Starting phenix.real_space_refine on Sun Feb 18 22:18:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4g_25676/02_2024/7t4g_25676.pdb" } resolution = 3.7 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= 0.040 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 14367 2.51 5 N 3696 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "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 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "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 "A TYR 515": "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 PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 100": "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 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "G PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 637": "OE1" <-> "OE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23045 Number of models: 1 Model: "" Number of chains: 57 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} 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: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "D" 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: "G" 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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" 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: "E" 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: "F" 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: "J" 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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: "Q" 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: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: "m" 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "p" 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: "q" 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: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" 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: 12.31, per 1000 atoms: 0.53 Number of scatterers: 23045 At special positions: 0 Unit cell: (156.4, 155.25, 124.2, 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 4835 8.00 N 3696 7.00 C 14367 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=2.06 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 459 " distance=2.04 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 C 101 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 211 " distance=2.02 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 168 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 263 " distance=2.05 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 255 " distance=2.08 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 395 " - pdb=" SG CYS C 459 " distance=2.04 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS G 100C" - pdb=" SG CYS G 100K" distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 211 " distance=1.79 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 168 " distance=2.02 Simple disulfide: pdb=" SG CYS E 194 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 263 " distance=2.04 Simple disulfide: pdb=" SG CYS E 243 " - pdb=" SG CYS E 255 " distance=2.05 Simple disulfide: pdb=" SG CYS E 311 " - pdb=" SG CYS E 344 " distance=2.07 Simple disulfide: pdb=" SG CYS E 395 " - pdb=" SG CYS E 459 " distance=2.06 Simple disulfide: pdb=" SG CYS E 402 " - pdb=" SG CYS E 432 " distance=2.02 Simple disulfide: pdb=" SG CYS J 100C" - pdb=" SG CYS J 100K" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 5 " - " MAN M 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN Z 5 " - " MAN Z 6 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN m 5 " - " MAN m 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " ALPHA1-3 " BMA M 3 " - " MAN M 8 " " MAN M 4 " - " MAN M 5 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 8 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA m 3 " - " MAN m 8 " " MAN m 4 " - " MAN m 5 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 7 " " BMA R 3 " - " MAN R 7 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 7 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Q 1 " - " FUC Q 3 " " NAG V 1 " - " FUC V 3 " " NAG b 1 " - " FUC b 3 " " NAG c 1 " - " FUC c 3 " " NAG d 1 " - " FUC d 3 " " NAG i 1 " - " FUC i 3 " " NAG o 1 " - " FUC o 3 " " NAG p 1 " - " FUC p 3 " " NAG q 1 " - " FUC q 3 " " NAG v 1 " - " FUC v 3 " NAG-ASN " 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 B 701 " - " ASN B 627 " " NAG B 702 " - " ASN B 636 " " NAG B 703 " - " ASN B 652 " " NAG C 601 " - " ASN C 70 " " NAG C 602 " - " ASN C 79 " " NAG C 603 " - " ASN C 171 " " NAG C 604 " - " ASN C 184 " " NAG C 605 " - " ASN C 198 " " NAG C 606 " - " ASN C 202 " " NAG C 607 " - " ASN C 244 " " NAG C 608 " - " ASN C 306 " " NAG C 609 " - " ASN C 476 " " NAG D 701 " - " ASN D 627 " " NAG D 702 " - " ASN D 636 " " NAG D 703 " - " ASN D 652 " " NAG E 601 " - " ASN E 70 " " NAG E 602 " - " ASN E 79 " " NAG E 603 " - " ASN E 171 " " NAG E 604 " - " ASN E 184 " " NAG E 605 " - " ASN E 198 " " NAG E 606 " - " ASN E 202 " " NAG E 607 " - " ASN E 244 " " NAG E 608 " - " ASN E 306 " " NAG E 609 " - " ASN E 476 " " NAG F 701 " - " ASN F 627 " " NAG F 702 " - " ASN F 636 " " NAG F 703 " - " ASN F 652 " " NAG M 1 " - " ASN A 37 " " NAG N 1 " - " ASN A 114 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 212 " " NAG R 1 " - " ASN A 278 " " NAG S 1 " - " ASN A 284 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 316 " " NAG V 1 " - " ASN A 371 " " NAG W 1 " - " ASN