Starting phenix.real_space_refine on Sun Feb 18 21:13:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2p_25621/02_2024/7t2p_25621.pdb" } resolution = 3.47 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= 0.049 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 147 5.16 5 C 14283 2.51 5 N 3693 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 637": "OE1" <-> "OE2" Residue "R GLU 665": "OE1" <-> "OE2" Residue "S PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 73": "OE1" <-> "OE2" Residue "6 TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 637": "OE1" <-> "OE2" Residue "7 GLU 665": "OE1" <-> "OE2" Residue "8 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 22896 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "B" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "R" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "0" 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: "1" 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: "2" 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: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "7" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "8" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "9" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.51, per 1000 atoms: 0.55 Number of scatterers: 22896 At special positions: 0 Unit cell: (154.1, 156.4, 121.9, 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 147 16.00 O 4773 8.00 N 3693 7.00 C 14283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 211 " distance=1.78 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 168 " distance=2.02 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 255 " distance=2.05 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS H 100C" - pdb=" SG CYS H 100K" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 108 " - pdb=" SG CYS Q 211 " distance=1.78 Simple disulfide: pdb=" SG CYS Q 113 " - pdb=" SG CYS Q 168 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 194 " - pdb=" SG CYS Q 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 233 " - pdb=" SG CYS Q 263 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 243 " - pdb=" SG CYS Q 255 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 311 " - pdb=" SG CYS Q 344 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 395 " - pdb=" SG CYS Q 459 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 402 " - pdb=" SG CYS Q 432 " distance=2.02 Simple disulfide: pdb=" SG CYS S 100C" - pdb=" SG CYS S 100K" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 101 " - pdb=" SG CYS 6 220 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 108 " - pdb=" SG CYS 6 211 " distance=1.78 Simple disulfide: pdb=" SG CYS 6 113 " - pdb=" SG CYS 6 168 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 194 " - pdb=" SG CYS 6 206 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 233 " - pdb=" SG CYS 6 263 " distance=2.04 Simple disulfide: pdb=" SG CYS 6 243 " - pdb=" SG CYS 6 255 " distance=2.05 Simple disulfide: pdb=" SG CYS 6 311 " - pdb=" SG CYS 6 344 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 395 " - pdb=" SG CYS 6 459 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 402 " - pdb=" SG CYS 6 432 " distance=2.02 Simple disulfide: pdb=" SG CYS 8 100C" - pdb=" SG CYS 8 100K" distance=2.03 Simple disulfide: pdb=" SG CYS 9 23 " - pdb=" SG CYS 9 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN C 5 " - " MAN C 6 " " MAN I 4 " - " MAN I 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 5 " - " MAN a 6 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA C 3 " - " MAN C 8 " " MAN C 4 " - " MAN C 5 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 8 " " MAN a 4 " - " MAN a 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 7 " " BMA I 3 " - " MAN I 6 " " BMA J 3 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 7 " " BMA Z 3 " - " MAN Z 6 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 7 " " BMA f 3 " - " MAN f 6 " " BMA g 3 " - " MAN g 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " " NAG G 1 " - " FUC G 3 " " NAG W 1 " - " FUC W 3 " " NAG X 1 " - " FUC X 3 " " NAG Y 1 " - " FUC Y 3 " " NAG c 1 " - " FUC c 3 " " NAG d 1 " - " FUC d 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG 0 1 " - " ASN Q 284 " " NAG 1 1 " - " ASN Q 295 " " NAG 2 1 " - " ASN Q 316 " " NAG 3 1 " - " ASN Q 377 " " NAG 4 1 " - " ASN Q 460 " " NAG 5 1 " - " ASN Q 479 " " NAG 6 601 " - " ASN 6 70 " " NAG 6 602 " - " ASN 6 79 " " NAG 6 603 " - " ASN 6 171 " " NAG 6 604 " - " ASN 6 184 " " NAG 6 605 " - " ASN 6 198 " " NAG 6 606 " - " ASN 6 202 " " NAG 6 607 " - " ASN 6 244 " " NAG 6 608 " - " ASN 6 306 " " NAG 6 609 " - " ASN 6 476 " " NAG 6 610 " - " ASN 6 371 " " NAG 7 701 " - " ASN 7 627 " " NAG 7 702 " - " ASN 7 636 " " NAG 7 703 " - " ASN 7 652 " " NAG A 601 " - " ASN A 70 " " NAG A 602 " - " ASN A 79 " " NAG A 603 " - " ASN A 171 " " NAG A 604 " - " ASN A 184 " " NAG A 605 " - " ASN A 198 " " NAG A 606 " - " ASN A 202 " " NAG A 607 " - " ASN A 244 " " NAG A 608 " - " ASN A 306 " " NAG A 609 " - " ASN A 476 " " NAG A 610 " - " ASN A 371 " " NAG B 701 " - " ASN B 627 " " NAG B 702 " - " ASN B 636 " " NAG B 703 " - " ASN B 652 " " NAG C 1 " - " ASN A 37 " " NAG D 1 " - " ASN A 114 " " NAG E 1 " - " ASN A 146 " " NAG F 1 " - " ASN A 156 " " NAG G 1 " - " ASN A 212 " " NAG I 1 " - " ASN A 278 " " NAG J 1 " - " ASN A 284 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 316 " " NAG N 1 " - " ASN A 377 " " NAG O 1 " - " ASN A 460 " " NAG P 1 " - " ASN A 479 " " NAG Q 601 " - " ASN Q 70 " " NAG Q 602 " - " ASN Q 79 " " NAG Q 603 " - " ASN Q 171 " " NAG Q 604 " - " ASN Q 184 " " NAG Q 605 " - " ASN Q 198 " " NAG Q 606 " - " ASN Q 202 " " NAG Q 607 " - " ASN Q 244 " " NAG Q 608 " - " ASN Q 306 " " NAG Q 609 " - " ASN Q 476 " " NAG Q 610 " - " ASN Q 371 " " NAG R 701 " - " ASN R 627 " " NAG R 702 " - " ASN R 636 " " NAG R 703 " - " ASN R 652 " " NAG U 1 " - " ASN Q 37 " " NAG V 1 " - " ASN Q 114 " " NAG W 1 " - " ASN Q 146 " " NAG X 1 " - " ASN Q 156 " " NAG Y 1 " - " ASN Q 212 " " NAG Z 1 " - " ASN Q 278 " " NAG a 1 " - " ASN 6 37 " " NAG b 1 " - " ASN 6 114 " " NAG c 1 " - " ASN 6 146 " " NAG d 1 " - " ASN 6 156 " " NAG e 1 " - " ASN 6 212 " " NAG f 1 " - " ASN 6 278 " " NAG g 1 " - " ASN 6 284 " " NAG h 1 " - " ASN 6 295 " " NAG i 1 " - " ASN 6 316 " " NAG j 1 " - " ASN 6 377 " " NAG k 1 " - " ASN 6 460 " " NAG l 1 " - " ASN 6 479 " Time building additional restraints: 11.26 Conformation dependent library (CDL) restraints added in 4.2 seconds 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 23.