Starting phenix.real_space_refine on Sun Apr 14 07:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2024/7l6o_23124_trim.pdb" } resolution = 3.9 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= 0.013 sd= 0.065 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: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 9717 2.51 5 N 2514 2.21 5 O 3336 1.98 5 H 13598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 32": "OE1" <-> "OE2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 83": "OE1" <-> "OE2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a ASP 99": "OD1" <-> "OD2" Residue "a GLU 169": "OE1" <-> "OE2" Residue "a TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "a GLU 293": "OE1" <-> "OE2" Residue "a TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 325": "OD1" <-> "OD2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 612": "OD1" <-> "OD2" Residue "b GLU 622": "OE1" <-> "OE2" Residue "b GLU 636": "OE1" <-> "OE2" Residue "c PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 83": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "c GLU 335": "OE1" <-> "OE2" Residue "c PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 464": "OE1" <-> "OE2" Residue "d PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ASP 612": "OD1" <-> "OD2" Residue "d GLU 636": "OE1" <-> "OE2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e ASP 99": "OD1" <-> "OD2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 211": "OE1" <-> "OE2" Residue "e GLU 293": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 612": "OD1" <-> "OD2" Residue "f GLU 636": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29270 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "b" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "c" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "d" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "e" Number of atoms: 7191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7191 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "f" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.52, per 1000 atoms: 0.46 Number of scatterers: 29270 At special positions: 0 Unit cell: (127.98, 139.711, 127.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 3336 8.00 N 2514 7.00 C 9717 6.00 H 13598 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 74 " distance=2.03 Simple disulfide: pdb=" SG CYS a 119 " - pdb=" SG CYS a 205 " distance=2.03 Simple disulfide: pdb=" SG CYS a 126 " - pdb=" SG CYS a 196 " distance=2.02 Simple disulfide: pdb=" SG CYS a 131 " - pdb=" SG CYS a 157 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 433 " distance=2.03 Simple disulfide: pdb=" SG CYS a 218 " - pdb=" SG CYS a 247 " distance=2.02 Simple disulfide: pdb=" SG CYS a 228 " - pdb=" SG CYS a 239 " distance=2.03 Simple disulfide: pdb=" SG CYS a 296 " - pdb=" SG CYS a 331 " distance=2.02 Simple disulfide: pdb=" SG CYS a 378 " - pdb=" SG CYS a 445 " distance=2.03 Simple disulfide: pdb=" SG CYS a 385 " - pdb=" SG CYS a 418 " distance=2.03 Simple disulfide: pdb=" SG CYS a 501 " - pdb=" SG CYS b 593 " distance=2.06 Simple disulfide: pdb=" SG CYS b 586 " - pdb=" SG CYS b 592 " distance=2.02 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.01 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.04 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.02 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.02 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 593 " distance=2.05 Simple disulfide: pdb=" SG CYS d 586 " - pdb=" SG CYS d 592 " distance=2.03 Simple disulfide: pdb=" SG CYS e 54 " - pdb=" SG CYS e 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 205 " distance=2.03 Simple disulfide: pdb=" SG CYS e 126 " - pdb=" SG CYS e 196 " distance=2.01 Simple disulfide: pdb=" SG CYS e 131 " - pdb=" SG CYS e 157 " distance=2.03 Simple disulfide: pdb=" SG CYS e 201 " - pdb=" SG CYS e 433 " distance=2.03 Simple disulfide: pdb=" SG CYS e 218 " - pdb=" SG CYS e 247 " distance=2.02 Simple disulfide: pdb=" SG CYS e 228 " - pdb=" SG CYS e 239 " distance=2.03 Simple disulfide: pdb=" SG CYS e 296 " - pdb=" SG CYS e 331 " distance=2.02 Simple disulfide: pdb=" SG CYS e 378 " - pdb=" SG CYS e 445 " distance=2.03 Simple disulfide: pdb=" SG CYS e 385 " - pdb=" SG CYS e 418 " distance=2.03 Simple disulfide: pdb=" SG CYS e 501 " - pdb=" SG CYS f 593 " distance=2.05 Simple disulfide: pdb=" SG CYS f 586 " - pdb=" SG CYS f 592 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA R 3 " - " MAN R 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA R 3 " - " MAN R 5 " " BMA k 3 " - " MAN k 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 1 " - " ASN a 362 " " NAG B 1 " - " ASN a 392 " " NAG C 1 " - " ASN a 234 " " NAG D 1 " - " ASN a 241 " " NAG E 1 " - " ASN a 262 " " NAG F 1 " - " ASN a 156 " " NAG H 1 " - " ASN a 301 " " NAG I 1 " - " ASN a 332 " " NAG J 1 " - " ASN a 339 " " NAG K 1 " - " ASN a 136 " " NAG L 1 " - " ASN a 160 " " NAG M 1 " - " ASN a 197 " " NAG N 1 " - " ASN c 362 " " NAG O 1 " - " ASN c 392 " " NAG P 1 " - " ASN c 234 " " NAG Q 1 " - " ASN c 241 " " NAG R 1 " - " ASN c 262 " " NAG S 1 " - " ASN c 156 " " NAG U 1 " - " ASN c 301 " " NAG V 1 " - " ASN c 332 " " NAG W 1 " - " ASN c 339 " " NAG X 1 " - " ASN c 136 " " NAG Y 1 " - " ASN c 160 " " NAG Z 1 " - " ASN c 197 " " NAG a 601 " - " ASN a 88 " " NAG a 602 " - " ASN a 276 " " NAG a 603 " - " ASN a 448 " " NAG a 604 " - " ASN a 442 " " NAG b 701 " - " ASN b 599 " " NAG b 702 " - " ASN b 625 " " NAG c 601 " - " ASN c 88 " " NAG c 602 " - " ASN c 276 " " NAG c 603 " - " ASN c 448 " " NAG c 604 " - " ASN c 442 " " NAG d 701 " - " ASN d 599 " " NAG d 702 " - " ASN d 625 " " NAG e 601 " - " ASN e 88 " " NAG e 602 " - " ASN e 276 " " NAG e 603 " - " ASN e 448 " " NAG e 604 " - " ASN e 442 " " NAG f 701 " - " ASN f 599 " " NAG f 702 " - " ASN f 625 " " NAG g 1 " - " ASN e 362 " " NAG h 1 " - " ASN e 392 " " NAG i 1 " - " ASN e 234 " " NAG j 1 " - " ASN e 241 " " NAG k 1 " - " ASN e 262 " " NAG l 1 " - " ASN e 156 " " NAG n 1 " - " ASN e 301 " " NAG o 1 " - " ASN e 332 " " NAG p 1 " - " ASN e 339 " " NAG q 1 " - " ASN e 136 " " NAG r 1 " - " ASN e 160 " " NAG s 1 " - " ASN e 197 " NAG-SER " NAG G 1 " - " SER a 388 " " NAG T 1 " - " SER c 388 " " NAG m 1 " - " SER e 388 " Time building additional restraints: 25.33 Conformation dependent library (CDL) restraints added in 2.7 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 27 sheets defined 25.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'a' and resid 59 through 63 removed outlier: 3.650A pdb=" N GLU a 62 " --> pdb=" O ARG a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 117 Processing helix chain 'a' and resid 122 through 126 removed outlier: 3.588A pdb=" N CYS a 126 " --> pdb=" O THR a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 198 Processing helix chain 'a' and resid 335 through 353 removed outlier: 3.787A pdb=" N HIS a 352 " --> pdb=" O GLU a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 368 through 373 Processing helix chain 'a' and resid 377 through 381 removed outlier: 3.860A pdb=" N GLY a 380 " --> pdb=" O ASN a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 401 Processing helix chain 'a' and resid 476 through 484 removed outlier: 4.754A pdb=" N GLU a 482 " --> pdb=" O ASN a 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 517 through 522 Processing helix chain 'b' and resid 524 through 530 removed outlier: 3.571A pdb=" N GLN b 528 " --> pdb=" O THR b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 559 through 584 removed outlier: 3.629A pdb=" N GLN b 563 " --> pdb=" O TRP b 559 " (cutoff:3.500A) Processing helix chain 'b' and resid 606 through 612 Processing helix chain 'b' and resid 615 through 624 removed outlier: 3.679A pdb=" N LYS b 621 " --> pdb=" O LEU b 617 " (cutoff:3.500A) Processing helix chain 'b' and resid 625 through 627 No H-bonds generated for 'chain 'b' and resid 625 through 627' Processing helix chain 'b' and resid 628 through 636 removed outlier: 4.042A pdb=" N GLU b 636 " --> pdb=" O GLY b 632 " (cutoff:3.500A) Processing helix chain 'b' and resid 638 through 651 Processing helix chain 'c' and resid 59 through 63 removed outlier: 3.961A pdb=" N GLU c 62 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 99 through 117 Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 351 removed outlier: 4.367A pdb=" N ASP c 340 " --> pdb=" O GLU c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 368 through 373 Processing helix chain 'c' and resid 377 through 381 removed outlier: 3.937A pdb=" N GLY c 380 " --> pdb=" O ASN c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 397 through 401 Processing helix chain 'c' and resid 476 through 484 removed outlier: 4.748A pdb=" N GLU c 482 " --> pdb=" O ASN c 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 517 through 522 Processing helix chain 'd' and resid 524 through 530 Processing helix