A 377 " " NAG X 1 " - " ASN A 460 " " NAG Y 1 " - " ASN A 479 " " NAG Z 1 " - " ASN C 37 " " NAG a 1 " - " ASN C 114 " " NAG b 1 " - " ASN C 146 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 212 " " NAG e 1 " - " ASN C 278 " " NAG f 1 " - " ASN C 284 " " NAG g 1 " - " ASN C 295 " " NAG h 1 " - " ASN C 316 " " NAG i 1 " - " ASN C 371 " " NAG j 1 " - " ASN C 377 " " NAG k 1 " - " ASN C 460 " " NAG l 1 " - " ASN C 479 " " NAG m 1 " - " ASN E 37 " " NAG n 1 " - " ASN E 114 " " NAG o 1 " - " ASN E 146 " " NAG p 1 " - " ASN E 156 " " NAG q 1 " - " ASN E 212 " " NAG r 1 " - " ASN E 278 " " NAG s 1 " - " ASN E 284 " " NAG t 1 " - " ASN E 295 " " NAG u 1 " - " ASN E 316 " " NAG v 1 " - " ASN E 371 " " NAG w 1 " - " ASN E 377 " " NAG x 1 " - " ASN E 460 " " NAG y 1 " - " ASN E 479 " Time building additional restraints: 11.00 Conformation dependent library (CDL) restraints added in 4.0 seconds 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 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: 64 helices and 45 sheets defined 23.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 80 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: 3.772A pdb=" N ILE A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.564A pdb=" N PHE A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'B' and resid 535 through 540 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 584 through 611 removed outlier: 3.705A pdb=" N THR B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 646 through 674 removed outlier: 3.748A pdb=" N ASN B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.012A 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 'L' and resid 79 through 83 removed outlier: 4.165A pdb=" N GLY L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 485 through 488 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 553 through 573 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 585 through 612 Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 646 through 674 removed outlier: 3.975A pdb=" N GLU D 651 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN D 652 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA D 655 " --> pdb=" O GLU D 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 80 through 99 removed outlier: 3.663A pdb=" N ILE E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 349 through 363 Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE E 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.599A pdb=" N PHE E 390 " --> pdb=" O PRO E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 485 through 488 Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'F' and resid 535 through 541 removed outlier: 4.305A pdb=" N THR F 540 " --> pdb=" O PHE F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 573 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 584 through 612 Processing helix chain 'F' and resid 638 through 644 Processing helix chain 'F' and resid 646 through 674 removed outlier: 3.942A pdb=" N GLU F 651 " --> pdb=" O ASP F 647 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN F 652 " --> pdb=" O PHE F 648 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.209A pdb=" N VAL A 258 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.668A pdb=" N CYS A 44 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.934A pdb=" N PHE A 75 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA7, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.740A pdb=" N GLN A 217 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 277 removed outlier: 7.322A pdb=" N THR A 379 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 290 removed outlier: 5.770A pdb=" N GLY A 455 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 315 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 399 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.441A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.848A pdb=" N GLY L 13 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 35 through 37 removed outlier: 4.099A pdb=" N VAL C 258 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AC1, first strand: chain 'C' and resid 73 through 76 removed outlier: 4.910A pdb=" N PHE C 75 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 188 Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AC4, first strand: chain 'C' and resid 217 through 218 removed outlier: 6.629A pdb=" N GLN C 217 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 275 through 277 removed outlier: 7.283A pdb=" N THR C 379 " --> pdb=" O MET C 482 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.043A pdb=" N GLY C 455 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY C 315 " --> pdb=" O GLY C 455 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 399 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 320 through 323 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.024A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=AD2, first strand: chain 'I' and resid 4 through 7 removed outlier: 5.440A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N ILE I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N SER I 65 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 13 removed outlier: 4.025A pdb=" N GLY I 13 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 29 through 30 Processing sheet with id=AD5, first strand: chain 'E' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL E 258 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.855A pdb=" N CYS E 44 