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.659A pdb=" N ILE A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 553 through 573 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 585 through 612 Processing helix chain 'B' and resid 638 through 644 removed outlier: 4.069A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU B 651 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'Q' and resid 51 through 57 Processing helix chain 'Q' and resid 81 through 99 Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'Q' and resid 114 through 121 Processing helix chain 'Q' and resid 149 through 154 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 302 through 306 Processing helix chain 'Q' and resid 349 through 363 Processing helix chain 'Q' and resid 372 through 376 removed outlier: 3.659A pdb=" N ILE Q 376 " --> pdb=" O THR Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 390 Processing helix chain 'Q' and resid 404 through 412 Processing helix chain 'Q' and resid 420 through 424 Processing helix chain 'Q' and resid 485 through 488 Processing helix chain 'Q' and resid 489 through 494 Processing helix chain 'R' and resid 537 through 541 Processing helix chain 'R' and resid 553 through 573 Processing helix chain 'R' and resid 574 through 576 No H-bonds generated for 'chain 'R' and resid 574 through 576' Processing helix chain 'R' and resid 585 through 612 Processing helix chain 'R' and resid 638 through 644 removed outlier: 4.068A pdb=" N ARG R 644 " --> pdb=" O GLN R 640 " (cutoff:3.500A) Processing helix chain 'R' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU R 651 " --> pdb=" O ASP R 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN R 652 " --> pdb=" O PHE R 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA R 655 " --> pdb=" O GLU R 651 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 81 through 99 Processing helix chain '6' and resid 104 through 108 Processing helix chain '6' and resid 114 through 121 Processing helix chain '6' and resid 149 through 154 Processing helix chain '6' and resid 190 through 192 No H-bonds generated for 'chain '6' and resid 190 through 192' Processing helix chain '6' and resid 302 through 306 Processing helix chain '6' and resid 349 through 363 Processing helix chain '6' and resid 372 through 376 removed outlier: 3.658A pdb=" N ILE 6 376 " --> pdb=" O THR 6 373 " (cutoff:3.500A) Processing helix chain '6' and resid 385 through 390 Processing helix chain '6' and resid 404 through 412 Processing helix chain '6' and resid 420 through 424 Processing helix chain '6' and resid 485 through 488 Processing helix chain '6' and resid 489 through 494 Processing helix chain '7' and resid 537 through 541 Processing helix chain '7' and resid 553 through 573 Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 585 through 612 Processing helix chain '7' and resid 638 through 644 removed outlier: 4.069A pdb=" N ARG 7 644 " --> pdb=" O GLN 7 640 " (cutoff:3.500A) Processing helix chain '7' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU 7 651 " --> pdb=" O ASP 7 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN 7 652 " --> pdb=" O PHE 7 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) Processing helix chain '8' and resid 61 through 64 Processing helix chain '8' and resid 83 through 87 Processing sheet with id= 1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id= 2, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL A 258 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS A 44 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE A 75 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 180 through 188 Processing sheet with id= 6, first strand: chain 'A' and resid 142 through 143 Processing sheet with id= 7, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.729A pdb=" N GLN A 217 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 275 through 277 removed outlier: 7.288A pdb=" N THR A 379 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY A 455 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY A 315 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 399 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 320 through 323 Processing sheet with id= 11, first strand: chain 'H' and resid 4 through 5 Processing sheet with id= 12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.001A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 96 through 97 Processing sheet with id= 14, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.043A pdb=" N GLY L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id= 17, first strand: chain 'Q' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL Q 258 " --> pdb=" O LEU Q 69 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Q' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS Q 44 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Q' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE Q 75 " --> pdb=" O PRO Q 253 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 180 through 188 Processing sheet with id= 21, first strand: chain 'Q' and resid 142 through 143 Processing sheet with id= 