 0.8332 (m-80) REVERT: D 190 MET cc_start: 0.0524 (tmm) cc_final: -0.0462 (ttp) REVERT: D 207 TYR cc_start: 0.1929 (OUTLIER) cc_final: 0.1009 (m-80) REVERT: D 213 ASP cc_start: 0.2106 (t0) cc_final: 0.1623 (m-30) REVERT: D 270 MET cc_start: 0.2715 (ttm) cc_final: 0.2216 (ttm) REVERT: D 480 MET cc_start: 0.0399 (mtt) cc_final: -0.0461 (ptt) REVERT: D 557 MET cc_start: 0.0596 (OUTLIER) cc_final: 0.0389 (ppp) REVERT: D 571 GLU cc_start: 0.3319 (OUTLIER) cc_final: 0.2914 (pt0) REVERT: F 150 GLU cc_start: 0.1481 (OUTLIER) cc_final: 0.0261 (pt0) REVERT: F 323 MET cc_start: -0.1816 (tpt) cc_final: -0.2422 (ppp) REVERT: F 351 LEU cc_start: 0.0688 (OUTLIER) cc_final: 0.0272 (mp) REVERT: F 459 TRP cc_start: 0.0289 (t60) cc_final: -0.0083 (t60) REVERT: F 579 MET cc_start: -0.0155 (pmm) cc_final: -0.0980 (ttp) REVERT: H 166 GLU cc_start: 0.4157 (tp30) cc_final: 0.3167 (tt0) REVERT: H 270 MET cc_start: 0.1247 (tpp) cc_final: 0.0720 (tpp) REVERT: H 383 MET cc_start: 0.1545 (mtp) cc_final: 0.0295 (tmm) outliers start: 174 outliers final: 114 residues processed: 425 average time/residue: 0.4542 time to fit residues: 336.5504 Evaluate side-chains 378 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 249 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 761 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 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 510 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 1.9990 chunk 412 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 269 optimal weight: 0.0470 chunk 113 optimal weight: 5.9990 chunk 458 optimal weight: 40.0000 chunk 380 optimal weight: 40.0000 chunk 212 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 240 optimal weight: 50.0000 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN H 101 GLN ** H 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 40543 Z= 0.312 Angle : 0.675 13.678 55114 Z= 0.332 Chirality : 0.047 0.487 6353 Planarity : 0.004 0.058 6984 Dihedral : 6.853 59.112 7324 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.99 % Allowed : 16.95 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4720 helix: 0.29 (0.13), residues: 1680 sheet: -1.28 (0.18), residues: 729 loop : -2.20 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 459 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE D 314 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG C 905 *********************** 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 380 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 254 time to evaluate : 4.644 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 379 CYS cc_start: 0.2945 (OUTLIER) cc_final: 0.2623 (p) REVERT: A 767 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 950 ASP cc_start: 0.8109 (m-30) cc_final: 0.7804 (m-30) REVERT: A 1010 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5687 (tp40) REVERT: B 1014 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7730 (ttm170) REVERT: C 398 ASP cc_start: 0.3169 (OUTLIER) cc_final: 0.1272 (t0) REVERT: D 190 MET cc_start: 0.0503 (tmm) cc_final: -0.0248 (ttp) REVERT: D 213 ASP cc_start: 0.1727 (t0) cc_final: 0.1452 (m-30) REVERT: D 376 MET cc_start: 0.2345 (tpp) cc_final: 0.2024 (tpt) REVERT: D 383 MET cc_start: 0.3469 (ptp) cc_final: 0.2721 (ppp) REVERT: D 480 MET cc_start: 0.0316 (mtt) cc_final: -0.0440 (ptp) REVERT: D 557 MET cc_start: 0.0620 (OUTLIER) cc_final: 0.0420 (ppp) REVERT: D 571 GLU cc_start: 0.3199 (OUTLIER) cc_final: 0.2860 (pt0) REVERT: F 150 GLU cc_start: 0.1367 (OUTLIER) cc_final: 0.0406 (pt0) REVERT: F 351 LEU cc_start: 0.0848 (OUTLIER) cc_final: 0.0424 (mp) REVERT: F 459 TRP cc_start: 0.0140 (t60) cc_final: -0.0070 (t60) REVERT: H 166 GLU cc_start: 0.4271 (tp30) cc_final: 0.3246 (tt0) REVERT: H 383 MET cc_start: 0.1484 (mtp) cc_final: 0.0251 (tmm) outliers start: 126 outliers final: 88 residues processed: 356 average time/residue: 0.4478 time to fit residues: 278.1217 Evaluate side-chains 339 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 242 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 510 TYR 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: 0.9980 chunk 261 optimal weight: 0.1980 chunk 334 