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 73 through 76 removed outlier: 4.907A pdb=" N PHE E 75 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 180 through 188 Processing sheet with id=AD9, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'E' and resid 217 through 218 removed outlier: 6.644A pdb=" N GLN E 217 " --> pdb=" O TYR E 449 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 275 through 277 removed outlier: 7.387A pdb=" N THR E 379 " --> pdb=" O MET E 482 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 288 through 290 removed outlier: 5.845A pdb=" N GLY E 455 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 315 " --> pdb=" O GLY E 455 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 399 " --> pdb=" O ARG E 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 320 through 323 Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 5.992A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 5.344A pdb=" N THR K 69 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLN K 27 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N SER K 67 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N ILE K 29 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N SER K 65 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.985A pdb=" N GLY K 13 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2049 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: 8.69 Time building geometry restraints manager: 11.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4718 1.32 - 1.47: 8416 1.47 - 1.61: 10194 1.61 - 1.76: 37 1.76 - 1.90: 169 Bond restraints: 23534 Sorted by residual: bond pdb=" CA VAL F 573 " pdb=" CB VAL F 573 " ideal model delta sigma weight residual 1.537 1.575 -0.038 5.00e-03 4.00e+04 5.83e+01 bond pdb=" CA VAL D 573 " pdb=" CB VAL D 573 " ideal model delta sigma weight residual 1.539 1.573 -0.034 5.40e-03 3.43e+04 4.08e+01 bond pdb=" CB LEU D 674 " pdb=" CG LEU D 674 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" CB LEU F 674 " pdb=" CG LEU F 674 " ideal model delta sigma weight residual 1.530 1.637 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 23529 not shown) Histogram of bond angle deviations from ideal: 94.91 - 102.82: 226 102.82 - 110.73: 8814 110.73 - 118.65: 10738 118.65 - 126.56: 11795 126.56 - 134.47: 422 Bond angle restraints: 31995 Sorted by residual: angle pdb=" N VAL E 32 " pdb=" CA VAL E 32 " pdb=" C VAL E 32 " ideal model delta sigma weight residual 108.63 116.68 -8.05 8.60e-01 1.35e+00 8.75e+01 angle pdb=" C VAL B 573 " pdb=" N PRO B 574 " pdb=" CA PRO B 574 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C VAL D 573 " pdb=" N PRO D 574 " pdb=" CA PRO D 574 " ideal model delta sigma weight residual 119.82 127.61 -7.79 9.80e-01 1.04e+00 6.32e+01 angle pdb=" C VAL F 573 " pdb=" N PRO F 574 " pdb=" CA PRO F 574 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" N THR B 588 " pdb=" CA THR B 588 " pdb=" C THR B 588 " ideal model delta sigma weight residual 113.41 103.86 9.55 1.22e+00 6.72e-01 6.13e+01 ... (remaining 31990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 15594 21.43 - 42.85: 403 42.85 - 64.28: 94 64.28 - 85.70: 117 85.70 - 107.13: 68 Dihedral angle restraints: 16276 sinusoidal: 8653 harmonic: 7623 Sorted by residual: dihedral pdb=" CB CYS E 243 " pdb=" SG CYS E 243 " pdb=" SG CYS E 255 " pdb=" CB CYS E 255 " ideal model delta sinusoidal sigma weight residual 93.00 -176.51 -90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 243 " pdb=" SG CYS C 243 " pdb=" SG CYS C 255 " pdb=" CB CYS C 255 " ideal model delta sinusoidal sigma weight residual -86.00 -176.32 90.32 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 255 " pdb=" CB CYS A 255 " ideal model delta sinusoidal sigma weight residual 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 16273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2544 0.107 - 0.214: 946 0.214 - 0.320: 361 0.320 - 0.427: 139 0.427 - 0.534: 68 Chirality restraints: 4058 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 6.11e+02 chirality pdb=" C1 MAN R 6 " pdb=" O2 MAN R 5 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 2.02 0.38 2.00e-02 2.50e+03 3.52e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.27e+02 ... (remaining 4055 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 2 " 0.217 2.00e-02 2.50e+03 1.80e-01 4.07e+02 pdb=" C7 NAG t 2 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG t 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG t 2 " -0.297 2.00e-02 2.50e+03 pdb=" O7 NAG t 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.168 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" C7 NAG R 1 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 371 " -0.137 2.00e-02 2.50e+03 1.36e-01 2.33e+02 pdb=" CG ASN C 371 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 371 " 0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN C 371 " 0.200 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.168 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7757 2.87 - 3.38: 20792 3.38 - 3.89: 39341 3.89 - 4.39: 45462 4.39 - 4.90: 72437 Nonbonded interactions: 185789 Sorted by model distance: nonbonded pdb=" OD1 ASP C 89 " pdb=" NZ LYS D 589 " model vdw 2.363 2.520 nonbonded pdb=" C4 BMA R 3 " pdb=" O6 BMA R 3 " model vdw 2.446 2.776 nonbonded pdb=" N THR C 246 " pdb=" N ASN C 247 " model vdw 2.447 2.560 nonbonded pdb=" N ARG B 582 " pdb=" N LEU B 583 " model vdw 2.451 2.560 nonbonded pdb=" N THR A 246 " pdb=" N ASN A 