22, first strand: chain 'Q' and resid 217 through 218 removed outlier: 6.729A pdb=" N GLN Q 217 " --> pdb=" O TYR Q 449 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 275 through 277 removed outlier: 7.289A pdb=" N THR Q 379 " --> pdb=" O MET Q 482 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY Q 455 " --> pdb=" O GLY Q 315 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY Q 315 " --> pdb=" O GLY Q 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE Q 399 " --> pdb=" O ARG Q 435 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 320 through 323 Processing sheet with id= 26, first strand: chain 'S' and resid 4 through 5 Processing sheet with id= 27, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.001A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 96 through 97 Processing sheet with id= 29, first strand: chain 'T' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR T 69 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN T 27 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER T 67 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE T 29 " --> pdb=" O SER T 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER T 65 " --> pdb=" O ILE T 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.043A pdb=" N GLY T 13 " --> pdb=" O ASP T 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '6' and resid 29 through 30 Processing sheet with id= 32, first strand: chain '6' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL 6 258 " --> pdb=" O LEU 6 69 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS 6 44 " --> pdb=" O LEU 6 58 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '6' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE 6 75 " --> pdb=" O PRO 6 253 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '6' and resid 180 through 188 Processing sheet with id= 36, first strand: chain '6' and resid 142 through 143 Processing sheet with id= 37, first strand: chain '6' and resid 217 through 218 removed outlier: 6.728A pdb=" N GLN 6 217 " --> pdb=" O TYR 6 449 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '6' and resid 275 through 277 removed outlier: 7.289A pdb=" N THR 6 379 " --> pdb=" O MET 6 482 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '6' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY 6 455 " --> pdb=" O GLY 6 315 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY 6 315 " --> pdb=" O GLY 6 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE 6 399 " --> pdb=" O ARG 6 435 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '6' and resid 320 through 323 Processing sheet with id= 41, first strand: chain '8' and resid 4 through 5 Processing sheet with id= 42, first strand: chain '8' and resid 11 through 12 removed outlier: 6.000A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '8' and resid 96 through 97 Processing sheet with id= 44, first strand: chain '9' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR 9 69 " --> pdb=" O ALA 9 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN 9 27 " --> pdb=" O SER 9 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER 9 67 " --> pdb=" O GLN 9 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE 9 29 " --> pdb=" O SER 9 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER 9 65 " --> pdb=" O ILE 9 29 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '9' and resid 10 through 13 removed outlier: 4.043A pdb=" N GLY 9 13 " --> pdb=" O ASP 9 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU 9 33 " --> pdb=" O TYR 9 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR 9 49 " --> pdb=" O LEU 9 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP 9 35 " --> pdb=" O LEU 9 47 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2007 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: 8.52 Time building geometry restraints manager: 11.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4393 1.32 - 1.47: 8428 1.47 - 1.61: 10345 1.61 - 1.76: 41 1.76 - 1.90: 169 Bond restraints: 23376 Sorted by residual: bond pdb=" NE1 TRP Q 290 " pdb=" CE2 TRP Q 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" NE1 TRP 6 290 " pdb=" CE2 TRP 6 290 " ideal model delta sigma weight residual 1.370 1.306 0.064 1.10e-02 8.26e+03 3.41e+01 bond pdb=" CB LEU R 674 " pdb=" CG LEU R 674 " ideal model delta sigma weight residual 1.530 1.641 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 99.57 - 111.69: 10968 111.69 - 123.81: 19496 123.81 - 135.93: 1297 135.93 - 148.05: 0 148.05 - 160.16: 3 Bond angle restraints: 31764 Sorted by residual: angle pdb=" C2 NAG A 610 " pdb=" N2 NAG A 610 " pdb=" C7 NAG A 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG 6 610 " pdb=" N2 NAG 6 610 " pdb=" C7 NAG 6 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG Q 610 " pdb=" N2 NAG Q 610 " pdb=" C7 NAG Q 610 " ideal model delta sigma weight residual 124.56 160.14 -35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL A 32 " pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 108.95 117.06 -8.11 9.80e-01 1.04e+00 6.84e+01 angle pdb=" N VAL Q 32 " pdb=" CA VAL Q 32 " pdb=" C VAL Q 32 " ideal model delta sigma weight residual 108.95 117.04 -8.09 9.80e-01 1.04e+00 6.81e+01 ... (remaining 31759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 15354 21.30 - 42.61: 438 42.61 - 63.91: 93 63.91 - 85.21: 84 85.21 - 106.51: 51 Dihedral angle restraints: 16020 sinusoidal: 8406 harmonic: 7614 Sorted by residual: dihedral pdb=" C PHE R 537 " pdb=" N PHE R 537 " pdb=" CA PHE R 537 " pdb=" CB PHE R 537 " ideal model delta harmonic sigma weight residual -122.60 -111.05 -11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE 7 537 " pdb=" N PHE 7 537 " pdb=" CA PHE 7 537 " pdb=" CB PHE 7 537 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE B 537 " pdb=" N PHE B 537 " pdb=" CA PHE B 537 " pdb=" CB PHE B 537 " ideal model delta harmonic