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 386 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 907 ASN C 913 GLN H 101 GLN H 210 ASN H 325 GLN H 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40543 Z= 0.197 Angle : 0.611 11.190 55114 Z= 0.298 Chirality : 0.046 0.872 6353 Planarity : 0.004 0.048 6984 Dihedral : 6.342 59.533 7324 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.51 % Favored : 94.22 % Rotamer: Outliers : 2.71 % Allowed : 17.37 % Favored : 79.92 % 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: -1.28 (0.12), residues: 4720 helix: 0.67 (0.13), residues: 1675 sheet: -0.98 (0.18), residues: 740 loop : -2.01 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 459 HIS 0.004 0.001 HIS A 954 PHE 0.028 0.001 PHE D 314 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG B 983 *********************** 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 383 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 269 time to evaluate : 4.381 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 379 CYS cc_start: 0.3042 (OUTLIER) cc_final: 0.2564 (p) REVERT: A 950 ASP cc_start: 0.7918 (m-30) cc_final: 0.7648 (m-30) REVERT: A 1010 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.5689 (tp40) REVERT: A 1119 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8702 (p0) REVERT: C 398 ASP cc_start: 0.2945 (OUTLIER) cc_final: 0.1171 (t0) REVERT: D 190 MET cc_start: 0.0558 (tmm) cc_final: -0.0999 (ttp) REVERT: D 207 TYR cc_start: 0.1543 (OUTLIER) cc_final: 0.0934 (m-80) REVERT: D 376 MET cc_start: 0.2356 (tpp) cc_final: 0.2075 (tpt) REVERT: D 383 MET cc_start: 0.3586 (ptp) cc_final: 0.2931 (ppp) REVERT: D 480 MET cc_start: 0.0144 (mtt) cc_final: -0.0562 (ptp) REVERT: D 571 GLU cc_start: 0.3061 (OUTLIER) cc_final: 0.2779 (pt0) REVERT: F 150 GLU cc_start: 0.1271 (OUTLIER) cc_final: 0.0684 (pt0) REVERT: F 323 MET cc_start: 0.0362 (OUTLIER) cc_final: -0.0352 (ttm) REVERT: F 351 LEU cc_start: 0.1307 (OUTLIER) cc_final: 0.0749 (mp) REVERT: F 474 MET cc_start: -0.2127 (mmp) cc_final: -0.3119 (ttm) REVERT: F 579 MET cc_start: -0.0378 (pmm) cc_final: -0.1239 (ttp) REVERT: H 166 GLU cc_start: 0.4230 (tp30) cc_final: 0.3261 (tt0) REVERT: H 383 MET cc_start: 0.1530 (mtp) cc_final: 0.0299 (tmm) outliers start: 114 outliers final: 74 residues processed: 357 average time/residue: 0.4912 time to fit residues: 304.9941 Evaluate side-chains 325 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 242 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN 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 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 510 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 359 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 40543 Z= 0.295 Angle : 0.645 11.201 55114 Z= 0.317 Chirality : 0.047 0.655 6353 Planarity : 0.004 0.053 6984 Dihedral : 6.298 59.537 7324 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.25 % Favored : 93.52 % Rotamer: Outliers : 2.87 % Allowed : 17.66 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4720 helix: 0.68 (0.13), residues: 1677 sheet: -0.98 (0.19), residues: 714 loop : -1.98 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 168 HIS 0.005 0.001 HIS C1064 PHE 0.025 0.002 PHE D 314 TYR 0.033 0.001 TYR C 674 ARG 0.007 0.000 ARG B 983 *********************** 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 365 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 244 time to evaluate : 4.565 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 379 CYS cc_start: 0.3052 (OUTLIER) cc_final: 0.2537 (p) REVERT: A 767 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 950 ASP cc_start: 0.8053 (m-30) cc_final: 0.7797 (m-30) REVERT: A 1010 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.5712 (tp40) REVERT: B 926 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: C 398 ASP cc_start: 0.2968 (OUTLIER) cc_final: 0.0994 (t0) REVERT: C 1002 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7193 (tp-100) REVERT: D 145 GLU cc_start: -0.0350 (mp0) cc_final: -0.0614 (mt-10) REVERT: D 190 MET cc_start: 0.0165 (tmm) cc_final: -0.1046 (ttp) REVERT: D 207 TYR cc_start: 0.1480 (OUTLIER) cc_final: 0.0883 (m-80) REVERT: D 