chain 'd' and resid 559 through 585 removed outlier: 3.903A pdb=" N GLN d 563 " --> pdb=" O TRP d 559 " (cutoff:3.500A) Processing helix chain 'd' and resid 606 through 612 Processing helix chain 'd' and resid 615 through 624 removed outlier: 3.853A pdb=" N LYS d 621 " --> pdb=" O LEU d 617 " (cutoff:3.500A) Processing helix chain 'd' and resid 628 through 636 removed outlier: 3.858A pdb=" N GLU d 636 " --> pdb=" O GLY d 632 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 651 Processing helix chain 'e' and resid 98 through 117 removed outlier: 4.262A pdb=" N ASP e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 198 Processing helix chain 'e' and resid 335 through 353 removed outlier: 3.751A pdb=" N HIS e 352 " --> pdb=" O GLU e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 368 through 373 Processing helix chain 'e' and resid 397 through 401 removed outlier: 3.532A pdb=" N SER e 401 " --> pdb=" O GLY e 398 " (cutoff:3.500A) Processing helix chain 'e' and resid 476 through 481 Processing helix chain 'e' and resid 482 through 484 No H-bonds generated for 'chain 'e' and resid 482 through 484' Processing helix chain 'f' and resid 517 through 522 Processing helix chain 'f' and resid 524 through 530 removed outlier: 3.528A pdb=" N GLN f 528 " --> pdb=" O THR f 524 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 584 removed outlier: 3.579A pdb=" N LEU f 569 " --> pdb=" O GLN f 565 " (cutoff:3.500A) Processing helix chain 'f' and resid 607 through 612 Processing helix chain 'f' and resid 615 through 624 Processing helix chain 'f' and resid 628 through 636 removed outlier: 3.510A pdb=" N LEU f 633 " --> pdb=" O ILE f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 638 through 651 Processing sheet with id=AA1, first strand: chain 'a' and resid 494 through 499 removed outlier: 5.353A pdb=" N VAL b 596 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL a 38 " --> pdb=" O THR b 594 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR b 594 " --> pdb=" O VAL a 38 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR a 40 " --> pdb=" O CYS b 592 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N CYS b 592 " --> pdb=" O TYR a 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 45 through 47 removed outlier: 3.579A pdb=" N ILE a 225 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'a' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'a' and resid 169 through 177 removed outlier: 9.219A pdb=" N GLU a 150 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N VAL a 139 " --> pdb=" O GLU a 150 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET a 154 " --> pdb=" O ALA a 137 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA a 137 " --> pdb=" O MET a 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 202 through 203 removed outlier: 6.510A pdb=" N THR a 202 " --> pdb=" O TYR a 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 259 through 261 removed outlier: 4.472A pdb=" N GLY a 451 " --> pdb=" O LEU a 260 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N THR a 444 " --> pdb=" O ILE a 294 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE a 294 " --> pdb=" O THR a 444 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG a 446 " --> pdb=" O VAL a 292 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL a 292 " --> pdb=" O ARG a 446 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ASN a 448 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR a 290 " --> pdb=" O ASN a 448 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR a 450 " --> pdb=" O LEU a 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 284 through 297 current: chain 'a' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'a' and resid 271 through 273 removed outlier: 6.934A pdb=" N THR a 450 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR a 290 " --> pdb=" O ASN a 448 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ASN a 448 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL a 292 " --> pdb=" O ARG a 446 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG a 446 " --> pdb=" O VAL a 292 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE a 294 " --> pdb=" O THR a 444 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N THR a 444 " --> pdb=" O ILE a 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 444 through 456 current: chain 'a' and resid 413 through 420 Processing sheet with id=AA9, first strand: chain 