sigma weight residual -122.60 -111.07 -11.53 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 16017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2533 0.107 - 0.213: 858 0.213 - 0.320: 380 0.320 - 0.426: 144 0.426 - 0.533: 78 Chirality restraints: 3993 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 3990 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG A 602 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG Q 602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG Q 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG Q 602 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG Q 602 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.85e+02 pdb=" C7 NAG 6 602 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG 6 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG 6 602 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG 6 602 " -0.022 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 9 2.04 - 2.75: 3260 2.75 - 3.47: 29380 3.47 - 4.18: 57781 4.18 - 4.90: 94807 Nonbonded interactions: 185237 Sorted by model distance: nonbonded pdb=" N SER 8 52 " pdb=" C TYR 8 52A" model vdw 1.320 3.350 nonbonded pdb=" N SER H 52 " pdb=" C TYR H 52A" model vdw 1.320 3.350 nonbonded pdb=" N SER S 52 " pdb=" C TYR S 52A" model vdw 1.320 3.350 nonbonded pdb=" C ILE H 51 " pdb=" N TYR H 52A" model vdw 1.326 3.350 nonbonded pdb=" C ILE S 51 " pdb=" N TYR S 52A" model vdw 1.326 3.350 ... (remaining 185232 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 '0' selection = chain 'J' selection = chain 'g' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain 'D' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = (chain '3' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = chain '6' selection = chain 'A' selection = chain 'Q' } ncs_group { reference = chain '7' selection = chain 'B' selection = chain 'R' } ncs_group { reference = chain '8' selection = chain 'H' selection = chain 'S' } ncs_group { reference = chain '9' selection = chain 'L' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'Z' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 7.090 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 63.260 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.023 0.150 23376 Z= 1.432 Angle : 1.855 35.605 31764 Z= 1.181 Chirality : 0.152 0.533 3993 Planarity : 0.011 0.251 3801 Dihedral : 13.523 106.514 11013 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 1.39 % Allowed : 3.14 % Favored : 95.47 % Rotamer: Outliers : 0.39 % Allowed : 1.04 % Favored : 98.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2583 helix: -0.23 (0.22), residues: 429 sheet: 0.31 (0.17), residues: 720 loop : -0.32 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.008 TRP A 290 HIS 0.008 0.002 HIS S 100N PHE 0.049 0.008 PHE R 537 TYR 0.057 0.009 TYR H 91 ARG 0.011 0.001 ARG 6 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 511 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7089 (t0) REVERT: A 338 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7347 (mmt180) REVERT: B 553 THR cc_start: 0.6849 (p) cc_final: 0.6330 (t) REVERT: B 590 ASN cc_start: 0.5725 (m-40) cc_final: 0.5139 (t0) REVERT: H 21 THR cc_start: 0.8477 (m) cc_final: 0.7922 (p) REVERT: H 32 CYS cc_start: 0.7015 (t) cc_final: 0.6748 (p) REVERT: H 82 ASN cc_start: 0.6998 (p0) cc_final: 0.6641 (p0) REVERT: Q 172 MET cc_start: 0.8144 (tpp) cc_final: 0.7897 (tpt) REVERT: Q 205 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7946 (mtm-85) REVERT: Q 306 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6917 (t0) REVERT: Q 338 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7169 (mmp80) REVERT: Q 473 ILE cc_start: 0.8710 (pt) cc_final: 0.8261 (mt) REVERT: R 553 THR cc_start: 0.6820 (p) cc_final: 0.6595 (t) REVERT: R 590 ASN cc_start: 0.5177 (m-40) cc_final: 0.4625 (t0) REVERT: R 625 TRP cc_start: 0.7375 (t-100) cc_final: 0.7128 (t-100) REVERT: R 668 MET cc_start: 0.6390 (tpp) cc_final: 0.5536 (mmp) REVERT: S 21 THR cc_start: 0.8218 (m) cc_final: 0.7835 (p) REVERT: S 32 CYS cc_start: 0.6893 (t) cc_final: 0.6649 (p) REVERT: S 69 ILE cc_start: 0.7347 (mt) cc_final: 0.7030 (mt) REVERT: S 73 MET cc_start: 0.7020 (mtt) cc_final: 0.6715 (mmm) REVERT: 6 306 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6818 (t0) REVERT: 6 338 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7291 (mmt-90) REVERT: 7 553 THR cc_start: 0.6745 (p) cc_final: 0.6468 (t) REVERT: 7 590 ASN cc_start: 0.5115 (m-40) cc_final: 0.4508 (t0) REVERT: 7 611 TRP cc_start: 0.7438 (m-10) cc_final: 0.7212 (m-10) REVERT: 7 625 TRP cc_start: 0.7239 (t-100) cc_final: 0.6964 (t-100) REVERT: 7 667 ASN cc_start: 0.7015 (m-40) cc_final: 0.6581 (t0) outliers start: 9 outliers final: 0 residues processed: 515 average time/residue: 0.3953 time to fit residues: 302.5699 Evaluate side-chains 271 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 265 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 338 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 223 HIS ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 77 GLN Q 223 HIS ** R 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 223 HIS ** 7 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23376 Z= 0.258 Angle : 0.784 12.561 31764 Z= 0.400 Chirality : 0.050 0.389 3993 Planarity : 0.005 0.052 3801 Dihedral : 11.203 84.027 6126 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.48 % Favored : 95.93 % Rotamer: Outliers : 1.99 % Allowed : 7.32 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2583 helix: 1.38 (0.25), residues: 435 sheet: 0.27 (0.17), residues: 750 loop : -0.74 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 6 91 HIS 0.005 0.001 HIS Q 210 PHE 0.025 0.002 PHE R 537 TYR 0.020 0.002 TYR A 401 ARG 0.008 0.001 ARG 6 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 334 