247 " model vdw 2.452 2.560 ... (remaining 185784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 2 or resid 5 through 8)) selection = (chain 'R' and (resid 1 or resid 4 through 7)) selection = (chain 'Z' and (resid 2 or resid 5 through 8)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 2 or resid 5 through 8)) selection = (chain 'r' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'u' selection = chain 'x' } ncs_group { reference = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) selection = (chain 'y' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 's' selection = chain 't' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 62.810 Find NCS groups from input model: 1.450 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.022 0.155 23534 Z= 1.373 Angle : 1.831 10.909 31995 Z= 1.174 Chirality : 0.149 0.534 4058 Planarity : 0.010 0.180 3813 Dihedral : 14.435 107.127 11269 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 1.35 % Allowed : 2.85 % Favored : 95.80 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % 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: -0.17 (0.16), residues: 2595 helix: -0.06 (0.21), residues: 471 sheet: 0.69 (0.19), residues: 654 loop : -0.45 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP F 586 HIS 0.008 0.003 HIS G 100N PHE 0.039 0.007 PHE B 537 TYR 0.055 0.008 TYR H 91 ARG 0.012 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 581 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8385 (m-10) cc_final: 0.8118 (m-10) REVERT: A 163 GLU cc_start: 0.7552 (tp30) cc_final: 0.7335 (tp30) REVERT: A 391 MET cc_start: 0.8515 (ttp) cc_final: 0.8133 (ttm) REVERT: B 592 GLN cc_start: 0.6083 (tp40) cc_final: 0.5639 (tm-30) REVERT: H 55 ASP cc_start: 0.8567 (m-30) cc_final: 0.8281 (p0) REVERT: H 60 ASN cc_start: 0.8382 (t0) cc_final: 0.8150 (t0) REVERT: H 69 ILE cc_start: 0.8910 (mt) cc_final: 0.8543 (mt) REVERT: L 101 THR cc_start: 0.7782 (p) cc_final: 0.7364 (t) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7772 (p0) REVERT: C 56 GLN cc_start: 0.7323 (mt0) cc_final: 0.7073 (mp10) REVERT: C 265 ARG cc_start: 0.8806 (ptp90) cc_final: 0.8022 (ptp-170) REVERT: D 559 LEU cc_start: 0.8780 (tp) cc_final: 0.8423 (tt) REVERT: D 589 LYS cc_start: 0.8421 (mtpt) cc_final: 0.7803 (mtmt) REVERT: D 603 LYS cc_start: 0.8929 (tttm) cc_final: 0.8662 (tptt) REVERT: D 631 ILE cc_start: 0.9224 (mm) cc_final: 0.8951 (pt) REVERT: G 55 ASP cc_start: 0.8689 (m-30) cc_final: 0.8469 (m-30) REVERT: G 90 TYR cc_start: 0.7696 (m-80) cc_final: 0.7377 (m-80) REVERT: I 19 VAL cc_start: 0.6728 (t) cc_final: 0.6517 (p) REVERT: I 74 THR cc_start: 0.7341 (m) cc_final: 0.6703 (p) REVERT: I 79 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6979 (tm-30) REVERT: I 87 TYR cc_start: 0.8943 (m-80) cc_final: 0.8581 (m-80) REVERT: E 290 TRP cc_start: 0.8699 (m100) cc_final: 0.8431 (m100) REVERT: E 391 MET cc_start: 0.8824 (ttp) cc_final: 0.8584 (ttt) REVERT: F 557 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7370 (ptt90) REVERT: F 588 THR cc_start: 0.7428 (m) cc_final: 0.7155 (p) REVERT: F 633 LYS cc_start: 0.7977 (mttp) cc_final: 0.7771 (mmtt) REVERT: F 668 MET cc_start: 0.8797 (mmm) cc_final: 0.8543 (mmp) REVERT: J 54 ASN cc_start: 0.8052 (t0) cc_final: 0.7800 (p0) REVERT: J 100 TYR cc_start: 0.8719 (m-80) cc_final: 0.8469 (m-80) REVERT: K 4 LEU cc_start: 0.8586 (tp) cc_final: 0.8368 (tp) REVERT: K 19 VAL cc_start: 0.8291 (t) cc_final: 0.7992 (t) REVERT: K 24 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7541 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 585 average time/residue: 0.3892 time to fit residues: 336.5989 Evaluate side-chains 291 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain E residue 476 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 291 HIS A 302 ASN A 336 ASN A 394 ASN B 566 GLN B 635 ASN B 661 GLN H 56 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 89 GLN C 210 HIS C 270 GLN C 291 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN E 291 HIS E 433 HIS ** F 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23534 Z= 0.241 Angle : 0.799 13.567 31995 Z= 0.404 Chirality : 0.050 0.541 4058 Planarity : 0.005 0.056 3813 Dihedral : 11.765 86.624 6368 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.89 % Favored : 95.61 % Rotamer: Outliers : 2.77 % Allowed : 8.18 % Favored : 89.05 % 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: 2595 helix: 1.27 (0.24), residues: 447 sheet: 0.54 (0.20), residues: 636 loop : -0.79 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 36 HIS 0.007 0.001 HIS A 291 PHE 0.020 0.002 PHE B 537 TYR 0.030 0.002 TYR L 91 ARG 0.007 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 343 time to evaluate : 2.723 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 48 ASN cc_start: 0.7796 (t0) cc_final: 0.6941 (m-40) REVERT: A 391 MET cc_start: 0.8378 (ttp) cc_final: 0.8043 (ttt) REVERT: B 545 MET cc_start: 0.8400 (mmm) cc_final: 0.7667 (mmm) REVERT: B 629 SER cc_start: 0.8237 (m) cc_final: 0.7808 (t) REVERT: H 54 ASN cc_start: 0.7952 (t0) cc_final: 0.7740 (t0) REVERT: H 55 ASP cc_start: 0.8671 (m-30) cc_final: 0.8256 (p0) REVERT: H 73 MET cc_start: 0.7338 (ppp) cc_final: 0.6758 (ppp) REVERT: L 48 ILE cc_start: 0.8655 (mm) cc_final: 0.8447 (mt) REVERT: L 91 TYR cc_start: 0.8483 (p90) cc_final: 0.8226 (p90) REVERT: C 232 TYR cc_start: 0.8321 (m-80) cc_final: 0.8096 (m-80) REVERT: D 559 LEU cc_start: 0.8667 (tp) cc_final: 0.8393 (tt) REVERT: D 593 THR cc_start: 