Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 02:58:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgf_11204/08_2023/6zgf_11204.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.072 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 117 5.16 5 C 16638 2.51 5 N 4218 2.21 5 O 5190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 986": "OE1" <-> "OE2" Residue "B GLU 1027": "OE1" <-> "OE2" Residue "B PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 776": "OE1" <-> "OE2" Residue "C PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 914": "OE1" <-> "OE2" Residue "C PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 986": "OE1" <-> "OE2" Residue "C GLU 1027": "OE1" <-> "OE2" Residue "C PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 26163 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 Chain: "B" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 Chain: "C" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1060, 8290 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8470 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 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 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 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 chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "W" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 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 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 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 chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 chiralities: 9 Time building chain proxies: 23.29, per 1000 atoms: 0.89 Number of scatterers: 26163 At special positions: 0 Unit cell: (140.14, 135.828, 175.714, 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 117 16.00 O 5190 8.00 N 4218 7.00 C 16638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 2 " " NAG R 1 " - " FUC R 3 " " NAG W 1 " - " FUC W 2 " " NAG b 1 " - " FUC b 3 " " NAG g 1 " - " FUC g 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG A1315 " - " ASN A 343 " " NAG A1316 " - " ASN A 616 " " NAG A1317 " - " ASN A 705 " " NAG A1321 " - " ASN A1070 " " NAG A1328 " - " ASN A 603 " " NAG A1331 " - " ASN A 657 " " NAG B1301 " - " ASN B 17 " " NAG B1304 " - " ASN B 61 " " NAG B1311 " - " ASN B 282 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B 616 " " NAG B1317 " - " ASN B 705 " " NAG B1321 " - " ASN B1070 " " NAG B1328 " - " ASN B 603 " " NAG B1331 " - " ASN B 657 " " NAG C1301 " - " ASN C 17 " " NAG C1304 " - " ASN C 61 " " NAG C1311 " - " ASN C 282 " " NAG C1315 " - " ASN C 343 " " NAG C1316 " - " ASN C 616 " " NAG C1317 " - " ASN C 705 " " NAG C1321 " - " ASN C1070 " " NAG C1328 " - " ASN C 603 " " NAG C1331 " - " ASN C 657 " " NAG D 1 " - " ASN A 30 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 713 " " NAG J 1 " - " ASN A1094 " " NAG K 1 " - " ASN A1130 " " NAG L 1 " - " ASN A 797 " " NAG M 1 " - " ASN A 370 " " NAG N 1 " - " ASN B 30 " " NAG O 1 " - " ASN B 122 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 713 " " NAG T 1 " - " ASN B1094 " " NAG U 1 " - " ASN B1130 " " NAG V 1 " - " ASN B 797 " " NAG W 1 " - " ASN B 370 " " NAG X 1 " - " ASN C 30 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN C 165 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 331 " " NAG c 1 " - " ASN C 713 " " NAG d 1 " - " ASN C1094 " " NAG e 1 " - " ASN C1130 " " NAG f 1 " - " ASN C 797 " " NAG g 1 " - " ASN C 370 " Time building additional restraints: 11.24 Conformation dependent library (CDL) restraints added in 8.0 seconds 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 24.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.544A pdb=" N ALA A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL A 635 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 636' Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 756 through 768 removed outlier: 3.774A pdb=" N ASN A 760 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 779 removed outlier: 3.989A pdb=" N LYS A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 811 Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.693A pdb=" N ASN A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 862 through 877 removed outlier: 3.832A pdb=" N ALA A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 869 " --> pdb=" O MET A 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.871A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 886 " --> pdb=" O THR A 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 886' Processing helix chain 'A' and resid 893 through 904 removed outlier: 3.943A pdb=" N TYR A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 removed outlier: 3.931A pdb=" N LYS A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA A 940 " --> pdb=" O THR A 937 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 941 " --> pdb=" O ALA A 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 937 through 941' Processing helix chain 'A' and resid 945 through 961 removed outlier: 3.885A pdb=" N GLN A 950 " --> pdb=" O ASP A 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 994 " --> pdb=" O ASP A 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 999 " --> pdb=" O GLY A 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1000 " --> pdb=" O ARG A 996 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.544A pdb=" N ALA B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 636' Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 756 through 768 removed outlier: 3.774A pdb=" N ASN B 760 " --> pdb=" O CYS B 756 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 779 removed outlier: 3.990A pdb=" N LYS B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 811 Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.692A pdb=" N ASN B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU B 837 " --> pdb=" O TYR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 862 through 877 removed outlier: 3.831A pdb=" N ALA B 867 " --> pdb=" O ASP B 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 869 " --> pdb=" O MET B 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.870A pdb=" N GLY B 885 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 886 " --> pdb=" O THR B 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 882 through 886' Processing helix chain 'B' and resid 893 through 904 