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 TRP cc_start: 0.8115 (m100) cc_final: 0.7819 (m100) REVERT: B 553 THR cc_start: 0.6401 (p) cc_final: 0.6036 (t) REVERT: B 668 MET cc_start: 0.6501 (tpt) cc_final: 0.6158 (tpp) REVERT: H 21 THR cc_start: 0.8286 (m) cc_final: 0.7814 (p) REVERT: H 82 ASN cc_start: 0.6661 (p0) cc_final: 0.6442 (p0) REVERT: Q 172 MET cc_start: 0.8226 (tpp) cc_final: 0.7881 (tpt) REVERT: R 590 ASN cc_start: 0.4991 (m-40) cc_final: 0.4730 (m-40) REVERT: R 599 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: R 625 TRP cc_start: 0.7327 (t-100) cc_final: 0.7000 (t-100) REVERT: R 667 ASN cc_start: 0.6887 (m-40) cc_final: 0.6608 (t0) REVERT: S 5 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8624 (tp-100) REVERT: S 6 GLU cc_start: 0.6033 (mp0) cc_final: 0.5751 (mp0) REVERT: 6 119 ASP cc_start: 0.8583 (m-30) cc_final: 0.8324 (m-30) REVERT: 6 257 LYS cc_start: 0.8478 (mttt) cc_final: 0.8238 (mtpt) REVERT: 6 281 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8001 (mtp-110) REVERT: 6 325 MET cc_start: 0.7838 (mtm) cc_final: 0.7556 (mtp) REVERT: 7 667 ASN cc_start: 0.6989 (m-40) cc_final: 0.6555 (t0) REVERT: 7 668 MET cc_start: 0.6439 (tpt) cc_final: 0.5698 (tpp) REVERT: 8 21 THR cc_start: 0.8267 (m) cc_final: 0.7654 (p) outliers start: 46 outliers final: 34 residues processed: 371 average time/residue: 0.3676 time to fit residues: 210.0585 Evaluate side-chains 299 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 418 ASN Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 82 ASN Chi-restraints excluded: chain 8 residue 87 THR Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN H 100NHIS ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23376 Z= 0.296 Angle : 0.707 12.011 31764 Z= 0.361 Chirality : 0.048 0.324 3993 Planarity : 0.005 0.043 3801 Dihedral : 9.775 76.409 6114 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.68 % Favored : 94.77 % Rotamer: Outliers : 2.77 % Allowed : 8.70 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2583 helix: 1.26 (0.24), residues: 453 sheet: 0.17 (0.19), residues: 684 loop : -1.11 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 6 91 HIS 0.004 0.001 HIS Q 364 PHE 0.024 0.003 PHE R 537 TYR 0.027 0.002 TYR 6 401 ARG 0.010 0.001 ARG R 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 265 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 TRP cc_start: 0.8225 (m100) cc_final: 0.7988 (m100) REVERT: B 545 MET cc_start: 0.7145 (mtp) cc_final: 0.6913 (mtp) REVERT: H 21 THR cc_start: 0.8304 (m) cc_final: 0.7940 (p) REVERT: H 32 CYS cc_start: 0.6632 (p) cc_final: 0.6425 (m) REVERT: H 72 ASP cc_start: 0.7377 (t0) cc_final: 0.7071 (t0) REVERT: H 82 ASN cc_start: 0.6830 (p0) cc_final: 0.6628 (p0) REVERT: L 33 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (tp) REVERT: Q 91 TRP cc_start: 0.7503 (t-100) cc_final: 0.7165 (t-100) REVERT: Q 95 GLU cc_start: 0.8469 (tp30) cc_final: 0.8219 (tp30) REVERT: Q 172 MET cc_start: 0.8440 (tpp) cc_final: 0.8205 (tpt) REVERT: R 590 ASN cc_start: 0.4559 (m-40) cc_final: 0.4150 (t0) REVERT: R 625 TRP cc_start: 0.7293 (t-100) cc_final: 0.7041 (t-100) REVERT: R 631 ILE cc_start: 0.8389 (tp) cc_final: 0.8031 (mt) REVERT: R 648 PHE cc_start: 0.7604 (p90) cc_final: 0.7306 (p90) REVERT: R 667 ASN cc_start: 0.6918 (m-40) cc_final: 0.6490 (t0) REVERT: R 668 MET cc_start: 0.5742 (tpt) cc_final: 0.5210 (tpp) REVERT: S 5 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8573 (tp-100) REVERT: T 104 LEU cc_start: 0.6711 (tp) cc_final: 0.6231 (tt) REVERT: 6 119 ASP cc_start: 0.8645 (m-30) cc_final: 0.8381 (m-30) REVERT: 6 257 LYS cc_start: 0.8535 (mttt) cc_final: 0.8291 (mtpt) REVERT: 6 290 TRP cc_start: 0.8309 (m100) cc_final: 0.8098 (m100) REVERT: 6 309 MET cc_start: 0.8536 (ttt) cc_final: 0.8277 (ttt) REVERT: 7 633 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7726 (mmtm) REVERT: 7 667 ASN cc_start: 0.7035 (m-40) cc_final: 0.6625 (t0) REVERT: 7 668 MET cc_start: 0.6371 (tpt) cc_final: 0.5896 (tpp) REVERT: 8 21 THR cc_start: 0.8146 (m) cc_final: 0.7882 (p) outliers start: 64 outliers final: 48 residues processed: 318 average time/residue: 0.3505 time to fit residues: 173.0477 Evaluate side-chains 284 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 418 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 471 ASP Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 202 ASN Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 388 VAL Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Chi-restraints excluded: chain 9 residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 249 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23376 Z= 0.211 Angle : 0.646 13.944 31764 Z= 0.322 Chirality : 0.046 0.416 3993 Planarity : 0.004 0.040 3801 Dihedral : 9.241 99.760 6112 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.76 % Favored : 94.77 % Rotamer: Outliers : 2.47 % Allowed : 9.83 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2583 helix: 1.64 (0.24), residues: 453 sheet: 0.24 (0.19), residues: 651 loop : -1.18 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 7 625 HIS 0.002 0.001 HIS Q 364 PHE 0.017 0.002 PHE R 537 TYR 0.019 0.001 TYR 6 401 ARG 0.006 0.000 ARG 7 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 253 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: B 635 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7660 (p0) REVERT: H 32 CYS cc_start: 0.6653 (p) cc_final: 0.6450 (m) REVERT: H 75 LYS cc_start: 0.7700 (pttp) cc_final: 0.7324 (pttp) REVERT: H 82 ASN cc_start: 0.6708 (p0) cc_final: 0.6496 (p0) REVERT: Q 172 MET cc_start: 0.8407 (tpp) cc_final: 0.8197 (tpt) REVERT: R 590 ASN cc_start: 0.4459 (m-40) cc_final: 0.4245 (t0) REVERT: R 599 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: R 625 TRP cc_start: 0.7193 (t-100) cc_final: 0.6830 (t-100) REVERT: R 631 ILE cc_start: 0.8415 (tp) cc_final: 0.8103 (mt) REVERT: R 667 ASN cc_start: 0.6906 (m-40) cc_final: 0.6518 (t0) REVERT: T 5 THR cc_start: 0.7667 (p) cc_final: 0.7464 (p) REVERT: 6 119 ASP cc_start: 0.8595 (m-30) cc_final: 0.8318 (m-30) REVERT: 6 257 LYS cc_start: 0.8411 (mttt) cc_final: 0.8165 (mtpt) REVERT: 6 309 MET cc_start: 0.8486 (ttt) cc_final: 0.8278 (ttt) REVERT: 7 625 TRP cc_start: 0.6885 (t-100) cc_final: 0.6336 (t-100) REVERT: 7 667 ASN cc_start: 0.6909 (m-40) cc_final: 0.6493 (t0) REVERT: 7 668 MET cc_start: 0.6237 (tpt) cc_final: 0.5771 (tpp) REVERT: 8 21 THR cc_start: 0.8030 (m) cc_final: 0.7826 (p) outliers start: 57 outliers final: 47 residues processed: 295 average time/residue: 0.3567 time to fit residues: 164.3615 Evaluate side-chains 275 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 418 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 471 ASP Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 46 GLU Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 23376 Z= 0.462 Angle : 0.767 10.442 31764 Z= 0.386 Chirality : 0.049 0.336 3993 Planarity : 0.005 0.047 3801 Dihedral : 9.316 88.456 6112 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.31 % Favored : 93.19 % Rotamer: Outliers : 3.16 % Allowed : 10.04 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2583 helix: 1.73 (0.24), residues: 453 sheet: -0.18 (0.19), residues: 687 loop : -1.61 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 7 625 HIS 0.005 0.001 HIS 6 364 PHE 0.026 0.003 PHE H 78 TYR 0.038 0.003 TYR 6 401 ARG 0.009 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 252 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8525 (ttt) cc_final: 0.8115 (ttt) REVERT: B 599 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: H 28 THR cc_start: 0.8664 (p) cc_final: 0.8358 (m) REVERT: Q 91 TRP cc_start: 0.7406 (t-100) cc_final: 0.7102 (t-100) REVERT: R 590 ASN cc_start: 0.4363 (m-40) cc_final: 0.4060 (t0) REVERT: R 631 ILE cc_start: 0.8376 (tp) cc_final: 0.8089 (mt) REVERT: R 667 ASN cc_start: 0.6946 (m-40) cc_final: 0.6496 (t0) REVERT: S 6 GLU cc_start: 0.5972 (mp0) cc_final: 0.5753 (mp0) REVERT: S 28 THR cc_start: 0.8501 (p) cc_final: 0.8234 (m) REVERT: S 32 CYS cc_start: 0.6853 (p) cc_final: 0.6633 (m) REVERT: S 46 GLU cc_start: 0.8219 (tt0) cc_final: 0.7943 (tt0) REVERT: T 33 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (tp) REVERT: T 69 THR cc_start: 0.8161 (p) cc_final: 0.7898 (p) REVERT: 6 91 TRP cc_start: 0.7260 (t-100) cc_final: 0.6541 (t-100) REVERT: 7 625 TRP cc_start: 0.6892 (t-100) cc_final: 0.6206 (t-100) REVERT: 7 668 MET cc_start: 0.6456 (tpt) cc_final: 0.6092 (tpp) REVERT: 8 28 THR cc_start: 0.8639 (p) cc_final: 0.8350 (m) REVERT: 8 52 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6836 (m) REVERT: 8 77 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7404 (mm110) REVERT: 9 69 THR cc_start: 0.8064 (p) cc_final: 0.7793 (p) outliers start: 73 outliers final: 58 residues processed: 314 average time/residue: 0.3463 time to fit residues: 172.2040 Evaluate side-chains 285 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 202 ASN Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 388 VAL Chi-restraints excluded: chain 6 residue 393 THR Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 5 THR Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 336 ASN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 GLN S 82AASN T 30 ASN T 37 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23376 Z= 0.223 Angle : 0.639 10.263 31764 Z= 0.324 Chirality : 0.045 0.322 3993 Planarity : 0.004 0.053 3801 Dihedral : 8.839 89.627 6108 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.77 % Favored : 93.81 % Rotamer: Outliers : 2.81 % Allowed : 11.60 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2583 helix: 1.92 (0.24), residues: 453 sheet: -0.18 (0.19), residues: 690 loop : -1.50 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 6 91 HIS 0.003 0.001 HIS A 223 PHE 0.018 0.002 PHE R 537 TYR 0.020 0.001 TYR 6 401 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 254 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 92 GLN cc_start: 0.8737 (tp40) cc_final: 0.8257 (tp40) REVERT: A 203 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: A 309 MET cc_start: 0.8326 (ttt) cc_final: 0.8080 (ttt) REVERT: B 599 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: Q 91 TRP cc_start: 0.7152 (t-100) cc_final: 0.6923 (t-100) REVERT: Q 309 MET cc_start: 0.8433 (ttt) cc_final: 0.8086 (ttt) REVERT: R 590 ASN cc_start: 0.4299 (m-40) cc_final: 0.4031 (t0) REVERT: R 599 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: R 667 ASN cc_start: 0.6891 (m-40) cc_final: 0.6475 (t0) REVERT: R 668 MET cc_start: 0.5714 (tpt) cc_final: 0.5362 (tpp) REVERT: S 28 THR cc_start: 0.8587 (p) cc_final: 0.8265 (m) REVERT: S 32 CYS cc_start: 0.6789 (p) cc_final: 0.6476 (m) REVERT: S 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7985 (tt0) REVERT: T 69 THR cc_start: 0.8110 (p) cc_final: 0.7839 (p) REVERT: 6 257 LYS cc_start: 0.8399 (mttt) cc_final: 0.8169 (mtpt) REVERT: 7 625 TRP cc_start: 0.6956 (t-100) cc_final: 0.6199 (t-100) REVERT: 7 667 ASN cc_start: 0.6912 (m-40) cc_final: 0.6528 (t0) REVERT: 7 668 MET cc_start: 0.6364 (tpt) cc_final: 0.5933 (tpp) REVERT: 8 21 THR cc_start: 0.8125 (m) cc_final: 0.7855 (p) REVERT: 8 28 THR cc_start: 0.8610 (p) cc_final: 0.8350 (m) REVERT: 8 77 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7529 (mm110) outliers start: 65 outliers final: 53 residues processed: 301 average time/residue: 0.3429 time to fit residues: 162.1727 Evaluate side-chains 286 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 230 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 393 THR Chi-restraints excluded: chain Q residue 471 ASP Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 202 ASN Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 