'a' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'c' and resid 494 through 499 removed outlier: 5.173A pdb=" N VAL d 596 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL c 38 " --> pdb=" O THR d 594 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR d 594 " --> pdb=" O VAL c 38 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR c 40 " --> pdb=" O CYS d 592 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N CYS d 592 " --> pdb=" O TYR c 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.504A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'c' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'c' and resid 169 through 177 removed outlier: 9.150A pdb=" N GLU c 150 " --> pdb=" O VAL c 139 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N VAL c 139 " --> pdb=" O GLU c 150 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET c 154 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA c 137 " --> pdb=" O MET c 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 202 through 203 removed outlier: 6.576A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 259 through 261 removed outlier: 3.769A pdb=" N GLY c 451 " --> pdb=" O LEU c 260 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N THR c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE c 294 " --> pdb=" O THR c 444 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL c 292 " --> pdb=" O ARG c 446 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR c 450 " --> pdb=" O LEU c 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 284 through 297 current: chain 'c' and resid 358 through 361 Processing sheet with id=AB8, first strand: chain 'c' and resid 271 through 273 removed outlier: 6.846A pdb=" N THR c 450 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL c 292 " --> pdb=" O ARG c 446 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE c 294 " --> pdb=" O THR c 444 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N THR c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 444 through 456 current: chain 'c' and resid 413 through 420 Processing sheet with id=AB9, first strand: chain 'c' and resid 304 through 307 Processing sheet with id=AC1, first strand: chain 'e' and resid 494 through 499 removed outlier: 5.135A pdb=" N VAL f 596 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL e 38 " --> pdb=" O THR f 594 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR f 594 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR e 40 " --> pdb=" O CYS f 592 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS f 592 " --> pdb=" O TYR e 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'e' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'e' and resid 91 through 94 removed outlier: 3.521A pdb=" N GLU e 91 " --> pdb=" O CYS e 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 169 through 177 removed outlier: 9.687A pdb=" N GLU e 150 " --> pdb=" O VAL e 139 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL e 139 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET e 154 " --> pdb=" O ALA e 137 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA e 137 " --> pdb=" O MET e 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 202 through 203 removed outlier: 6.513A pdb=" N THR e 202 " --> pdb=" O TYR e 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 259 through 261 removed outlier: 4.160A pdb=" N GLY e 451 " --> pdb=" O LEU e 260 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 284 through 297 current: chain 'e' and resid 358 through 361 Processing sheet with id=AC8, first strand: chain 'e' and resid 271 through 273 removed outlier: 6.818A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 444 through 456 current: chain 'e' and resid 413 through 421 removed outlier: 3.698A pdb=" N LYS e 421 " --> pdb=" O PHE e 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE e 382 " --> pdb=" O LYS e 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 301 through 306 removed outlier: 7.389A pdb=" N ASN e 301 " --> pdb=" O ILE e 323 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE e 323 " --> pdb=" O ASN e 301 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR e 303 " --> pdb=" O GLY e 321 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1260 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: 12.83 Time building geometry restraints manager: 26.