Starting phenix.real_space_refine on Mon Feb 19 15:16:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epn_28531/02_2024/8epn_28531.pdb" } resolution = 2.8 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= 0.000 sd= 0.002 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 99 5.16 5 C 15915 2.51 5 N 3993 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 747": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25077 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 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: 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: 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: "G" 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" 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: "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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "c" 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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 12.92, per 1000 atoms: 0.52 Number of scatterers: 25077 At special positions: 0 Unit cell: (145.39, 143.38, 175.54, 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 99 16.00 O 5070 8.00 N 3993 7.00 C 15915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA h 3 " - " MAN h 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 Z 1 " - " NAG Z 2 " " 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 234 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 234 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 234 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 657 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B 657 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 657 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C 331 " Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 3.8 seconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 43 sheets defined 26.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.967A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.518A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.518A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.540A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.530A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.290A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.076A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.295A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.113A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.525A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.641A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.511A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.512A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.514A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.163A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.517A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.303A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 5.841A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.114A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.813A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.938A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.120A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.270A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.968A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.926A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.730A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.118A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.048A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.786A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.249A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.907A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.678A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.869A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.077A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.008A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.816A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.272A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 1007 hydrogen bonds defined for protein. 2757 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: 12.66 Time building geometry restraints manager: 11.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7757 1.34 - 1.46: 6330 1.46 - 1.58: 11395 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 25605 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.16e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 25600 not shown) Histogram of bond angle deviations from ideal: 100.20 - 107.03: 807 107.03 - 113.86: 14986 113.86 - 120.69: 9847 120.69 - 127.52: 9013 127.52 - 134.35: 171 Bond angle restraints: 34824 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 121.70 133.36 -11.66 1.80e+00 3.09e-01 4.20e+01 angle pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ASN B1135 " pdb=" N THR B1136 " pdb=" CA THR B1136 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 117.23 111.18 6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 ... (remaining 34819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 15660 24.98 - 49.96: 826 49.96 - 74.94: 162 74.94 - 99.93: 134 99.93 - 124.91: 51 Dihedral angle restraints: 16833 sinusoidal: 8118 harmonic: 8715 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.99 75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.95 75.95 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 16830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3685 0.072 - 0.144: 611 0.144 - 0.215: 12 0.215 - 0.287: 13 0.287 - 0.359: 14 Chirality restraints: 4335 