0.8877 (m) cc_final: 0.8573 (p) REVERT: D 620 CYS cc_start: 0.7641 (m) cc_final: 0.7213 (p) REVERT: D 631 ILE cc_start: 0.9138 (mm) cc_final: 0.8867 (pt) REVERT: G 6 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: G 55 ASP cc_start: 0.8779 (m-30) cc_final: 0.8570 (m-30) REVERT: I 74 THR cc_start: 0.7141 (m) cc_final: 0.6876 (p) REVERT: I 87 TYR cc_start: 0.8843 (m-80) cc_final: 0.8566 (m-80) REVERT: E 391 MET cc_start: 0.8613 (ttp) cc_final: 0.8331 (ttt) REVERT: F 557 ARG cc_start: 0.7583 (ptt180) cc_final: 0.7157 (ptt90) REVERT: F 633 LYS cc_start: 0.7898 (mttp) cc_final: 0.7643 (mmtt) REVERT: F 668 MET cc_start: 0.8727 (mmm) cc_final: 0.8522 (mmt) REVERT: J 75 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8382 (tptp) REVERT: K 24 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7196 (mtm-85) outliers start: 64 outliers final: 33 residues processed: 389 average time/residue: 0.3530 time to fit residues: 210.6001 Evaluate side-chains 291 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 257 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain K residue 103 LEU 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: 9.9990 chunk 194 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 635 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN C 223 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 433 HIS ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 23534 Z= 0.579 Angle : 0.930 10.787 31995 Z= 0.470 Chirality : 0.054 0.538 4058 Planarity : 0.006 0.074 3813 Dihedral : 10.295 79.141 6368 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.43 % Favored : 94.03 % Rotamer: Outliers : 3.51 % Allowed : 10.13 % Favored : 86.36 % 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: -1.10 (0.16), residues: 2595 helix: 0.69 (0.23), residues: 469 sheet: 0.00 (0.18), residues: 726 loop : -1.68 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 625 HIS 0.008 0.002 HIS J 100N PHE 0.029 0.003 PHE E 330 TYR 0.036 0.003 TYR C 401 ARG 0.009 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 268 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: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7832 (t0) cc_final: 0.7138 (m-40) REVERT: A 391 MET cc_start: 0.8732 (ttp) cc_final: 0.8501 (ttt) REVERT: H 55 ASP cc_start: 0.8838 (m-30) cc_final: 0.8626 (p0) REVERT: H 77 GLN cc_start: 0.7867 (mp10) cc_final: 0.6976 (mp10) REVERT: L 91 TYR cc_start: 0.8772 (p90) cc_final: 0.8262 (p90) REVERT: C 325 MET cc_start: 0.8909 (mmm) cc_final: 0.8551 (mmt) REVERT: D 556 SER cc_start: 0.9006 (m) cc_final: 0.8365 (t) REVERT: D 620 CYS cc_start: 0.7582 (m) cc_final: 0.6958 (m) REVERT: D 625 TRP cc_start: 0.8422 (t-100) cc_final: 0.7376 (t-100) REVERT: I 55 GLN cc_start: 0.8195 (tp40) cc_final: 0.7896 (tp-100) REVERT: I 74 THR cc_start: 0.7282 (m) cc_final: 0.6856 (p) REVERT: E 391 MET cc_start: 0.8883 (ttp) cc_final: 0.8646 (ttt) REVERT: F 668 MET cc_start: 0.8737 (mmm) cc_final: 0.8431 (mmt) REVERT: J 75 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8558 (tptp) REVERT: J 94 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7265 (mtm-85) REVERT: K 24 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7251 (mtt-85) outliers start: 81 outliers final: 53 residues processed: 321 average time/residue: 0.3457 time to fit residues: 173.0095 Evaluate side-chains 283 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 229 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 394 ASN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 394 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23534 Z= 0.178 Angle : 0.675 9.100 31995 Z= 0.337 Chirality : 0.046 0.489 4058 Planarity : 0.004 0.043 3813 Dihedral : 8.838 71.448 6366 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.55 % Favored : 94.95 % Rotamer: Outliers : 2.38 % Allowed : 12.34 % Favored : 85.28 % 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: -0.81 (0.16), residues: 2595 helix: 1.05 (0.24), residues: 475 sheet: 0.11 (0.19), residues: 711 loop : -1.49 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 345 HIS 0.004 0.001 HIS E 364 PHE 0.023 0.002 PHE D 537 TYR 0.031 0.002 TYR I 91 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 2.774 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: A 48 ASN cc_start: 0.7876 (t0) cc_final: 0.7091 (m-40) REVERT: A 391 MET cc_start: 0.8593 (ttp) cc_final: 0.8377 (ttt) REVERT: B 545 MET cc_start: 0.8617 (mmm) cc_final: 0.7862 (tpp) REVERT: H 55 ASP cc_start: 0.8820 (m-30) cc_final: 0.8585 (p0) REVERT: H 75 LYS cc_start: 0.8954 (mppt) cc_final: 0.8612 (mtmm) REVERT: H 77 GLN cc_start: 0.7697 (mp10) cc_final: 0.6884 (mp10) REVERT: L 18 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7509 (mmm-85) REVERT: L 91 TYR cc_start: 0.8569 (p90) cc_final: 0.7935 (p90) REVERT: C 325 MET cc_start: 0.8797 (mmm) cc_final: 0.8407 (mmt) REVERT: C 407 PHE cc_start: 0.9384 (t80) cc_final: 0.9012 (t80) REVERT: C 497 TYR cc_start: 0.9277 (m-80) cc_final: 0.8478 (m-80) REVERT: D 556 SER cc_start: 0.8767 (m) cc_final: 0.8246 (t) REVERT: D 620 CYS cc_start: 0.7195 (m) cc_final: 0.6512 (m) REVERT: I 58 VAL cc_start: 0.8665 (t) cc_final: 0.8261 (p) REVERT: I 74 THR cc_start: 0.7234 (m) cc_final: 0.6814 (p) REVERT: I 103 LEU cc_start: 0.8522 (tp) cc_final: 0.8314 (tt) REVERT: E 391 MET cc_start: 0.8805 (ttp) cc_final: 0.8381 (ttt) REVERT: F 633 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8225 (mmtp) REVERT: F 668 MET cc_start: 0.8657 (mmm) cc_final: 0.8322 (mmt) REVERT: J 75 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8457 (tptp) outliers start: 55 outliers final: 39 residues processed: 311 average time/residue: 0.3639 time to fit residues: 175.0776 Evaluate side-chains 277 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 23534 Z= 0.364 Angle : 0.724 8.495 31995 Z= 0.362 Chirality : 0.048 0.466 4058 Planarity : 0.005 0.049 3813 Dihedral : 8.493 69.917 6366 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.70 % Favored : 93.83 % Rotamer: Outliers : 3.20 % Allowed : 12.55 % Favored : 84.24 % 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: -1.03 (0.16), residues: 2595 helix: 1.06 (0.24), residues: 467 sheet: -0.03 (0.19), residues: 711 loop : -1.70 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 52 HIS 0.006 0.001 HIS E 364 PHE 0.024 0.002 PHE E 346 TYR 0.028 0.002 TYR K 91 ARG 0.007 0.001 ARG F 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 254 time to evaluate : 2.317 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 48 ASN cc_start: 0.7839 (t0) cc_final: 0.7148 (m-40) REVERT: A 482 MET cc_start: 0.8673 (mmm) cc_final: 0.7928 (mmm) REVERT: B 545 MET cc_start: 0.8687 (mmm) cc_final: 0.8260 (tpp) REVERT: B 669 TYR cc_start: 0.7817 (t80) cc_final: 0.7289 (t80) REVERT: H 27 ASP cc_start: 0.7572 (t0) cc_final: 0.7181 (t0) REVERT: H 73 MET cc_start: 0.7531 (ppp) cc_final: 0.6957 (ppp) REVERT: H 77 GLN cc_start: 0.7834 (mp10) cc_final: 0.7557 (mp10) REVERT: L 91 TYR cc_start: 0.8648 (p90) cc_final: 0.8253 (p90) REVERT: C 325 MET cc_start: 0.8880 (mmm) cc_final: 0.8500 (mmt) REVERT: C 366 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8225 (mtp180) REVERT: C 400 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9068 (mt) REVERT: C 497 TYR cc_start: 0.9317 (m-80) cc_final: 0.8427 (m-80) REVERT: D 556 SER cc_start: 0.9063 (m) cc_final: 0.8420 (t) REVERT: D 620 CYS cc_start: 0.7344 (m) cc_final: 0.6753 (m) REVERT: D 625 TRP cc_start: 0.8409 (t-100) cc_final: 0.8130 (t-100) REVERT: I 55 GLN cc_start: 0.8047 (tp40) cc_final: 0.7674 (tp-100) REVERT: I 87 TYR cc_start: 0.8846 (m-80) cc_final: 0.8318 (m-80) REVERT: E 203 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8063 (mm-30) REVERT: E 391 MET cc_start: 0.8845 (ttp) cc_final: 0.8605 (ttt) REVERT: F 557 ARG cc_start: 0.7460 (ptt90) cc_final: 0.6663 (ptp90) REVERT: F 668 MET cc_start: 0.8644 (mmm) cc_final: 0.8233 (mmp) REVERT: J 75 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8548 (tptp) REVERT: K 3 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8438 (pp) outliers start: 74 outliers final: 55 residues processed: 301 average time/residue: 0.3409 time to fit residues: 160.4958 Evaluate side-chains 292 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100NHIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23534 Z= 0.247 Angle : 0.658 8.853 31995 Z= 0.328 Chirality : 0.046 0.459 4058 Planarity : 0.004 0.046 3813 Dihedral : 7.947 66.221 6366 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.32 % Favored : 94.18 % Rotamer: Outliers : 3.51 % Allowed : 12.99 % Favored : 83.51 % 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: -0.99 (0.16), residues: 2595 helix: 1.17 (0.24), residues: 474 sheet: -0.04 (0.19), residues: 705 loop : -1.69 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 PHE 0.024 0.002 PHE D 537 TYR 0.029 0.002 TYR I 91 ARG 0.005 0.000 ARG F 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 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: 81 poor density : 248 time to evaluate : 2.529 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 48 ASN cc_start: 0.7731 (t0) cc_final: 0.7158 (m-40) REVERT: B 545 MET cc_start: 0.8700 (mmm) cc_final: 0.8135 (tpp) REVERT: H 27 ASP cc_start: 0.7665 (t0) cc_final: 0.7211 (t0) REVERT: H 73 MET cc_start: 0.7480 (ppp) cc_final: 0.6807 (ppp) REVERT: H 77 GLN cc_start: 0.7856 (mp10) cc_final: 0.7637 (mp10) REVERT: L 91 TYR cc_start: 0.8636 (p90) cc_final: 0.8173 (p90) REVERT: C 325 MET cc_start: 0.8880 (mmm) cc_final: 0.8446 (mmt) REVERT: C 352 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7222 (t0) REVERT: C 497 TYR cc_start: 0.9289 (m-80) cc_final: 0.8364 (m-80) REVERT: D 556 SER cc_start: 0.9016 (m) cc_final: 0.8348 (t) REVERT: D 571 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7253 (tt) REVERT: D 586 TRP cc_start: 0.8019 (m100) cc_final: 0.7788 (m100) REVERT: D 620 CYS cc_start: 0.7046 (m) cc_final: 0.6561 (m) REVERT: I 78 LEU cc_start: 0.8215 (tp) cc_final: 0.7990 (tp) REVERT: I 82 ASP cc_start: 0.7788 (m-30) cc_final: 0.7272 (p0) REVERT: I 87 TYR cc_start: 0.8788 (m-80) cc_final: 0.8213 (m-80) REVERT: E 203 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7974 (mm-30) REVERT: E 391 MET cc_start: 0.8812 (ttp) cc_final: 0.8567 (ttt) REVERT: F 668 MET cc_start: 0.8611 (mmm) cc_final: 0.8187 (mmp) REVERT: J 75 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8425 (tptp) REVERT: K 3 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8433 (pp) REVERT: K 81 GLU cc_start: 0.8309 (pm20) cc_final: 0.8086 (pm20) outliers start: 81 outliers final: 59 residues processed: 304 average time/residue: 0.3417 time to fit residues: 164.3323 Evaluate side-chains 293 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 151 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 394 ASN A 433 HIS ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN E 56 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23534 Z= 0.210 Angle : 0.630 8.927 31995 Z= 0.312 Chirality : 0.045 