376 MET cc_start: 0.2410 (tpp) cc_final: 0.2150 (tpt) REVERT: D 383 MET cc_start: 0.3878 (ptp) cc_final: 0.2630 (ppp) REVERT: D 474 MET cc_start: 0.2084 (mpp) cc_final: 0.1433 (mtp) REVERT: D 571 GLU cc_start: 0.3131 (OUTLIER) cc_final: 0.2825 (pt0) REVERT: F 150 GLU cc_start: 0.0982 (OUTLIER) cc_final: 0.0392 (pt0) REVERT: F 351 LEU cc_start: 0.1218 (OUTLIER) cc_final: 0.0714 (mp) REVERT: F 459 TRP cc_start: 0.0049 (t60) cc_final: -0.0342 (t60) REVERT: F 474 MET cc_start: -0.2045 (mmp) cc_final: -0.3076 (ttm) REVERT: F 579 MET cc_start: -0.0267 (pmm) cc_final: -0.1053 (ttp) REVERT: H 166 GLU cc_start: 0.4351 (tp30) cc_final: 0.3347 (tt0) REVERT: H 383 MET cc_start: 0.1541 (mtp) cc_final: 0.0322 (tmm) outliers start: 121 outliers final: 90 residues processed: 346 average time/residue: 0.4539 time to fit residues: 273.4491 Evaluate side-chains 335 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 235 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 756 TYR 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 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 510 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 40.0000 chunk 437 optimal weight: 8.9990 chunk 399 optimal weight: 10.0000 chunk 425 optimal weight: 50.0000 chunk 256 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 334 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 402 optimal weight: 40.0000 chunk 424 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 370 ASN B 394 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN D 340 GLN H 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.7300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 40543 Z= 0.596 Angle : 0.822 16.997 55114 Z= 0.410 Chirality : 0.053 0.712 6353 Planarity : 0.005 0.082 6984 Dihedral : 7.039 59.325 7324 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.75 % Favored : 91.99 % Rotamer: Outliers : 3.13 % Allowed : 17.78 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4720 helix: 0.27 (0.13), residues: 1673 sheet: -1.26 (0.18), residues: 737 loop : -2.18 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 459 HIS 0.011 0.001 HIS B1048 PHE 0.046 0.003 PHE A 275 TYR 0.035 0.002 TYR B 707 ARG 0.009 0.001 ARG C1107 *********************** 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 384 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 252 time to evaluate : 4.801 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 379 CYS cc_start: 0.2685 (OUTLIER) cc_final: 0.2324 (p) REVERT: A 767 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8049 (mm) REVERT: A 1010 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.5718 (tp40) REVERT: B 569 ILE cc_start: 0.8734 (mp) cc_final: 0.8531 (mt) REVERT: B 926 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: B 1005 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7789 (tp40) REVERT: B 1014 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: C 398 ASP cc_start: 0.3241 (OUTLIER) cc_final: 0.0804 (t0) REVERT: C 917 TYR cc_start: 0.8529 (m-80) cc_final: 0.8218 (m-80) REVERT: C 1002 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7346 (tp-100) REVERT: D 190 MET cc_start: -0.0176 (tmm) cc_final: -0.1222 (ttp) REVERT: D 207 TYR cc_start: 0.1578 (OUTLIER) cc_final: 0.1094 (m-80) REVERT: D 376 MET cc_start: 0.2527 (tpp) cc_final: 0.2294 (tpt) REVERT: D 383 MET cc_start: 0.3771 (ptp) cc_final: 0.2841 (ppp) REVERT: D 474 MET cc_start: 0.2196 (mpp) cc_final: 0.1520 (mtt) REVERT: D 480 MET cc_start: 0.0211 (mtt) cc_final: -0.0463 (mtm) REVERT: D 571 GLU cc_start: 0.3327 (OUTLIER) cc_final: 0.2895 (pt0) REVERT: F 459 TRP cc_start: -0.0159 (t60) cc_final: -0.0608 (t60) REVERT: F 579 MET cc_start: -0.0244 (pmm) cc_final: -0.1036 (ttp) REVERT: H 383 MET cc_start: 0.1514 (mtp) cc_final: 0.0290 (tmm) outliers start: 132 outliers final: 98 residues processed: 369 average time/residue: 0.4564 time to fit residues: 294.4023 Evaluate side-chains 345 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 237 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 756 TYR 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 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 510 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.9980 chunk 450 optimal weight: 50.0000 chunk 274 optimal weight: 0.7980 chunk 213 optimal weight: 20.0000 chunk 312 optimal weight: 40.0000 chunk 472 optimal weight: 6.9990 chunk 434 optimal weight: 50.0000 chunk 376 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 290 optimal weight: 0.2980 chunk 230 optimal weight: 3.