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 4332 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1132 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE B1132 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1132 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ILE C1132 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 139 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2685 2.75 - 3.29: 23064 3.29 - 3.83: 39662 3.83 - 4.36: 45309 4.36 - 4.90: 79566 Nonbonded interactions: 190286 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.243 2.440 nonbonded pdb=" NZ LYS C 825 " pdb=" O THR C 941 " model vdw 2.269 2.520 ... (remaining 190281 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 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.810 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: 29.090 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 68.670 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.470 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.005 0.081 25605 Z= 0.305 Angle : 0.751 11.663 34824 Z= 0.355 Chirality : 0.053 0.359 4335 Planarity : 0.004 0.043 4314 Dihedral : 18.173 124.907 11130 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 12.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2931 helix: 1.64 (0.21), residues: 669 sheet: 0.67 (0.21), residues: 543 loop : -1.06 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.001 PHE A 140 TYR 0.021 0.001 TYR A 453 ARG 0.008 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7629 (m-80) cc_final: 0.7167 (m-80) REVERT: C 133 PHE cc_start: 0.7579 (m-80) cc_final: 0.7115 (m-80) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 1.0494 time to fit residues: 149.4415 Evaluate side-chains 92 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 173 optimal weight: 0.3980 chunk 269 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25605 Z= 0.166 Angle : 0.562 8.730 34824 Z= 0.283 Chirality : 0.047 0.341 4335 Planarity : 0.004 0.043 4314 Dihedral : 13.972 111.938 5786 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.95 % Allowed : 11.38 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2931 helix: 1.96 (0.21), residues: 687 sheet: 0.88 (0.22), residues: 543 loop : -1.12 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS A 207 PHE 0.014 0.001 PHE C 192 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 92 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 TYR cc_start: 0.8104 (m-80) cc_final: 0.7796 (m-10) REVERT: B 133 PHE cc_start: 0.7608 (m-80) cc_final: 0.7137 (m-80) REVERT: B 957 GLN cc_start: 0.8715 (tt0) cc_final: 0.8479 (tt0) REVERT: C 133 PHE cc_start: 0.7604 (m-80) cc_final: 0.7131 (m-80) REVERT: C 957 GLN cc_start: 0.8738 (tt0) cc_final: 0.8531 (tt0) outliers start: 51 outliers final: 24 residues processed: 139 average time/residue: 0.8793 time to fit residues: 155.0568 Evaluate side-chains 101 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 240 optimal weight: 30.0000 chunk 267 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 25605 Z= 0.382 Angle : 0.667 9.714 34824 Z= 0.335 Chirality : 0.052 0.353 4335 Planarity : 0.005 0.048 4314 Dihedral : 12.846 116.653 5778 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.30 % Allowed : 11.26 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2931 helix: 1.80 (0.21), residues: 684 sheet: 0.77 (0.21), residues: 573 loop : -1.12 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 353 HIS 0.006 0.001 HIS C1058 PHE 0.017 0.002 PHE B 541 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 79 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7869 (ttpt) REVERT: A 314 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: B 133 PHE cc_start: 0.7748 (m-80) cc_final: 0.7310 (m-80) REVERT: B 314 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: B 401 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6356 (p) REVERT: C 133 PHE cc_start: 0.7601 (m-80) cc_final: 0.7233 (m-80) REVERT: C 314 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (tp40) REVERT: C 380 TYR cc_start: 0.6674 (m-10) cc_final: 0.6431 (m-10) REVERT: C 740 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8254 (tpt) REVERT: C 1144 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7765 (mm-30) outliers start: 86 outliers final: 28 residues processed: 158 average time/residue: 0.8958 time to fit residues: 176.6708 Evaluate side-chains 101 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 67 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25605 Z= 0.286 Angle : 0.614 9.688 34824 Z= 0.303 Chirality : 0.050 0.340 4335 Planarity : 0.004 0.047 4314 Dihedral : 11.729 114.445 5770 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.15 % Allowed : 13.14 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2931 helix: 1.90 (0.21), residues: 687 sheet: 0.70 (0.20), residues: 648 loop : -1.10 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 PHE 0.015 0.001 PHE A 400 TYR 0.020 0.001 TYR A 707 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 74 time to evaluate : 2.708 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7709 (m-80) cc_final: 0.7285 (m-80) REVERT: A 314 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: B 133 PHE cc_start: 0.7744 (m-80) cc_final: 0.7317 (m-80) REVERT: B 227 VAL cc_start: 0.8829 (t) cc_final: 0.8589 (p) REVERT: B 314 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: B 401 VAL cc_start: 0.6599 (OUTLIER) cc_final: 0.6382 (p) REVERT: C 133 PHE cc_start: 0.7603 (m-80) cc_final: 0.7250 (m-80) REVERT: C 314 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: C 380 TYR cc_start: 0.6680 (m-10) cc_final: 0.6464 (m-10) REVERT: C 740 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8183 (tpt) REVERT: C 1144 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7797 (mm-30) outliers start: 56 outliers final: 26 residues processed: 125 average time/residue: 0.9140 time to fit residues: 143.0663 Evaluate side-chains 101 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25605 Z= 0.253 Angle : 0.597 9.744 34824 Z= 0.292 Chirality : 0.049 0.337 4335 Planarity : 0.004 0.045 4314 Dihedral : 10.779 113.728 5770 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.64 % Allowed : 12.68 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 2931 helix: 2.00 (0.21), residues: 687 sheet: 0.80 (0.20), residues: 642 loop : -1.09 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.015 0.001 PHE A 238 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 83 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7821 (tmmt) REVERT: A 133 PHE cc_start: 0.7755 (m-80) cc_final: 0.7258 (m-80) REVERT: A 227 VAL cc_start: 0.8787 (t) cc_final: 0.8584 (p) REVERT: A 314 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: B 133 PHE cc_start: 0.7745 (m-80) cc_final: 0.7312 (m-80) REVERT: B 190 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7060 (ttm110) REVERT: B 227 VAL cc_start: 0.8819 (t) cc_final: 0.8588 (p) REVERT: B 314 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: B 401 VAL cc_start: 0.6595 (OUTLIER) cc_final: 0.6380 (p) REVERT: B 707 TYR cc_start: 0.8044 (m-80) cc_final: 0.7678 (m-10) REVERT: C 133 PHE cc_start: 0.7607 (m-80) cc_final: 0.7259 (m-80) REVERT: C 314 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: C 1144 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 69 outliers final: 44 residues processed: 149 average time/residue: 0.8946 time to fit residues: 167.8932 Evaluate side-chains 122 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 73 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.4980 chunk 258 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 287 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25605 Z= 0.153 Angle : 0.557 9.768 34824 Z= 0.269 Chirality : 0.047 0.325 4335 Planarity : 0.004 0.041 4314 Dihedral : 9.939 111.505 5768 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.11 % Allowed : 13.45 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2931 helix: 2.22 (0.21), residues: 684 sheet: 0.89 (0.20), residues: 627 loop : -1.00 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 353 HIS 0.002 0.000 HIS A1064 PHE 0.020 0.001 PHE B 238 TYR 0.022 0.001 TYR A 453 ARG 0.002 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 95 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (tmmt) REVERT: A 133 PHE cc_start: 0.7713 (m-80) cc_final: 0.7158 (m-80) REVERT: A 227 VAL cc_start: 0.8770 (t) cc_final: 0.8566 (p) REVERT: A 1144 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 133 PHE cc_start: 0.7732 (m-80) cc_final: 0.7287 (m-80) REVERT: B 190 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7024 (ttm110) REVERT: B 227 VAL cc_start: 0.8785 (t) cc_final: 0.8560 (p) REVERT: B 314 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: B 707 TYR cc_start: 0.8062 (m-80) cc_final: 0.7558 (m-10) REVERT: B 957 GLN cc_start: 0.8703 (tt0) cc_final: 0.8460 (tt0) REVERT: C 133 PHE cc_start: 0.7620 (m-80) cc_final: 0.7266 (m-80) REVERT: C 314 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8213 (tp40) REVERT: C 454 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6119 (tmt90) REVERT: C 1144 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7851 (mm-30) outliers start: 55 outliers final: 34 residues processed: 147 average time/residue: 0.9436 time to fit residues: 172.7260 Evaluate side-chains 117 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 79 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 0.0980 chunk 241 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 286 optimal weight: 0.4980 chunk 179 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25605 Z= 0.138 Angle : 0.533 9.806 34824 Z= 0.256 Chirality : 0.046 0.325 4335 Planarity : 0.004 0.039 4314 Dihedral : 8.924 109.599 5767 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.80 % Allowed : 13.91 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 2931 helix: 2.43 (0.21), residues: 684 sheet: 0.95 (0.20), residues: 630 loop : -0.91 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 353 HIS 0.002 0.000 HIS A 66 PHE 0.021 0.001 PHE A 541 TYR 0.022 0.001 TYR A 453 ARG 0.003 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7817 (tmmt) REVERT: A 133 PHE cc_start: 0.7687 (m-80) cc_final: 0.7109 (m-80) REVERT: A 227 VAL cc_start: 0.8747 (t) cc_final: 0.8544 (p) REVERT: A 957 GLN cc_start: 0.8744 (tt0) cc_final: 0.8529 (tt0) REVERT: B 65 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: B 133 PHE cc_start: 0.7714 (m-80) cc_final: 0.7223 (m-80) REVERT: B 227 VAL cc_start: 0.8754 (t) cc_final: 0.8550 (p) REVERT: B 707 TYR cc_start: 0.8063 (m-80) cc_final: 0.7537 (m-10) REVERT: B 957 GLN cc_start: 0.8700 (tt0) cc_final: 0.8452 (tt0) REVERT: C 133 PHE cc_start: 0.7615 (m-80) cc_final: 0.7266 (m-80) REVERT: C 386 LYS cc_start: 0.7795 (mttt) cc_final: 0.7173 (mtpt) REVERT: C 454 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6162 (tmm-80) REVERT: C 1144 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7842 (mm-30) outliers start: 47 outliers final: 34 residues processed: 140 average time/residue: 0.9378 time to fit residues: 163.9376 Evaluate side-chains 117 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 80 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 225 optimal weight: 