removed outlier: 3.943A pdb=" N TYR B 900 " --> pdb=" O MET B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 936 " --> pdb=" O ASP B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA B 940 " --> pdb=" O THR B 937 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 941 " --> pdb=" O ALA B 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 937 through 941' Processing helix chain 'B' and resid 945 through 961 removed outlier: 3.885A pdb=" N GLN B 950 " --> pdb=" O ASP B 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 951 " --> pdb=" O VAL B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 955 " --> pdb=" O ASN B 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 994 " --> pdb=" O ASP B 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 998 " --> pdb=" O THR B 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 999 " --> pdb=" O GLY B 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B1000 " --> pdb=" O ARG B 996 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B1012 " --> pdb=" O LEU B1008 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B1013 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.557A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.174A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.977A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.244A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.543A pdb=" N ALA C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.728A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 636' Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 756 through 768 removed outlier: 3.775A pdb=" N ASN C 760 " --> pdb=" O CYS C 756 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 762 " --> pdb=" O GLN C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 779 removed outlier: 3.990A pdb=" N LYS C 772 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 811 Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.693A pdb=" N ASN C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 837 removed outlier: 3.638A pdb=" N LEU C 837 " --> pdb=" O TYR C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 851 Processing helix chain 'C' and resid 862 through 877 removed outlier: 3.831A pdb=" N ALA C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 869 " --> pdb=" O MET C 865 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 886 removed outlier: 3.870A pdb=" N GLY C 885 " --> pdb=" O TRP C 882 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 886 " --> pdb=" O THR C 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 882 through 886' Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.942A pdb=" N TYR C 900 " --> pdb=" O MET C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.088A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 removed outlier: 3.931A pdb=" N LYS C 929 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 936 " --> pdb=" O ASP C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 941 removed outlier: 3.572A pdb=" N ALA C 940 " --> pdb=" O THR C 937 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 941 " --> pdb=" O ALA C 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 937 through 941' Processing helix chain 'C' and resid 945 through 961 removed outlier: 3.886A pdb=" N GLN C 950 " --> pdb=" O ASP C 946 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 951 " --> pdb=" O VAL C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.596A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 994 " --> pdb=" O ASP C 990 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 998 " --> pdb=" O THR C 994 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 999 " --> pdb=" O GLY C 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C1012 " --> pdb=" O LEU C1008 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C1013 " --> pdb=" O ILE C1009 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.164A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.346A pdb=" N ASP A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASN A 542 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.084A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.912A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 697 through 699 Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.845A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A1098 " --> pdb=" O GLN A1109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN A1109 " --> pdb=" O TRP A1098 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A1100 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1107 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A1102 " --> pdb=" O PHE A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET A1046 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.691A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.642A pdb=" N ILE A 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.165A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.345A pdb=" N ASP B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN B 542 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.085A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.911A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 697 through 699 Processing sheet with id=AD3, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.846A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP B1098 " --> pdb=" O GLN B1109 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN B1109 " --> pdb=" O TRP B1098 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B1100 " --> pdb=" O GLU B1107 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B1107 " --> pdb=" O VAL B1100 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B1102 " --> pdb=" O PHE B1105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET B1046 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.690A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.592A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N SER C 221 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG C 34 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N LEU C 223 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.894A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.165A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.387A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.816A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.346A pdb=" N ASP C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN C 542 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 595 through 598 removed outlier: 3.912A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.373A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.844A pdb=" N THR C1072 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP C1098 " --> pdb=" O GLN C1109 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C1109 " --> pdb=" O TRP C1098 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C1100 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU C1107 " --> pdb=" O VAL C1100 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN C1102 " --> pdb=" O PHE C1105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 714 through 724 removed outlier: 3.624A pdb=" N MET C1046 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.691A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1116 through 1118 853 hydrogen bonds defined for protein. 2307 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: 12.14 Time building geometry restraints manager: 12.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4229 1.32 - 1.44: 7573 1.44 - 1.57: 14793 1.57 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 26739 Sorted by residual: bond pdb=" C ASN B 713 " pdb=" O ASN B 713 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" C ASN A 713 " pdb=" O ASN A 713 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" C ASN C 713 " pdb=" O ASN C 713 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" N ILE C 790 " pdb=" CA ILE C 790 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.47e+00 bond pdb=" N ILE A 790 " pdb=" CA ILE A 790 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.35e+00 ... (remaining 26734 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.41: 821 106.41 - 113.32: 14825 113.32 - 120.24: 9477 120.24 - 127.16: 11030 127.16 - 134.07: 246 Bond angle restraints: 36399 Sorted by residual: angle pdb=" C ASN C 370 " pdb=" CA ASN C 370 " pdb=" CB ASN C 370 " ideal model delta sigma weight residual 110.56 103.01 7.55 1.69e+00 3.50e-01 2.00e+01 angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 110.56 103.02 7.54 1.69e+00 3.50e-01 1.99e+01 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 110.56 103.03 7.53 1.69e+00 3.50e-01 1.98e+01 angle pdb=" CA ASN B 331 " pdb=" C ASN B 331 " pdb=" O ASN B 331 " ideal model delta sigma weight residual 122.37 117.26 5.11 1.15e+00 7.56e-01 1.98e+01 angle pdb=" CA ASN C 331 " pdb=" C ASN C 331 " pdb=" O ASN C 331 " ideal model delta sigma weight residual 122.37 117.31 5.06 1.15e+00 7.56e-01 1.94e+01 ... (remaining 36394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14047 17.87 - 35.74: 941 35.74 - 53.61: 165 53.61 - 71.48: 42 71.48 - 89.35: 18 Dihedral angle restraints: 15213 sinusoidal: 5934 harmonic: 9279 Sorted by residual: 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 -86.00 -135.26 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.26 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.21 49.21 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4401 0.329 - 0.658: 9 0.658 - 0.987: 0 0.987 - 1.317: 0 1.317 - 1.646: 3 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.42e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.33e+02 ... (remaining 4410 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG R 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG H 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG b 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.118 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 443 2.67 - 3.23: 22961 3.23 - 3.78: 35540 3.78 - 4.34: 50563 4.34 - 4.90: 87994 Nonbonded interactions: 197501 Sorted by model distance: nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.113 2.440 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.113 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.214 2.440 ... (remaining 197496 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 14 through 156 or resid 158 through 1140 or resid 1301 thr \ ough 1331)) selection = (chain 'B' and (resid 14 through 156 or resid 158 through 1140 or resid 1301 thr \ ough 1331)) selection = (chain 'C' and (resid 14 through 156 or resid 158 through 1140 or resid 1301 thr \ ough 1331)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.020 Extract box with map and model: 15.240 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 86.640 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.210 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.041 26739 Z= 0.453 Angle : 0.860 7.894 36399 Z= 0.472 Chirality : 0.074 1.646 4413 Planarity : 0.021 0.284 4572 Dihedral : 12.803 89.347 9102 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.76 % 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: -2.49 (0.14), residues: 3129 helix: -1.97 (0.19), residues: 675 sheet: 0.22 (0.20), residues: 714 loop : -2.43 (0.13), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 314 average time/residue: 0.3917 time to fit residues: 194.6181 Evaluate side-chains 199 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 3.269 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2413 time to fit residues: 9.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 0.0370 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26739 Z= 0.195 Angle : 0.653 10.898 36399 Z= 0.322 Chirality : 0.048 0.425 4413 Planarity : 0.004 0.059 4572 Dihedral : 5.452 38.348 3408 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.14 (0.14), residues: 3129 helix: -1.46 (0.20), residues: 690 sheet: 0.16 (0.19), residues: 756 loop : -2.23 (0.14), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 240 average time/residue: 0.3812 time to fit residues: 147.4370 Evaluate side-chains 207 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2533 time to fit residues: 17.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 26739 Z= 0.229 Angle : 0.630 9.566 36399 Z= 0.313 Chirality : 0.047 0.406 4413 Planarity : 0.004 0.057 4572 Dihedral : 5.348 43.577 3408 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3129 helix: -1.20 (0.20), residues: 690 sheet: 0.20 (0.19), residues: 756 loop : -2.14 (0.14), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 3.227 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 218 average time/residue: 0.4107 time to fit residues: 143.4489 Evaluate side-chains 189 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3137 time to fit residues: 12.