0.434 4058 Planarity : 0.004 0.066 3813 Dihedral : 7.275 62.797 6366 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.82 % Favored : 93.80 % Rotamer: Outliers : 2.90 % Allowed : 13.72 % Favored : 83.38 % 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: -0.96 (0.16), residues: 2595 helix: 1.31 (0.24), residues: 474 sheet: 0.01 (0.20), residues: 681 loop : -1.71 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 52 HIS 0.003 0.001 HIS E 364 PHE 0.022 0.002 PHE D 537 TYR 0.032 0.002 TYR I 91 ARG 0.009 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 253 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7692 (t0) cc_final: 0.7107 (m-40) REVERT: A 482 MET cc_start: 0.8525 (mmm) cc_final: 0.8144 (mmm) REVERT: B 545 MET cc_start: 0.8719 (mmm) cc_final: 0.8129 (tpp) REVERT: H 67 ILE cc_start: 0.9000 (tt) cc_final: 0.8697 (tp) REVERT: H 73 MET cc_start: 0.7442 (ppp) cc_final: 0.6889 (ppp) REVERT: H 77 GLN cc_start: 0.7741 (mp10) cc_final: 0.7508 (mp-120) REVERT: L 70 GLU cc_start: 0.8354 (pm20) cc_final: 0.8022 (pm20) REVERT: L 91 TYR cc_start: 0.8611 (p90) cc_final: 0.8162 (p90) REVERT: C 325 MET cc_start: 0.8907 (mmm) cc_final: 0.8492 (mmt) REVERT: C 352 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7166 (t0) REVERT: C 497 TYR cc_start: 0.9267 (m-80) cc_final: 0.8306 (m-80) REVERT: D 556 SER cc_start: 0.8990 (m) cc_final: 0.8329 (t) REVERT: D 571 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7297 (tt) REVERT: D 620 CYS cc_start: 0.6881 (m) cc_final: 0.6452 (m) REVERT: D 625 TRP cc_start: 0.8290 (t-100) cc_final: 0.7971 (t-100) REVERT: I 87 TYR cc_start: 0.8785 (m-80) cc_final: 0.8197 (m-80) REVERT: E 203 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7813 (mm-30) REVERT: E 391 MET cc_start: 0.8828 (ttp) cc_final: 0.8549 (ttt) REVERT: F 668 MET cc_start: 0.8565 (mmm) cc_final: 0.8121 (mmp) REVERT: J 75 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8453 (tptp) REVERT: K 3 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (pp) outliers start: 67 outliers final: 55 residues processed: 297 average time/residue: 0.3390 time to fit residues: 158.9894 Evaluate side-chains 291 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 233 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 9.9990 chunk 99 optimal weight: 0.0050 chunk 148 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 341 GLN A 394 ASN L 90 GLN E 56 GLN E 336 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23534 Z= 0.166 Angle : 0.613 8.559 31995 Z= 0.304 Chirality : 0.044 0.423 4058 Planarity : 0.004 0.046 3813 Dihedral : 6.814 59.942 6366 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.36 % Favored : 94.30 % Rotamer: Outliers : 2.68 % Allowed : 13.85 % Favored : 83.46 % 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: -0.90 (0.16), residues: 2595 helix: 1.39 (0.24), residues: 474 sheet: 0.01 (0.20), residues: 681 loop : -1.66 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 52 HIS 0.003 0.001 HIS E 291 PHE 0.021 0.001 PHE D 537 TYR 0.032 0.001 TYR I 91 ARG 0.007 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 250 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7692 (t0) cc_final: 0.7107 (m-40) REVERT: A 482 MET cc_start: 0.8588 (mmm) cc_final: 0.7919 (mmm) REVERT: B 545 MET cc_start: 0.8698 (mmm) cc_final: 0.8081 (tpp) REVERT: H 67 ILE cc_start: 0.8990 (tt) cc_final: 0.8697 (tp) REVERT: H 73 MET cc_start: 0.7465 (ppp) cc_final: 0.6912 (ppp) REVERT: H 77 GLN cc_start: 0.7617 (mp10) cc_final: 0.7413 (mp-120) REVERT: L 70 GLU cc_start: 0.8332 (pm20) cc_final: 0.7992 (pm20) REVERT: L 91 TYR cc_start: 0.8550 (p90) cc_final: 0.8163 (p90) REVERT: C 325 MET cc_start: 0.8889 (mmm) cc_final: 0.8432 (mmt) REVERT: C 352 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7159 (t0) REVERT: D 556 SER cc_start: 0.8937 (m) cc_final: 0.8263 (t) REVERT: D 620 CYS cc_start: 0.6631 (m) cc_final: 0.6250 (m) REVERT: D 625 TRP cc_start: 0.8242 (t-100) cc_final: 0.7893 (t-100) REVERT: I 87 TYR cc_start: 0.8727 (m-80) cc_final: 0.8140 (m-80) REVERT: E 203 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7612 (mm-30) REVERT: E 391 MET cc_start: 0.8781 (ttp) cc_final: 0.8470 (ttt) REVERT: F 545 MET cc_start: 0.8324 (mmm) cc_final: 0.7918 (mtp) REVERT: F 668 MET cc_start: 0.8538 (mmm) cc_final: 0.8089 (mmp) REVERT: J 75 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8492 (tptp) REVERT: K 3 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8386 (pp) outliers start: 62 outliers final: 52 residues processed: 291 average time/residue: 0.3355 time to fit residues: 153.8039 Evaluate side-chains 289 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 103 LEU 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: 2.9990 chunk 231 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 209 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN E 56 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23534 Z= 0.242 Angle : 0.644 8.645 31995 Z= 0.319 Chirality : 0.045 0.416 4058 Planarity : 0.004 0.044 3813 Dihedral : 6.729 57.079 6366 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.51 % Favored : 93.14 % Rotamer: Outliers : 2.68 % Allowed : 14.07 % Favored : 83.25 % 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: -0.99 (0.16), residues: 2595 helix: 1.36 (0.24), residues: 474 sheet: -0.07 (0.20), residues: 681 loop : -1.72 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 PHE 0.020 0.002 PHE D 537 TYR 0.036 0.002 TYR I 91 ARG 0.005 0.000 ARG F 