20.0000 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25605 Z= 0.141 Angle : 0.530 9.811 34824 Z= 0.255 Chirality : 0.046 0.329 4335 Planarity : 0.004 0.038 4314 Dihedral : 8.378 110.015 5767 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.80 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2931 helix: 2.48 (0.21), residues: 681 sheet: 0.88 (0.20), residues: 672 loop : -0.88 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 353 HIS 0.002 0.000 HIS A1064 PHE 0.020 0.001 PHE B 541 TYR 0.021 0.001 TYR A 453 ARG 0.002 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7812 (tmmt) REVERT: A 133 PHE cc_start: 0.7680 (m-80) cc_final: 0.7105 (m-80) REVERT: A 957 GLN cc_start: 0.8751 (tt0) cc_final: 0.8537 (tt0) REVERT: B 133 PHE cc_start: 0.7719 (m-80) cc_final: 0.7191 (m-80) REVERT: B 227 VAL cc_start: 0.8743 (t) cc_final: 0.8542 (p) REVERT: B 707 TYR cc_start: 0.8073 (m-80) cc_final: 0.7571 (m-10) REVERT: B 957 GLN cc_start: 0.8718 (tt0) cc_final: 0.8477 (tt0) REVERT: C 133 PHE cc_start: 0.7636 (m-80) cc_final: 0.7294 (m-80) REVERT: C 386 LYS cc_start: 0.7783 (mttt) cc_final: 0.7159 (mtpt) REVERT: C 454 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6165 (tmm-80) REVERT: C 541 PHE cc_start: 0.5671 (m-10) cc_final: 0.5110 (m-10) REVERT: C 1144 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7840 (mm-30) outliers start: 47 outliers final: 40 residues processed: 131 average time/residue: 0.9281 time to fit residues: 153.7800 Evaluate side-chains 121 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25605 Z= 0.286 Angle : 0.607 9.891 34824 Z= 0.300 Chirality : 0.048 0.344 4335 Planarity : 0.004 0.041 4314 Dihedral : 8.460 113.884 5767 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.15 % Allowed : 13.79 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2931 helix: 2.11 (0.21), residues: 705 sheet: 0.91 (0.20), residues: 630 loop : -0.93 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 353 HIS 0.005 0.001 HIS B1058 PHE 0.027 0.002 PHE B 400 TYR 0.021 0.001 TYR B 453 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 87 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7798 (tmmt) REVERT: A 133 PHE cc_start: 0.7735 (m-80) cc_final: 0.7186 (m-80) REVERT: B 133 PHE cc_start: 0.7786 (m-80) cc_final: 0.7339 (m-80) REVERT: B 227 VAL cc_start: 0.8767 (t) cc_final: 0.8554 (p) REVERT: B 314 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: B 707 TYR cc_start: 0.8116 (m-80) cc_final: 0.7706 (m-10) REVERT: C 133 PHE cc_start: 0.7683 (m-80) cc_final: 0.7373 (m-80) REVERT: C 380 TYR cc_start: 0.6523 (m-10) cc_final: 0.6291 (m-10) REVERT: C 454 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6343 (tmt90) REVERT: C 1144 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7865 (mm-30) outliers start: 56 outliers final: 37 residues processed: 140 average time/residue: 0.8305 time to fit residues: 146.8114 Evaluate side-chains 116 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 76 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 24 optimal weight: 0.0020 chunk 181 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 493 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25605 Z= 0.168 Angle : 0.551 9.853 34824 Z= 0.269 Chirality : 0.046 0.323 4335 Planarity : 0.004 0.040 4314 Dihedral : 8.178 111.798 5767 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.46 % Allowed : 14.52 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2931 helix: 2.28 (0.21), residues: 684 sheet: 1.05 (0.22), residues: 549 loop : -0.95 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 353 HIS 0.003 0.000 HIS A1064 PHE 0.022 0.001 PHE A 541 TYR 0.022 0.001 TYR A 453 ARG 0.003 0.000 ARG C 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7809 (tmmt) REVERT: A 133 PHE cc_start: 0.7721 (m-80) cc_final: 0.7165 (m-80) REVERT: B 133 PHE cc_start: 0.7735 (m-80) cc_final: 0.7265 (m-80) REVERT: B 227 VAL cc_start: 0.8758 (t) cc_final: 0.8551 (p) REVERT: B 707 TYR cc_start: 0.8075 (m-80) cc_final: 0.7644 (m-10) REVERT: B 957 GLN cc_start: 0.8724 (tt0) cc_final: 0.8471 (tt0) REVERT: C 133 PHE cc_start: 0.7701 (m-80) cc_final: 0.7362 (m-80) REVERT: C 314 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8253 (tp40) REVERT: C 380 TYR cc_start: 0.6542 (m-10) cc_final: 0.6338 (m-10) REVERT: C 454 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6318 (tmt90) REVERT: C 1144 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7879 (mm-30) outliers start: 38 outliers final: 33 residues processed: 120 average time/residue: 0.9423 time to fit residues: 142.2934 Evaluate side-chains 116 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.0030 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 overall best weight: 0.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.123007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077307 restraints weight = 59784.111| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.28 r_work: 0.3062 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 25605 Z= 0.145 Angle : 0.540 9.889 34824 Z= 0.261 Chirality : 0.045 0.323 4335 Planarity : 0.004 0.040 4314 Dihedral : 7.854 110.900 5767 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 14.44 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 2931 helix: 2.57 (0.21), residues: 666 sheet: 1.08 (0.22), residues: 549 loop : -0.84 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 353 HIS 0.002 0.000 HIS A1064 PHE 0.016 0.001 PHE A 374 TYR 0.016 0.001 TYR B 453 ARG 0.002 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6148.13 seconds wall clock time: 112 minutes 46.61 seconds (6766.61 seconds total)