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN B 474 GLN C1001 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 26739 Z= 0.288 Angle : 0.633 9.667 36399 Z= 0.318 Chirality : 0.048 0.399 4413 Planarity : 0.004 0.059 4572 Dihedral : 5.379 42.648 3408 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.96 (0.14), residues: 3129 helix: -1.16 (0.20), residues: 690 sheet: 0.21 (0.19), residues: 756 loop : -2.16 (0.14), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 2.963 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 19 residues processed: 193 average time/residue: 0.3813 time to fit residues: 119.2407 Evaluate side-chains 189 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2394 time to fit residues: 12.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 3.9990 chunk 174 optimal weight: 0.0870 chunk 4 optimal weight: 0.2980 chunk 228 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 0.0870 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 474 GLN C1001 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 26739 Z= 0.134 Angle : 0.544 9.508 36399 Z= 0.272 Chirality : 0.044 0.352 4413 Planarity : 0.004 0.050 4572 Dihedral : 4.903 38.657 3408 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3129 helix: -0.83 (0.20), residues: 687 sheet: 0.42 (0.20), residues: 735 loop : -2.02 (0.14), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 205 average time/residue: 0.3965 time to fit residues: 131.2413 Evaluate side-chains 185 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2342 time to fit residues: 6.6178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN B 474 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 26739 Z= 0.170 Angle : 0.557 9.573 36399 Z= 0.279 Chirality : 0.045 0.395 4413 Planarity : 0.004 0.049 4572 Dihedral : 4.844 37.616 3408 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 3129 helix: -0.68 (0.20), residues: 687 sheet: 0.29 (0.20), residues: 726 loop : -1.96 (0.14), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 195 average time/residue: 0.3899 time to fit residues: 122.8427 Evaluate side-chains 183 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2836 time to fit residues: 7.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 141 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 GLN B 474 GLN C 998 GLN C1115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 26739 Z= 0.157 Angle : 0.545 9.558 36399 Z= 0.274 Chirality : 0.044 0.348 4413 Planarity : 0.004 0.048 4572 Dihedral : 4.776 41.904 3408 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.50 (0.15), residues: 3129 helix: -0.55 (0.20), residues: 687 sheet: 0.48 (0.20), residues: 705 loop : -1.89 (0.14), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 194 average time/residue: 0.4029 time to fit residues: 126.0080 Evaluate side-chains 174 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2358 time to fit residues: 6.8763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 151 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 240 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C1115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 26739 Z= 0.163 Angle : 0.548 9.570 36399 Z= 0.275 Chirality : 0.045 0.366 4413 Planarity : 0.004 0.048 4572 Dihedral : 4.734 39.811 3408 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.49 (0.15), residues: 3129 helix: -0.48 (0.20), residues: 687 sheet: 0.33 (0.20), residues: 726 loop : -1.87 (0.14), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 188 average time/residue: 0.3943 time to fit residues: 120.3847 Evaluate side-chains 179 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 3.230 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2569 time to fit residues: 6.2640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.5980 chunk 293 optimal weight: 0.7980 chunk 267 optimal weight: 0.0670 chunk 285 optimal weight: 0.0270 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 0.4980 chunk 270 optimal weight: 0.5980 chunk 284 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 474 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 26739 Z= 0.141 Angle : 0.535 9.715 36399 Z= 0.269 Chirality : 0.044 0.345 4413 Planarity : 0.004 0.048 4572 Dihedral : 4.683 44.376 3408 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.15), residues: 3129 helix: -0.35 (0.20), residues: 687 sheet: 0.35 (0.20), residues: 726 loop : -1.83 (0.14), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 192 average time/residue: 0.3853 time to fit residues: 120.1182 Evaluate side-chains 182 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 3.017 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2549 time to fit residues: 6.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.2980 chunk 302 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C1115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 26739 Z= 0.179 Angle : 0.552 9.599 36399 Z= 0.278 Chirality : 0.045 0.347 4413 Planarity : 0.004 0.049 4572 Dihedral : 4.734 43.462 3408 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 3129 helix: -0.35 (0.20), residues: 684 sheet: 0.35 (0.20), residues: 726 loop : -1.81 (0.14), residues: 1719 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 180 average time/residue: 0.4103 time to fit residues: 120.1918 Evaluate side-chains 178 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4766 time to fit residues: 5.4903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.7980 chunk 268 optimal weight: 0.0770 chunk 77 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 474 GLN C1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108782 restraints weight = 47790.303| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.87 r_work: 0.3012 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 26739 Z= 0.144 Angle : 0.533 9.549 36399 Z= 0.269 Chirality : 0.044 0.338 4413 Planarity : 0.004 0.048 4572 Dihedral : 4.659 42.426 3408 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.31 (0.15), residues: 3129 helix: -0.22 (0.21), residues: 684 sheet: 0.37 (0.20), residues: 726 loop : -1.77 (0.14), residues: 1719 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.49 seconds wall clock time: 89 minutes 10.85 seconds (5350.85 seconds total)