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7712 (t0) cc_final: 0.7129 (m-40) REVERT: A 404 MET cc_start: 0.8135 (mtm) cc_final: 0.7898 (ptp) REVERT: A 482 MET cc_start: 0.8636 (mmm) cc_final: 0.8079 (mmm) REVERT: B 545 MET cc_start: 0.8741 (mmm) cc_final: 0.8172 (tpp) REVERT: H 67 ILE cc_start: 0.8987 (tt) cc_final: 0.8694 (tp) REVERT: H 73 MET cc_start: 0.7487 (ppp) cc_final: 0.6955 (ppp) REVERT: H 77 GLN cc_start: 0.7688 (mp10) cc_final: 0.7453 (mp-120) REVERT: L 18 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: L 70 GLU cc_start: 0.8317 (pm20) cc_final: 0.7983 (pm20) REVERT: L 91 TYR cc_start: 0.8635 (p90) cc_final: 0.8246 (p90) REVERT: C 325 MET cc_start: 0.8899 (mmm) cc_final: 0.8451 (mmt) REVERT: C 366 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8306 (mtp180) REVERT: C 497 TYR cc_start: 0.9211 (m-80) cc_final: 0.8412 (m-10) REVERT: D 556 SER cc_start: 0.9019 (m) cc_final: 0.8329 (t) REVERT: D 620 CYS cc_start: 0.6615 (m) cc_final: 0.6306 (m) REVERT: D 625 TRP cc_start: 0.8305 (t-100) cc_final: 0.7971 (t-100) REVERT: I 87 TYR cc_start: 0.8779 (m-80) cc_final: 0.8120 (m-80) REVERT: E 203 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7605 (mm-30) REVERT: E 391 MET cc_start: 0.8867 (ttp) cc_final: 0.8618 (ttt) REVERT: F 545 MET cc_start: 0.8371 (mmm) cc_final: 0.7936 (mtp) REVERT: F 668 MET cc_start: 0.8434 (mmm) cc_final: 0.8054 (mmp) REVERT: J 75 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8551 (tptp) REVERT: K 3 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (pp) outliers start: 62 outliers final: 55 residues processed: 280 average time/residue: 0.3499 time to fit residues: 156.9344 Evaluate side-chains 286 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 236 optimal weight: 0.0970 chunk 204 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN E 56 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23534 Z= 0.165 Angle : 0.624 8.986 31995 Z= 0.309 Chirality : 0.044 0.417 4058 Planarity : 0.004 0.043 3813 Dihedral : 6.556 55.400 6366 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.93 % Favored : 93.76 % Rotamer: Outliers : 2.16 % Allowed : 14.59 % Favored : 83.25 % 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: -0.95 (0.16), residues: 2595 helix: 1.40 (0.24), residues: 474 sheet: -0.07 (0.20), residues: 681 loop : -1.69 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 52 HIS 0.004 0.001 HIS E 291 PHE 0.020 0.001 PHE D 537 TYR 0.035 0.001 TYR I 91 ARG 0.005 0.000 ARG F 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7692 (t0) cc_final: 0.7121 (m-40) REVERT: A 482 MET cc_start: 0.8586 (mmm) cc_final: 0.7896 (mmm) REVERT: B 545 MET cc_start: 0.8727 (mmm) cc_final: 0.8137 (tpp) REVERT: B 668 MET cc_start: 0.8109 (tpt) cc_final: 0.7894 (tpt) REVERT: B 669 TYR cc_start: 0.7702 (t80) cc_final: 0.7464 (t80) REVERT: H 67 ILE cc_start: 0.8992 (tt) cc_final: 0.8676 (tp) REVERT: H 73 MET cc_start: 0.7584 (ppp) cc_final: 0.7032 (ppp) REVERT: L 18 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8124 (mmm-85) REVERT: L 70 GLU cc_start: 0.8321 (pm20) cc_final: 0.7985 (pm20) REVERT: L 91 TYR cc_start: 0.8573 (p90) cc_final: 0.8197 (p90) REVERT: C 325 MET cc_start: 0.8869 (mmm) cc_final: 0.8391 (mmt) REVERT: C 352 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7141 (t0) REVERT: C 497 TYR cc_start: 0.9162 (m-80) cc_final: 0.8329 (m-10) REVERT: D 556 SER cc_start: 0.8992 (m) cc_final: 0.8310 (t) REVERT: D 620 CYS cc_start: 0.6504 (m) cc_final: 0.6200 (m) REVERT: D 625 TRP cc_start: 0.8252 (t-100) cc_final: 0.7911 (t-100) REVERT: I 87 TYR cc_start: 0.8709 (m-80) cc_final: 0.8077 (m-80) REVERT: E 203 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7570 (mm-30) REVERT: E 391 MET cc_start: 0.8818 (ttp) cc_final: 0.8503 (ttt) REVERT: F 545 MET cc_start: 0.8330 (mmm) cc_final: 0.7875 (mtp) REVERT: F 668 MET cc_start: 0.8414 (mmm) cc_final: 0.8024 (mmp) REVERT: J 75 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8522 (tptp) REVERT: K 3 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (pp) outliers start: 50 outliers final: 43 residues processed: 273 average time/residue: 0.3382 time to fit residues: 147.3607 Evaluate side-chains 275 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain F residue 635 ASN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 chunk 56 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN C 425 HIS E 56 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN E 418 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079694 restraints weight = 52469.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080629 restraints weight = 43224.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081231 restraints weight = 42396.620| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23534 Z= 0.272 Angle : 0.663 9.057 31995 Z= 0.329 Chirality : 0.045 0.415 4058 Planarity : 0.004 0.047 3813 Dihedral : 6.665 58.807 6366 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.90 % Favored : 92.79 % Rotamer: Outliers : 2.34 % Allowed : 14.68 % Favored : 82.99 % 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: -1.08 (0.16), residues: 2595 helix: 1.37 (0.24), residues: 474 sheet: -0.16 (0.20), residues: 708 loop : -1.82 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 52 HIS 0.005 0.001 HIS E 364 PHE 0.021 0.002 PHE E 346 TYR 0.036 0.002 TYR I 91 ARG 0.006 0.001 ARG F 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.61 seconds wall clock time: 78 minutes 32.09 seconds (4712.09 seconds total)