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 954 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN D 572 ASN H 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40543 Z= 0.296 Angle : 0.667 12.867 55114 Z= 0.328 Chirality : 0.047 0.556 6353 Planarity : 0.004 0.053 6984 Dihedral : 6.707 59.919 7324 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.04 % Favored : 93.73 % Rotamer: Outliers : 2.49 % Allowed : 18.30 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4720 helix: 0.54 (0.13), residues: 1685 sheet: -0.99 (0.19), residues: 676 loop : -2.09 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 459 HIS 0.006 0.001 HIS F 535 PHE 0.026 0.002 PHE A 275 TYR 0.021 0.001 TYR C1067 ARG 0.010 0.000 ARG B 983 ********************** 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 343 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 238 time to evaluate : 4.302 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 379 CYS cc_start: 0.2669 (OUTLIER) cc_final: 0.2352 (p) REVERT: A 767 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8004 (mm) REVERT: A 950 ASP cc_start: 0.8176 (m-30) cc_final: 0.7843 (m-30) REVERT: A 1010 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5680 (tp40) REVERT: B 578 ASP cc_start: 0.6354 (t70) cc_final: 0.5920 (t0) REVERT: B 926 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: C 398 ASP cc_start: 0.3260 (OUTLIER) cc_final: 0.0911 (t0) REVERT: C 1002 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7141 (tp-100) REVERT: D 145 GLU cc_start: -0.0480 (mp0) cc_final: -0.0742 (mt-10) REVERT: D 190 MET cc_start: -0.0143 (tmm) cc_final: -0.1191 (ttp) REVERT: D 207 TYR cc_start: 0.1485 (OUTLIER) cc_final: 0.1026 (m-80) REVERT: D 376 MET cc_start: 0.2480 (tpp) cc_final: 0.2271 (tpt) REVERT: D 383 MET cc_start: 0.3653 (ptp) cc_final: 0.2696 (ppp) REVERT: D 474 MET cc_start: 0.2251 (mpp) cc_final: 0.1564 (mtt) REVERT: D 480 MET cc_start: -0.0004 (mtt) cc_final: -0.0298 (mtm) REVERT: D 571 GLU cc_start: 0.3443 (OUTLIER) cc_final: 0.2960 (pt0) REVERT: F 459 TRP cc_start: 0.0076 (t60) cc_final: -0.0342 (t60) REVERT: F 579 MET cc_start: -0.0279 (pmm) cc_final: -0.1060 (ttp) REVERT: H 166 GLU cc_start: 0.4415 (tp30) cc_final: 0.3757 (tm-30) REVERT: H 383 MET cc_start: 0.1590 (mtp) cc_final: 0.0372 (tmm) outliers start: 105 outliers final: 91 residues processed: 329 average time/residue: 0.4719 time to fit residues: 269.8127 Evaluate side-chains 331 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 232 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 207 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 50.0000 chunk 400 optimal weight: 50.0000 chunk 115 optimal weight: 0.6980 chunk 346 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 376 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 0.2980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.255774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.205888 restraints weight = 60944.078| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 4.18 r_work: 0.3440 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 40543 Z= 0.177 Angle : 0.607 11.451 55114 Z= 0.296 Chirality : 0.045 0.415 6353 Planarity : 0.004 0.054 6984 Dihedral : 6.230 59.889 7324 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.51 % Favored : 94.26 % Rotamer: Outliers : 2.04 % Allowed : 18.92 % Favored : 79.04 % 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: -1.08 (0.12), residues: 4720 helix: 0.83 (0.13), residues: 1689 sheet: -0.76 (0.19), residues: 678 loop : -1.92 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 459 HIS 0.004 0.001 HIS F 535 PHE 0.029 0.001 PHE A 55 TYR 0.021 0.001 TYR A1067 ARG 0.010 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8417.15 seconds wall clock time: 155 minutes 36.94 seconds (9336.94 seconds total)