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 2415 1.01 - 1.21: 11201 1.21 - 1.41: 6164 1.41 - 1.62: 9637 1.62 - 1.82: 138 Bond restraints: 29555 Sorted by residual: bond pdb=" N ALA c 436 " pdb=" H ALA c 436 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" N TRP e 427 " pdb=" H TRP e 427 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" NE2 HIS c 249 " pdb=" HE2 HIS c 249 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" N ASN d 639 " pdb=" H ASN d 639 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CE2 PHE c 468 " pdb=" HE2 PHE c 468 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 ... (remaining 29550 not shown) Histogram of bond angle deviations from ideal: 97.10 - 105.09: 449 105.09 - 113.07: 33275 113.07 - 121.06: 13585 121.06 - 129.05: 5138 129.05 - 137.04: 135 Bond angle restraints: 52582 Sorted by residual: angle pdb=" C GLY a 312 " pdb=" N PRO a 313 " pdb=" CA PRO a 313 " ideal model delta sigma weight residual 119.84 133.28 -13.44 1.25e+00 6.40e-01 1.16e+02 angle pdb=" N GLY c 314 " pdb=" CA GLY c 314 " pdb=" C GLY c 314 " ideal model delta sigma weight residual 111.62 130.59 -18.97 1.77e+00 3.19e-01 1.15e+02 angle pdb=" N GLN e 315 " pdb=" CA GLN e 315 " pdb=" C GLN e 315 " ideal model delta sigma weight residual 108.76 125.45 -16.69 1.58e+00 4.01e-01 1.12e+02 angle pdb=" N GLY a 314 " pdb=" CA GLY a 314 " pdb=" C GLY a 314 " ideal model delta sigma weight residual 111.62 129.26 -17.64 1.77e+00 3.19e-01 9.93e+01 angle pdb=" C GLY c 312 " pdb=" N PRO c 313 " pdb=" CA PRO c 313 " ideal model delta sigma weight residual 119.84 131.93 -12.09 1.25e+00 6.40e-01 9.36e+01 ... (remaining 52577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.85: 14230 20.85 - 41.71: 898 41.71 - 62.56: 356 62.56 - 83.42: 254 83.42 - 104.27: 128 Dihedral angle restraints: 15866 sinusoidal: 9909 harmonic: 5957 Sorted by residual: dihedral pdb=" CB CYS a 378 " pdb=" SG CYS a 378 " pdb=" SG CYS a 445 " pdb=" CB CYS a 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.11 57.11 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS e 378 " pdb=" SG CYS e 378 " pdb=" SG CYS e 445 " pdb=" CB CYS e 445 " ideal model delta sinusoidal sigma weight residual -86.00 -139.42 53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CA PRO c 313 " pdb=" C PRO c 313 " pdb=" N GLY c 314 " pdb=" CA GLY c 314 " ideal model delta harmonic sigma weight residual -180.00 -149.00 -31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 15863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1698 0.107 - 0.214: 1003 0.214 - 0.321: 118 0.321 - 0.428: 27 0.428 - 0.535: 4 Chirality restraints: 2850 Sorted by residual: chirality pdb=" C1 BMA h 3 " pdb=" O4 NAG h 2 " pdb=" C2 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.05e+02 ... (remaining 2847 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP d 598 " -0.372 2.00e-02 2.50e+03 1.29e-01 6.62e+02 pdb=" CG TRP d 598 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP d 598 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TRP d 598 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP d 598 " 0.127 2.00e-02 2.50e+03 pdb=" CE2 TRP d 598 " 0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP d 598 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 598 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 598 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP d 598 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP d 598 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP d 598 " 0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP d 598 " 0.131 2.00e-02 2.50e+03 pdb=" HZ2 TRP d 598 " -0.141 2.00e-02 2.50e+03 pdb=" HZ3 TRP d 598 " 0.053 2.00e-02 2.50e+03 pdb=" HH2 TRP d 598 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 598 " 0.354 2.00e-02 2.50e+03 1.25e-01 6.27e+02 pdb=" CG TRP b 598 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP b 598 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP b 598 " -0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP b 598 " -0.129 2.00e-02 2.50e+03 pdb=" CE2 TRP b 598 " -0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP b 598 " -0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 598 " 0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 598 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP b 598 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TRP b 598 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TRP b 598 " -0.109 2.00e-02 2.50e+03 pdb=" HE3 TRP b 598 " -0.134 2.00e-02 2.50e+03 pdb=" HZ2 TRP b 598 " 0.116 2.00e-02 