7 SER Chi-restraints excluded: chain 8 residue 46 GLU Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN H 77 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 23376 Z= 0.462 Angle : 0.754 10.576 31764 Z= 0.379 Chirality : 0.049 0.323 3993 Planarity : 0.005 0.068 3801 Dihedral : 9.085 86.202 6108 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.20 % Favored : 92.37 % Rotamer: Outliers : 3.16 % Allowed : 12.38 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2583 helix: 1.79 (0.24), residues: 453 sheet: -0.44 (0.19), residues: 699 loop : -1.81 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 345 HIS 0.005 0.001 HIS 6 364 PHE 0.022 0.003 PHE A 330 TYR 0.032 0.002 TYR 6 401 ARG 0.009 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 229 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8480 (ttt) cc_final: 0.8071 (ttt) REVERT: B 599 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: H 5 GLN cc_start: 0.8653 (tp40) cc_final: 0.8267 (tp-100) REVERT: Q 91 TRP cc_start: 0.7083 (t-100) cc_final: 0.6879 (t-100) REVERT: R 590 ASN cc_start: 0.4360 (m-40) cc_final: 0.4023 (t0) REVERT: R 667 ASN cc_start: 0.6839 (m-40) cc_final: 0.6455 (t0) REVERT: R 668 MET cc_start: 0.5827 (tpt) cc_final: 0.5467 (tpp) REVERT: S 5 GLN cc_start: 0.8710 (tp40) cc_final: 0.8173 (tp-100) REVERT: S 28 THR cc_start: 0.8804 (p) cc_final: 0.8566 (m) REVERT: S 32 CYS cc_start: 0.6933 (p) cc_final: 0.6662 (m) REVERT: S 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7956 (tt0) REVERT: T 33 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8465 (tp) REVERT: T 69 THR cc_start: 0.8323 (p) cc_final: 0.8058 (p) REVERT: 6 91 TRP cc_start: 0.7340 (t-100) cc_final: 0.6460 (t-100) REVERT: 6 95 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: 6 221 ASP cc_start: 0.8026 (t0) cc_final: 0.7659 (t0) REVERT: 7 616 ARG cc_start: 0.5961 (mtp180) cc_final: 0.5730 (ttp80) REVERT: 7 625 TRP cc_start: 0.6843 (t-100) cc_final: 0.6033 (t-100) REVERT: 7 668 MET cc_start: 0.6538 (tpt) cc_final: 0.6056 (tpp) REVERT: 8 52 SER cc_start: 0.7342 (OUTLIER) cc_final: 0.7067 (m) REVERT: 8 77 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7409 (mm110) REVERT: 9 69 THR cc_start: 0.8293 (p) cc_final: 0.8001 (p) outliers start: 73 outliers final: 55 residues processed: 289 average time/residue: 0.3503 time to fit residues: 159.6682 Evaluate side-chains 279 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 393 THR Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 95 GLU Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 202 ASN Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 388 VAL Chi-restraints excluded: chain 6 residue 393 THR Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 7 SER Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN H 77 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 640 GLN S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23376 Z= 0.199 Angle : 0.611 11.062 31764 Z= 0.308 Chirality : 0.044 0.313 3993 Planarity : 0.004 0.053 3801 Dihedral : 8.496 83.328 6108 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.77 % Favored : 93.92 % Rotamer: Outliers : 2.38 % Allowed : 13.38 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.92 (0.17), residues: 2583 helix: 1.97 (0.25), residues: 453 sheet: -0.35 (0.20), residues: 672 loop : -1.65 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 6 91 HIS 0.003 0.001 HIS A 364 PHE 0.018 0.002 PHE 7 537 TYR 0.017 0.001 TYR 6 401 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 325 MET cc_start: 0.8371 (mtp) cc_final: 0.8132 (mtp) REVERT: B 599 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: Q 309 MET cc_start: 0.8402 (ttt) cc_final: 0.8097 (ttt) REVERT: R 590 ASN cc_start: 0.4417 (m-40) cc_final: 0.4118 (t0) REVERT: R 599 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: R 667 ASN cc_start: 0.6801 (m-40) cc_final: 0.6445 (t0) REVERT: R 668 MET cc_start: 0.5736 (tpt) cc_final: 0.5371 (tpp) REVERT: S 28 THR cc_start: 0.8696 (p) cc_final: 0.8447 (m) REVERT: S 32 CYS cc_start: 0.6808 (p) cc_final: 0.6582 (m) REVERT: S 46 GLU cc_start: 0.8295 (tt0) cc_final: 0.8005 (tt0) REVERT: T 69 THR cc_start: 0.8266 (p) cc_final: 0.7994 (p) REVERT: 6 88 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7258 (tm-30) REVERT: 6 221 ASP cc_start: 0.7724 (t0) cc_final: 0.7298 (t70) REVERT: 6 257 LYS cc_start: 0.8329 (mttt) cc_final: 0.8113 (mtpt) REVERT: 6 293 ARG cc_start: 0.7960 (mpt180) cc_final: 0.7698 (mtt90) REVERT: 7 625 TRP cc_start: 0.6745 (t-100) cc_final: 0.5876 (t-100) REVERT: 7 667 ASN cc_start: 0.6948 (m-40) cc_final: 0.6541 (t0) REVERT: 7 668 MET cc_start: 0.6228 (tpt) cc_final: 0.5840 (tpp) REVERT: 8 52 SER cc_start: 0.7174 (OUTLIER) cc_final: 0.6944 (m) REVERT: 8 77 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7476 (mm110) REVERT: 9 69 THR cc_start: 0.8227 (p) cc_final: 0.7942 (p) outliers start: 55 outliers final: 45 residues processed: 287 average time/residue: 0.3436 time to fit residues: 153.9211 Evaluate side-chains 287 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 239 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 293 ARG Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 393 THR Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 545 MET Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 7 SER Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 42 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 0.0060 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 209 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 230 optimal weight: 0.0370 chunk 152 optimal weight: 6.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 GLN S 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23376 Z= 0.171 Angle : 0.593 11.395 31764 Z= 0.297 Chirality : 0.044 0.304 3993 Planarity : 0.004 0.048 3801 Dihedral : 7.994 76.745 6108 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.74 % Favored : 92.95 % Rotamer: Outliers : 2.21 % Allowed : 13.90 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2583 helix: 2.00 (0.24), residues: 453 sheet: -0.21 (0.19), residues: 669 loop : -1.53 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 6 91 HIS 0.002 0.001 HIS 6 433 PHE 0.015 0.001 PHE 7 537 TYR 0.021 0.001 TYR 6 401 ARG 0.011 0.000 ARG 6 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8420 (mtp) cc_final: 0.8206 (mtp) REVERT: B 599 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: Q 95 GLU cc_start: 0.8427 (tp30) cc_final: 0.7612 (mp0) REVERT: Q 186 THR cc_start: 0.9085 (m) cc_final: 0.8602 (p) REVERT: Q 221 ASP cc_start: 0.7404 (t0) cc_final: 0.6956 (t70) REVERT: Q 309 MET cc_start: 0.8374 (ttt) cc_final: 0.8103 (ttt) REVERT: R 590 ASN cc_start: 0.4366 (m-40) cc_final: 0.4118 (t0) REVERT: R 599 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: R 667 ASN cc_start: 0.6778 (m-40) cc_final: 0.6451 (t0) REVERT: R 668 MET cc_start: 0.5686 (tpt) cc_final: 0.5369 (tpp) REVERT: S 28 THR cc_start: 0.8681 (p) cc_final: 0.8436 (m) REVERT: S 46 GLU cc_start: 0.8229 (tt0) cc_final: 0.7970 (tt0) REVERT: T 69 THR cc_start: 0.8213 (p) cc_final: 0.7936 (p) REVERT: 6 91 TRP cc_start: 0.7035 (t-100) cc_final: 0.6307 (t-100) REVERT: 6 293 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7575 (mtt90) REVERT: 7 625 TRP cc_start: 0.6756 (t-100) cc_final: 0.6346 (t-100) REVERT: 7 667 ASN cc_start: 0.6854 (m-40) cc_final: 0.6465 (t0) REVERT: 7 668 MET cc_start: 0.6131 (tpt) cc_final: 0.5743 (tpp) REVERT: 8 52 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6957 (m) REVERT: 8 77 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7474 (mm110) REVERT: 9 69 THR cc_start: 0.8161 (p) cc_final: 0.7893 (p) outliers start: 51 outliers final: 37 residues processed: 288 average time/residue: 0.3413 time to fit residues: 155.8277 Evaluate side-chains 273 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 233 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain R residue 638 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 361 ILE Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 7 SER Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 90 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23376 Z= 0.204 Angle : 0.603 11.546 31764 Z= 0.302 Chirality : 0.044 0.303 3993 Planarity : 0.004 0.049 3801 Dihedral : 7.798 65.576 6108 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.46 % Rotamer: Outliers : 2.16 % Allowed : 14.11 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2583 helix: 2.05 (0.24), residues: 453 sheet: -0.16 (0.20), residues: 666 loop : -1.55 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 187 HIS 0.003 0.001 HIS 6 364 PHE 0.015 0.002 PHE 7 537 TYR 0.027 0.001 TYR 9 91 ARG 0.008 0.000 ARG R 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8437 (mtp) cc_final: 0.8235 (mtp) REVERT: A 485 GLU cc_start: 0.7886 (tp30) cc_final: 0.7627 (mm-30) REVERT: B 599 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: L 90 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7875 (pp30) REVERT: Q 95 GLU cc_start: 0.8453 (tp30) cc_final: 0.7528 (mp0) REVERT: Q 152 ILE cc_start: 0.8544 (mt) cc_final: 0.8167 (mt) REVERT: Q 221 ASP cc_start: 0.7467 (t0) cc_final: 0.7054 (t70) REVERT: Q 309 MET cc_start: 0.8404 (ttt) cc_final: 0.8135 (ttt) REVERT: R 590 ASN cc_start: 0.4391 (m-40) cc_final: 0.4154 (t0) REVERT: R 599 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: R 667 ASN cc_start: 0.6783 (m-40) cc_final: 0.6468 (t0) REVERT: R 668 MET cc_start: 0.5722 (tpt) cc_final: 0.5397 (tpp) REVERT: S 28 THR cc_start: 0.8694 (p) cc_final: 0.8492 (m) REVERT: S 46 GLU cc_start: 0.8227 (tt0) cc_final: 0.7953 (tt0) REVERT: T 69 THR cc_start: 0.8258 (p) cc_final: 0.7986 (p) REVERT: 6 293 ARG cc_start: 0.7860 (mpt180) cc_final: 0.7577 (mtt90) REVERT: 7 625 TRP cc_start: 0.6763 (t-100) cc_final: 0.6328 (t-100) REVERT: 7 667 ASN cc_start: 0.6849 (m-40) cc_final: 0.6468 (t0) REVERT: 7 668 MET cc_start: 0.6254 (tpt) cc_final: 0.6033 (tpp) REVERT: 8 52 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.7054 (m) REVERT: 8 77 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7479 (mm110) REVERT: 9 69 THR cc_start: 0.8240 (p) cc_final: 0.7955 (p) outliers start: 50 outliers final: 43 residues processed: 274 average time/residue: 0.3337 time to fit residues: 146.4850 Evaluate side-chains 279 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain R residue 638 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 44 CYS Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 220 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 7 residue 638 THR Chi-restraints excluded: chain 8 residue 52 SER Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 chunk 210 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 90 GLN ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 GLN S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128646 restraints weight = 32181.245| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.80 r_work: 0.3352 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23376 Z= 0.239 Angle : 0.756 59.200 31764 Z= 0.414 Chirality : 0.046 0.870 3993 Planarity : 0.004 0.050 3801 Dihedral : 7.806 65.461 6108 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.39 % Favored : 93.38 % Rotamer: Outliers : 2.29 % Allowed : 14.33 % Favored : 83.38 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2583 helix: 2.06 (0.24), residues: 453 sheet: -0.17 (0.20), residues: 666 loop : -1.56 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP Q 345 HIS 0.002 0.001 HIS 6 364 PHE 0.015 0.002 PHE 7 537 TYR 0.022 0.001 TYR 9 91 ARG 0.020 0.000 ARG R 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.58 seconds wall clock time: 86 minutes 9.69 seconds (5169.69 seconds total)