2.50e+03 pdb=" HZ3 TRP b 598 " -0.035 2.00e-02 2.50e+03 pdb=" HH2 TRP b 598 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 598 " 0.324 2.00e-02 2.50e+03 1.21e-01 5.85e+02 pdb=" CG TRP f 598 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP f 598 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP f 598 " -0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP f 598 " -0.126 2.00e-02 2.50e+03 pdb=" CE2 TRP f 598 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP f 598 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 598 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 598 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" HD1 TRP f 598 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 TRP f 598 " -0.136 2.00e-02 2.50e+03 pdb=" HE3 TRP f 598 " -0.137 2.00e-02 2.50e+03 pdb=" HZ2 TRP f 598 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP f 598 " -0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP f 598 " 0.137 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2159 2.21 - 2.81: 50648 2.81 - 3.41: 76186 3.41 - 4.00: 100725 4.00 - 4.60: 147629 Nonbonded interactions: 377347 Sorted by model distance: nonbonded pdb=" H THR c 162 " pdb="HG23 ILE c 309 " model vdw 1.614 2.270 nonbonded pdb=" HG1 THR a 161 " pdb=" OE2 GLU a 172 " model vdw 1.626 1.850 nonbonded pdb=" H THR a 162 " pdb="HG23 ILE a 309 " model vdw 1.629 2.270 nonbonded pdb=" HG1 THR c 161 " pdb=" OE2 GLU c 172 " model vdw 1.644 1.850 nonbonded pdb=" HG1 THR e 161 " pdb=" OE2 GLU e 172 " model vdw 1.652 1.850 ... (remaining 377342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'i' selection = chain 'n' selection = chain 'q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'k' } ncs_group { reference = (chain 'a' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 604)) selection = (chain 'c' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 604)) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.430 Extract box with map and model: 5.040 Check model and map are aligned: 0.460 Set scattering table: 0.240 Process input model: 93.600 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.590 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.016 0.087 15957 Z= 0.993 Angle : 1.999 18.975 21693 Z= 1.270 Chirality : 0.119 0.535 2850 Planarity : 0.019 0.182 2583 Dihedral : 21.219 104.271 7893 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.19 % Favored : 91.07 % Rotamer: Outliers : 0.70 % Allowed : 3.58 % Favored : 95.71 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.29 % 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: -1.91 (0.18), residues: 1758 helix: -1.58 (0.23), residues: 360 sheet: 0.05 (0.29), residues: 309 loop : -1.61 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.263 0.032 TRP d 598 HIS 0.014 0.004 HIS e 287 PHE 0.087 0.017 PHE d 510 TYR 0.149 0.022 TYR e 39 ARG 0.009 0.001 ARG a 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 MET cc_start: 0.8828 (ptm) cc_final: 0.8219 (ptm) REVERT: c 114 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: d 518 MET cc_start: 0.8295 (mtm) cc_final: 0.7891 (mtp) REVERT: f 518 MET cc_start: 0.8208 (mtm) cc_final: 0.7945 (mtm) REVERT: f 614 MET cc_start: 0.8825 (ptp) cc_final: 0.8584 (ptp) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.6351 time to fit residues: 71.5139 Evaluate side-chains 60 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 376 PHE Chi-restraints excluded: chain a residue 442 ASN Chi-restraints excluded: chain c residue 114 GLN Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 376 PHE Chi-restraints excluded: chain c residue 442 ASN Chi-restraints excluded: chain e residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 66 HIS ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 531 ASN f 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15957 Z= 0.283 Angle : 0.862 8.869 21693 Z= 0.427 Chirality : 0.051 0.333 2850 Planarity : 0.005 0.045 2583 Dihedral : 17.457 86.645 4613 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.09 % Allowed : 4.29 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.53 (0.19), residues: 1758 helix: -0.70 (0.25), residues: 372 sheet: 0.10 (0.27), residues: 357 loop : -1.60 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 598 HIS 0.007 0.002 HIS c 374 PHE 0.015 0.002 PHE f 510 TYR 0.031 0.002 TYR b 626 ARG 0.003 0.001 ARG a 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 114 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7920 (tt0) outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.5884 time to fit residues: 62.8353 Evaluate side-chains 61 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 287 HIS Chi-restraints excluded: chain a residue 309 ILE Chi-restraints excluded: chain a residue 317 PHE Chi-restraints excluded: chain a residue 376 PHE Chi-restraints excluded: chain a residue 442 ASN Chi-restraints excluded: chain b residue 598 TRP Chi-restraints excluded: chain b residue 652 ASP Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 114 GLN Chi-restraints excluded: chain c residue 309 ILE Chi-restraints excluded: chain c residue 376 PHE Chi-restraints excluded: chain c residue 442 ASN Chi-restraints excluded: chain f residue 594 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15957 Z= 0.286 Angle : 0.721 6.813 21693 Z= 0.350 Chirality : 0.051 0.291 2850 Planarity : 0.004 0.039 2583 Dihedral : 10.739 87.916 4610 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.23 % Rotamer: Outliers : 1.66 % Allowed : 4.29 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1758 helix: 0.09 (0.28), residues: 372 sheet: 0.11 (0.28), residues: 327 loop : -1.72 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 598 HIS 0.009 0.001 HIS c 374 PHE 0.015 0.002 PHE e 159 TYR 0.025 0.002 TYR f 626 ARG 0.007 0.001 ARG c 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 51 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 114 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: d 518 MET cc_start: 0.8313 (mtm) cc_final: 0.8044 (mtp) REVERT: e 104 MET cc_start: 0.9484 (ttm) cc_final: 0.9248 (ttm) outliers start: 26 outliers final: 19 residues processed: 74 average time/residue: 0.6687 time to fit residues: 74.5828 Evaluate side-chains 66 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 287 HIS Chi-restraints excluded: chain a residue 376 PHE Chi-restraints excluded: chain a residue 442 ASN Chi-restraints excluded: chain b residue 598 TRP Chi-restraints excluded: chain b residue 652 ASP Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 114 GLN Chi-restraints excluded: chain c residue 287 HIS Chi-restraints excluded: chain c residue 309 ILE Chi-restraints excluded: chain c residue 325 ASP Chi-restraints excluded: chain c residue 376 PHE Chi-restraints excluded: chain c residue 442 ASN Chi-restraints excluded: chain d residue 652 ASP Chi-restraints excluded: chain e residue 63 LYS Chi-restraints excluded: chain e residue 287 HIS Chi-restraints excluded: chain e residue 309 ILE Chi-restraints excluded: chain f residue 594 THR Chi-restraints excluded: chain f residue 621 LYS Chi-restraints excluded: chain f residue 652 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15957 Z= 0.174 Angle : 0.596 6.195 21693 Z= 0.292 Chirality : 0.046 0.298 2850 Planarity : 0.003 0.032 2583 Dihedral : 9.018 87.873 4610 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.15 % Allowed : 5.18 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1758 helix: 0.42 (0.29), residues: 372 sheet: 0.24 (0.27), residues: 357 loop : -1.59 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 598 HIS 0.008 0.001 HIS c 374 PHE 0.009 0.001 PHE c 317 TYR 0.018 0.001 TYR f 626 ARG 0.003 0.000 ARG e 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 114 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: d 518 MET cc_start: 0.8244 (mtm) cc_final: 0.8012 (mtp) REVERT: e 104 MET cc_start: 0.9463 (ttm) cc_final: 0.9228 (ttm) outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.5776 time to fit residues: 58.7095 Evaluate side-chains 64 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 287 HIS Chi-restraints excluded: chain a residue 376 PHE Chi-restraints excluded: chain a residue 442 ASN Chi-restraints excluded: chain b residue 598 TRP Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 114 GLN Chi-restraints excluded: chain c residue 287 HIS Chi-restraints excluded: chain c residue 309 ILE Chi-restraints excluded: chain c residue 376 PHE Chi-restraints excluded: chain c residue 442 ASN Chi-restraints excluded: chain e residue 63 LYS Chi-restraints excluded: chain e residue 287 HIS Chi-restraints excluded: chain e residue 309 ILE Chi-restraints excluded: chain e residue 316 THR Chi-restraints excluded: chain f residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 66 HIS e 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3148 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: