Starting phenix.real_space_refine on Sun Feb 18 01:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p65_20260/02_2024/6p65_20260.pdb" } resolution = 3.94 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= 0.010 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 129 5.16 5 C 12705 2.51 5 N 3291 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 30": "OE1" <-> "OE2" 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 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20319 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 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: "n" 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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "s" 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: 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: "0" 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: "1" 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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 Time building chain proxies: 11.14, per 1000 atoms: 0.55 Number of scatterers: 20319 At special positions: 0 Unit cell: (132.25, 136.85, 148.35, 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 129 16.00 O 4194 8.00 N 3291 7.00 C 12705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.13 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.13 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.13 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA Q 3 " - " MAN Q 5 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 5 " " BMA n 3 " - " MAN n 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " BETA1-6 " NAG 1 1 " - " FUC 1 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " " NAG m 1 " - " FUC m 3 " NAG-ASN " NAG 0 1 " - " ASN E 392 " " NAG 1 1 " - " ASN E 625 " " NAG A 710 " - " ASN A 187 " " NAG A 729 " - " ASN A 301 " " NAG A 738 " - " ASN A 398 " " NAG A 739 " - " ASN A 442 " " NAG A 740 " - " ASN A 448 " " NAG A 741 " - " ASN A 611 " " NAG A 745 " - " ASN A 637 " " NAG B 710 " - " ASN B 187 " " NAG B 729 " - " ASN B 301 " " NAG B 738 " - " ASN B 398 " " NAG B 739 " - " ASN B 442 " " NAG B 740 " - " ASN B 448 " " NAG B 741 " - " ASN B 611 " " NAG B 745 " - " ASN B 637 " " NAG E 710 " - " ASN E 187 " " NAG E 729 " - " ASN E 301 " " NAG E 738 " - " ASN E 398 " " NAG E 739 " - " ASN E 442 " " NAG E 740 " - " ASN E 448 " " NAG E 741 " - " ASN E 611 " " NAG E 745 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 230 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 289 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 359 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 625 " " NAG Y 1 " - " ASN B 88 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 160 " " NAG b 1 " - " ASN B 197 " " NAG c 1 " - " ASN B 230 " " NAG d 1 " - " ASN B 234 " " NAG e 1 " - " ASN B 241 " " NAG f 1 " - " ASN B 262 " " NAG g 1 " - " ASN B 276 " " NAG h 1 " - " ASN B 289 " " NAG i 1 " - " ASN B 332 " " NAG j 1 " - " ASN B 359 " " NAG k 1 " - " ASN B 386 " " NAG l 1 " - " ASN B 392 " " NAG m 1 " - " ASN B 625 " " NAG n 1 " - " ASN E 88 " " NAG o 1 " - " ASN E 156 " " NAG p 1 " - " ASN E 160 " " NAG q 1 " - " ASN E 197 " " NAG r 1 " - " ASN E 230 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 276 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 359 " " NAG z 1 " - " ASN E 386 " Time building additional restraints: 9.67 Conformation dependent library (CDL) restraints added in 3.3 seconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 20.8% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.655A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 568 through 568 No H-bonds generated for 'chain 'A' and resid 568 through 568' Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.868A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 568 through 568 No H-bonds generated for 'chain 'B' and resid 568 through 568' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 539 " --> pdb=" O ILE E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 548 Processing helix chain 'E' and resid 568 through 568 No H-bonds generated for 'chain 'E' and resid 568 through 568' Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS E 658 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 663 No H-bonds generated for 'chain 'E' and resid 661 through 663' Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 468 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA H 96 " --> pdb=" O PHE H 100J" (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE H 100J" --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR H 98 " --> pdb=" O LYS H 100H" (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS H 100H" --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY L 91 " --> pdb=" O LEU H 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS H 100I" --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU L 89 " --> pdb=" O HIS H 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN H 101 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR L 87 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP H 103 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR L 85 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 14 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE B 468 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS C 92 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG C 94 " --> pdb=" O PHE C 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE C 100J" --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 96 " --> pdb=" O LYS C 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY D 91 " --> pdb=" O LEU C 100G" (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS C 100I" --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU D 89 " --> pdb=" O HIS C 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN C 101 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR D 87 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP C 103 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR D 85 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 14 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.150A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.571A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.650A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE E 468 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 303 through 312 removed outlier: 6.421A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.615A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS F 92 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU F 102 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG F 94 " --> pdb=" O PHE F 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE F 100J" --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA F 96 " --> pdb=" O LYS F 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY G 91 " --> pdb=" O LEU F 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS F 100I" --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N LEU G 89 " --> pdb=" O HIS F 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN F 101 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR G 87 " --> pdb=" O ASN F 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP F 103 " --> pdb=" O THR G 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR G 85 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 14 Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 7 791 hydrogen bonds defined for protein. 2112 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: 7.86 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4117 1.32 - 1.44: 5694 1.44 - 1.57: 10692 1.57 - 1.70: 32 1.70 - 1.83: 168 Bond restraints: 20703 Sorted by residual: bond pdb=" CB PHE B 159 " pdb=" CG PHE B 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB TYR D 49 " pdb=" CG TYR D 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR G 49 " pdb=" CG TYR G 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.74e+01 ... (remaining 20698 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.65: 407 104.65 - 112.00: 10230 112.00 - 119.35: 7630 119.35 - 126.69: 9576 126.69 - 134.04: 261 Bond angle restraints: 28104 Sorted by residual: angle pdb=" C LYS A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.74 -8.18 1.02e+00 9.61e-01 6.43e+01 angle pdb=" C LYS E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C LYS B 492 " pdb=" N PRO B 493 " pdb=" CA PRO B 493 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.02e+00 9.61e-01 6.33e+01 angle pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.31e+01 angle pdb=" CA PHE G 98 " pdb=" CB PHE G 98 " pdb=" CG PHE G 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.30e+01 ... (remaining 28099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 13475 21.72 - 43.45: 435 43.45 - 65.17: 82 65.17 - 86.89: 75 86.89 - 108.61: 36 Dihedral angle restraints: 14103 sinusoidal: 7281 harmonic: 6822 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 14100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2669 0.114 - 0.227: 784 0.227 - 0.341: 93 0.341 - 0.455: 9 0.455 - 0.569: 9 Chirality restraints: 3564 Sorted by residual: 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 -2.58 0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 NAG x 2 " pdb=" O4 NAG x 1 " pdb=" C2 NAG x 2 " pdb=" O5 NAG x 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.87e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.78e+01 ... (remaining 3561 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG i 1 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.072 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.132 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG T 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG x 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.20e+01 pdb=" C7 NAG x 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG x 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG x 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG x 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6824 2.84 - 3.35: 17991 3.35 - 3.87: 34923 3.87 - 4.38: 39887 4.38 - 4.90: 64499 Nonbonded interactions: 164124 Sorted by model distance: nonbonded pdb=" N ASN E 398 " pdb=" OD1 ASN E 398 " model vdw 2.319 2.520 nonbonded pdb=" N ASN A 398 " pdb=" OD1 ASN A 398 " model vdw 2.319 2.520 nonbonded pdb=" N ASN B 398 " pdb=" OD1 ASN B 398 " model vdw 2.320 2.520 nonbonded pdb=" O4 NAG Z 2 " pdb=" O6 NAG Z 2 " model vdw 2.339 2.440 nonbonded pdb=" O4 NAG o 2 " pdb=" O6 NAG o 2 " model vdw 2.339 2.440 ... (remaining 164119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain '1' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'Y' selection = chain 'f' selection = chain 'n' selection = chain 'u' } 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: 1.290 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: 6.370 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 55.290 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.450 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.021 0.137 20703 Z= 1.354 Angle : 1.854 10.392 28104 Z= 1.168 Chirality : 0.104 0.569 3564 Planarity : 0.010 0.081 3372 Dihedral : 13.671 108.612 9612 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.44 % Allowed : 0.74 % Favored : 98.82 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % 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: 0.08 (0.16), residues: 2325 helix: -0.98 (0.21), residues: 426 sheet: 0.69 (0.21), residues: 540 loop : 0.27 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP E 35 HIS 0.015 0.003 HIS B 374 PHE 0.045 0.007 PHE D 98 TYR 0.059 0.008 TYR D 87 ARG 0.005 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 517 time to evaluate : 2.230 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 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7957 (ttm) REVERT: A 207 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8137 (tptp) REVERT: A 387 THR cc_start: 0.8811 (p) cc_final: 0.8467 (t) REVERT: A 426 MET cc_start: 0.8776 (tpp) cc_final: 0.8457 (mmm) REVERT: A 536 THR cc_start: 0.8903 (m) cc_final: 0.8680 (p) REVERT: A 571 TRP cc_start: 0.7758 (m100) cc_final: 0.7362 (m100) REVERT: H 11 LEU cc_start: 0.6083 (tt) cc_final: 0.5834 (mp) REVERT: H 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7849 (t0) REVERT: H 108 LEU cc_start: 0.6739 (tp) cc_final: 0.6389 (tt) REVERT: L 74 THR cc_start: 0.8623 (m) cc_final: 0.8388 (p) REVERT: B 84 MET cc_start: 0.8164 (ttp) cc_final: 0.7931 (ttm) REVERT: B 207 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8322 (tmtt) REVERT: B 358 ILE cc_start: 0.9043 (mt) cc_final: 0.8737 (mm) REVERT: B 387 THR cc_start: 0.8757 (p) cc_final: 0.8366 (t) REVERT: B 426 MET cc_start: 0.8867 (tpp) cc_final: 0.8581 (mmm) REVERT: B 500 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7364 (tpm170) REVERT: B 536 THR cc_start: 0.8811 (m) cc_final: 0.8584 (p) REVERT: B 571 TRP cc_start: 0.7558 (m100) cc_final: 0.7158 (m100) REVERT: C 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7609 (t0) REVERT: C 108 LEU cc_start: 0.6949 (tp) cc_final: 0.6591 (tt) REVERT: D 74 THR cc_start: 0.8548 (m) cc_final: 0.8245 (p) REVERT: E 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7932 (ttm) REVERT: E 207 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8240 (tmtt) REVERT: E 387 THR cc_start: 0.8889 (p) cc_final: 0.8468 (t) REVERT: E 426 MET cc_start: 0.8787 (tpp) cc_final: 0.8258 (mmm) REVERT: E 530 MET cc_start: 0.8908 (mtm) cc_final: 0.8687 (mtm) REVERT: E 536 THR cc_start: 0.8875 (m) cc_final: 0.8653 (p) REVERT: E 571 TRP cc_start: 0.7778 (m100) cc_final: 0.7181 (m100) REVERT: F 33 ASP cc_start: 0.8150 (m-30) cc_final: 0.7659 (t0) REVERT: F 108 LEU cc_start: 0.6900 (tp) cc_final: 0.6562 (tt) REVERT: G 74 THR cc_start: 0.8542 (m) cc_final: 0.8226 (p) outliers start: 9 outliers final: 3 residues processed: 526 average time/residue: 0.3730 time to fit residues: 287.0335 Evaluate side-chains 278 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain E residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.6980 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN L 70 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN E 195 ASN E 352 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20703 Z= 0.225 Angle : 0.766 10.299 28104 Z= 0.387 Chirality : 0.051 0.349 3564 Planarity : 0.004 0.028 3372 Dihedral : 10.747 76.319 5340 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.19 % Allowed : 8.48 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.08 (0.16), residues: 2325 helix: -0.04 (0.24), residues: 423 sheet: 0.44 (0.19), residues: 612 loop : 0.01 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 479 HIS 0.015 0.002 HIS C 100I PHE 0.016 0.002 PHE B 159 TYR 0.021 0.002 TYR D 92 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 333 time to evaluate : 2.506 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: A 104 MET cc_start: 0.9033 (ttp) cc_final: 0.8576 (tpt) REVERT: A 207 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8009 (tmtt) REVERT: A 387 THR cc_start: 0.8730 (p) cc_final: 0.8395 (t) REVERT: A 426 MET cc_start: 0.8415 (tpp) cc_final: 0.7884 (mmm) REVERT: H 11 LEU cc_start: 0.6433 (tt) cc_final: 0.6225 (mp) REVERT: H 31 TRP cc_start: 0.7422 (m-10) cc_final: 0.7016 (m-10) REVERT: H 100 HIS cc_start: 0.6616 (m-70) cc_final: 0.6336 (m-70) REVERT: H 102 LEU cc_start: 0.8436 (mm) cc_final: 0.8171 (mm) REVERT: H 108 LEU cc_start: 0.7114 (tp) cc_final: 0.6694 (tt) REVERT: L 49 TYR cc_start: 0.6991 (m-80) cc_final: 0.6268 (m-80) REVERT: L 87 TYR cc_start: 0.4776 (m-80) cc_final: 0.4467 (m-80) REVERT: L 96 PHE cc_start: 0.7717 (m-80) cc_final: 0.7241 (m-10) REVERT: B 207 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7887 (tptm) REVERT: B 387 THR cc_start: 0.8709 (p) cc_final: 0.8373 (t) REVERT: B 426 MET cc_start: 0.8506 (tpp) cc_final: 0.8129 (mmm) REVERT: B 500 ARG cc_start: 0.7541 (ptt90) cc_final: 0.7253 (tpm170) REVERT: C 66 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7449 (ttm110) REVERT: C 67 LEU cc_start: 0.7314 (tp) cc_final: 0.6673 (mt) REVERT: C 108 LEU cc_start: 0.7232 (tp) cc_final: 0.6694 (tt) REVERT: D 70 GLN cc_start: 0.7785 (tp-100) cc_final: 0.6816 (pp30) REVERT: D 71 PHE cc_start: 0.8796 (m-80) cc_final: 0.8587 (m-80) REVERT: D 90 TYR cc_start: 0.7286 (t80) cc_final: 0.7064 (t80) REVERT: E 207 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8151 (tmtt) REVERT: E 387 THR cc_start: 0.8733 (p) cc_final: 0.8426 (t) REVERT: E 426 MET cc_start: 0.8518 (tpp) cc_final: 0.8128 (mmm) REVERT: F 31 TRP cc_start: 0.7583 (m-10) cc_final: 0.7192 (m-10) REVERT: F 71 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6712 (ttmt) REVERT: G 19 VAL cc_start: 0.7370 (t) cc_final: 0.6810 (t) REVERT: G 37 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: G 87 TYR cc_start: 0.4433 (m-80) cc_final: 0.3966 (m-80) outliers start: 65 outliers final: 24 residues processed: 375 average time/residue: 0.3368 time to fit residues: 190.5420 Evaluate side-chains 280 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN B 287 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN E 287 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20703 Z= 0.346 Angle : 0.757 8.096 28104 Z= 0.381 Chirality : 0.050 0.306 3564 Planarity : 0.005 0.053 3372 Dihedral : 9.540 70.093 5340 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.12 % Allowed : 8.87 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.07 (0.17), residues: 2325 helix: 0.25 (0.26), residues: 435 sheet: 0.31 (0.19), residues: 678 loop : -0.27 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 479 HIS 0.009 0.002 HIS F 100I PHE 0.021 0.003 PHE B 159 TYR 0.016 0.002 TYR D 92 ARG 0.006 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 262 time to evaluate : 2.328 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: A 80 ASN cc_start: 0.6678 (t0) cc_final: 0.5753 (p0) REVERT: A 104 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8524 (tpt) REVERT: A 207 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8115 (tmtt) REVERT: A 387 THR cc_start: 0.9055 (p) cc_final: 0.8659 (t) REVERT: H 11 LEU cc_start: 0.6499 (tt) cc_final: 0.6229 (mp) REVERT: H 35 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7551 (mmp) REVERT: H 102 LEU cc_start: 0.8487 (mm) cc_final: 0.8167 (mm) REVERT: H 108 LEU cc_start: 0.6957 (tp) cc_final: 0.6413 (tt) REVERT: L 49 TYR cc_start: 0.7351 (m-80) cc_final: 0.6900 (m-80) REVERT: L 87 TYR cc_start: 0.5032 (m-80) cc_final: 0.4681 (m-80) REVERT: B 80 ASN cc_start: 0.6649 (t0) cc_final: 0.6082 (p0) REVERT: B 84 MET cc_start: 0.8138 (tmm) cc_final: 0.7629 (tmm) REVERT: B 207 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8027 (tmtt) REVERT: B 387 THR cc_start: 0.8953 (p) cc_final: 0.8637 (t) REVERT: B 426 MET cc_start: 0.8393 (tpp) cc_final: 0.7981 (mmm) REVERT: B 500 ARG cc_start: 0.7917 (ptt90) cc_final: 0.7351 (tpm170) REVERT: C 2 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: D 4 MET cc_start: 0.5803 (ttp) cc_final: 0.5582 (ttp) REVERT: D 24 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: D 95 ASP cc_start: 0.7902 (t0) cc_final: 0.7432 (t0) REVERT: E 80 ASN cc_start: 0.6711 (t0) cc_final: 0.5952 (p0) REVERT: E 104 MET cc_start: 0.9214 (ttt) cc_final: 0.8977 (tpp) REVERT: E 207 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7935 (tmtt) REVERT: E 387 THR cc_start: 0.8893 (p) cc_final: 0.8600 (t) REVERT: E 426 MET cc_start: 0.8465 (tpp) cc_final: 0.8192 (mmm) REVERT: E 620 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6783 (t0) REVERT: E 629 MET cc_start: 0.8637 (mmm) cc_final: 0.8430 (mmm) REVERT: F 36 TRP cc_start: 0.6856 (m100) cc_final: 0.5879 (m100) REVERT: F 71 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6389 (ttmt) REVERT: G 37 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: G 63 LYS cc_start: 0.7380 (tptp) cc_final: 0.7036 (mptt) REVERT: G 87 TYR cc_start: 0.4882 (m-80) cc_final: 0.4568 (m-80) outliers start: 84 outliers final: 44 residues processed: 324 average time/residue: 0.3262 time to fit residues: 160.7542 Evaluate side-chains 274 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN B 300 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 61 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN E 651 ASN E 652 GLN F 2 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.005 0.061 20703 Z= 0.310 Angle : 0.714 8.504 28104 Z= 0.356 Chirality : 0.049 0.292 3564 Planarity : 0.004 0.038 3372 Dihedral : 9.048 64.615 5340 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.43 % Allowed : 10.88 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.19 (0.17), residues: 2325 helix: 0.18 (0.26), residues: 435 sheet: 0.49 (0.20), residues: 636 loop : -0.51 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 62 HIS 0.007 0.002 HIS B 105 PHE 0.019 0.003 PHE B 376 TYR 0.017 0.002 TYR D 92 ARG 0.009 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 245 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6869 (t0) cc_final: 0.5824 (p0) REVERT: A 104 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8551 (tpt) REVERT: A 207 LYS cc_start: 0.8634 (mmtt) cc_final: 0.7882 (tptp) REVERT: A 387 THR cc_start: 0.9156 (p) cc_final: 0.8718 (t) REVERT: A 475 MET cc_start: 0.8603 (mmm) cc_final: 0.8210 (mmt) REVERT: A 629 MET cc_start: 0.8839 (mmm) cc_final: 0.8315 (mmm) REVERT: H 35 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7287 (mmp) REVERT: L 4 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5745 (mtp) REVERT: L 49 TYR cc_start: 0.7316 (m-80) cc_final: 0.6773 (m-80) REVERT: L 63 LYS cc_start: 0.7439 (tptp) cc_final: 0.7142 (mptt) REVERT: L 87 TYR cc_start: 0.5171 (m-80) cc_final: 0.4797 (m-80) REVERT: L 95 ASP cc_start: 0.7697 (t70) cc_final: 0.7390 (t0) REVERT: B 42 VAL cc_start: 0.9319 (t) cc_final: 0.8970 (p) REVERT: B 80 ASN cc_start: 0.6676 (t0) cc_final: 0.6070 (p0) REVERT: B 84 MET cc_start: 0.8114 (tmm) cc_final: 0.7626 (tmm) REVERT: B 207 LYS cc_start: 0.8549 (mmtt) cc_final: 0.7931 (tptm) REVERT: B 387 THR cc_start: 0.9019 (p) cc_final: 0.8616 (t) REVERT: B 426 MET cc_start: 0.8222 (tpp) cc_final: 0.7998 (mmm) REVERT: B 475 MET cc_start: 0.8773 (mmm) cc_final: 0.8284 (mmm) REVERT: C 36 TRP cc_start: 0.6472 (m100) cc_final: 0.6207 (m100) REVERT: D 27 GLU cc_start: 0.6074 (mp0) cc_final: 0.5781 (mp0) REVERT: D 63 LYS cc_start: 0.7462 (tptp) cc_final: 0.7217 (mptt) REVERT: D 70 GLN cc_start: 0.7813 (tp-100) cc_final: 0.6832 (pp30) REVERT: D 71 PHE cc_start: 0.8612 (m-80) cc_final: 0.8223 (m-80) REVERT: D 95 ASP cc_start: 0.7945 (t70) cc_final: 0.7628 (t0) REVERT: E 207 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7997 (tmtt) REVERT: E 387 THR cc_start: 0.8914 (p) cc_final: 0.8592 (t) REVERT: E 426 MET cc_start: 0.8323 (tpp) cc_final: 0.7952 (mmm) REVERT: F 66 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7122 (ttp-110) REVERT: G 37 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: G 63 LYS cc_start: 0.7481 (tptp) cc_final: 0.7195 (mptt) REVERT: G 86 TYR cc_start: 0.7913 (m-10) cc_final: 0.7568 (m-10) outliers start: 70 outliers final: 41 residues processed: 292 average time/residue: 0.3350 time to fit residues: 148.9479 Evaluate side-chains 265 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 652 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 2 GLN C 61 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20703 Z= 0.193 Angle : 0.661 11.932 28104 Z= 0.329 Chirality : 0.047 0.256 3564 Planarity : 0.004 0.047 3372 Dihedral : 8.477 60.850 5340 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.33 % Allowed : 10.74 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.07 (0.17), residues: 2325 helix: 0.30 (0.26), residues: 435 sheet: 0.57 (0.20), residues: 645 loop : -0.44 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 62 HIS 0.005 0.001 HIS A 105 PHE 0.019 0.002 PHE L 71 TYR 0.017 0.001 TYR D 92 ARG 0.006 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 228 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6812 (t0) cc_final: 0.5727 (p0) REVERT: A 104 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8503 (tpt) REVERT: A 201 CYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6299 (p) REVERT: A 207 LYS cc_start: 0.8566 (mmtt) cc_final: 0.7753 (tptp) REVERT: A 387 THR cc_start: 0.9139 (p) cc_final: 0.8689 (t) REVERT: A 475 MET cc_start: 0.8597 (mmm) cc_final: 0.8157 (mmt) REVERT: A 629 MET cc_start: 0.8713 (mmm) cc_final: 0.8327 (mmm) REVERT: H 35 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7174 (mmp) REVERT: L 4 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.5664 (mtp) REVERT: L 27 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: L 49 TYR cc_start: 0.7273 (m-80) cc_final: 0.6683 (m-80) REVERT: L 63 LYS cc_start: 0.7557 (tptp) cc_final: 0.7230 (mptt) REVERT: L 87 TYR cc_start: 0.5253 (m-80) cc_final: 0.4895 (m-80) REVERT: L 95 ASP cc_start: 0.7657 (t70) cc_final: 0.7338 (t0) REVERT: B 80 ASN cc_start: 0.6791 (t0) cc_final: 0.6074 (p0) REVERT: B 84 MET cc_start: 0.8055 (tmm) cc_final: 0.7585 (tmm) REVERT: B 207 LYS cc_start: 0.8535 (mmtt) cc_final: 0.7903 (tmtt) REVERT: B 376 PHE cc_start: 0.8418 (t80) cc_final: 0.8090 (t80) REVERT: B 387 THR cc_start: 0.9002 (p) cc_final: 0.8582 (t) REVERT: B 530 MET cc_start: 0.8948 (mtm) cc_final: 0.8681 (mtm) REVERT: B 629 MET cc_start: 0.8761 (mmm) cc_final: 0.8203 (mmm) REVERT: C 47 TRP cc_start: 0.6668 (t-100) cc_final: 0.6446 (t-100) REVERT: D 27 GLU cc_start: 0.6114 (mp0) cc_final: 0.5883 (mp0) REVERT: D 63 LYS cc_start: 0.7525 (tptp) cc_final: 0.7143 (mptt) REVERT: D 70 GLN cc_start: 0.7687 (tp-100) cc_final: 0.6899 (pp30) REVERT: D 71 PHE cc_start: 0.8606 (m-80) cc_final: 0.8255 (m-80) REVERT: D 95 ASP cc_start: 0.7952 (t70) cc_final: 0.7614 (t0) REVERT: E 104 MET cc_start: 0.9031 (tpp) cc_final: 0.8829 (tpt) REVERT: E 207 LYS cc_start: 0.8536 (mmtt) cc_final: 0.7883 (tmtt) REVERT: E 387 THR cc_start: 0.8940 (p) cc_final: 0.8578 (t) REVERT: E 426 MET cc_start: 0.8214 (tpp) cc_final: 0.7819 (mmm) REVERT: E 629 MET cc_start: 0.8922 (mmm) cc_final: 0.8605 (mmm) REVERT: F 67 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6736 (mt) REVERT: G 37 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: G 63 LYS cc_start: 0.7648 (tptp) cc_final: 0.7350 (mptt) REVERT: G 86 TYR cc_start: 0.7876 (m-10) cc_final: 0.7609 (m-10) outliers start: 68 outliers final: 43 residues processed: 276 average time/residue: 0.3176 time to fit residues: 135.5681 Evaluate side-chains 270 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN C 61 ASN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 20703 Z= 0.394 Angle : 0.751 7.554 28104 Z= 0.371 Chirality : 0.049 0.283 3564 Planarity : 0.004 0.054 3372 Dihedral : 8.620 59.334 5340 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.48 % Allowed : 11.18 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.37 (0.17), residues: 2325 helix: 0.04 (0.26), residues: 432 sheet: 0.44 (0.20), residues: 642 loop : -0.67 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 62 HIS 0.009 0.002 HIS A 105 PHE 0.021 0.003 PHE L 71 TYR 0.018 0.002 TYR B 217 ARG 0.008 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 223 time to evaluate : 2.220 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 42 VAL cc_start: 0.9312 (t) cc_final: 0.8825 (p) REVERT: A 104 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8741 (tpt) REVERT: A 207 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7907 (tptp) REVERT: A 387 THR cc_start: 0.9208 (p) cc_final: 0.8793 (t) REVERT: A 475 MET cc_start: 0.8686 (mmm) cc_final: 0.8398 (mmt) REVERT: A 629 MET cc_start: 0.8881 (mmm) cc_final: 0.8554 (mmm) REVERT: H 35 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7242 (mmp) REVERT: H 66 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7488 (mtp85) REVERT: H 67 LEU cc_start: 0.7520 (tp) cc_final: 0.6917 (mt) REVERT: L 4 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5713 (mtp) REVERT: L 27 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5917 (mp0) REVERT: L 49 TYR cc_start: 0.7339 (m-80) cc_final: 0.6774 (m-80) REVERT: L 63 LYS cc_start: 0.7589 (tptp) cc_final: 0.7371 (mptt) REVERT: L 87 TYR cc_start: 0.5497 (m-80) cc_final: 0.5140 (m-80) REVERT: L 95 ASP cc_start: 0.7687 (t70) cc_final: 0.7379 (t0) REVERT: B 84 MET cc_start: 0.8177 (tmm) cc_final: 0.7711 (tmm) REVERT: B 104 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8636 (tmm) REVERT: B 207 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7974 (tmtt) REVERT: B 629 MET cc_start: 0.8913 (mmm) cc_final: 0.8444 (mmm) REVERT: C 81 MET cc_start: 0.7019 (tpp) cc_final: 0.6779 (mmm) REVERT: D 27 GLU cc_start: 0.6171 (mp0) cc_final: 0.5754 (mp0) REVERT: D 70 GLN cc_start: 0.7748 (tp-100) cc_final: 0.6930 (pp30) REVERT: D 71 PHE cc_start: 0.8591 (m-80) cc_final: 0.8262 (m-80) REVERT: D 95 ASP cc_start: 0.7970 (t70) cc_final: 0.7569 (t0) REVERT: E 207 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8070 (tmtt) REVERT: E 387 THR cc_start: 0.9002 (p) cc_final: 0.8630 (t) REVERT: E 426 MET cc_start: 0.8169 (tpp) cc_final: 0.7773 (mmm) REVERT: E 629 MET cc_start: 0.9055 (mmm) cc_final: 0.8748 (mmm) REVERT: E 650 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: G 63 LYS cc_start: 0.7679 (tptp) cc_final: 0.7422 (mptt) outliers start: 71 outliers final: 51 residues processed: 275 average time/residue: 0.3114 time to fit residues: 132.8538 Evaluate side-chains 264 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 207 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 chunk 137 optimal weight: 0.0270 chunk 104 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 101 ASN B 195 ASN B 425 ASN C 2 GLN C 61 ASN C 80 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20703 Z= 0.173 Angle : 0.641 10.571 28104 Z= 0.318 Chirality : 0.046 0.247 3564 Planarity : 0.004 0.054 3372 Dihedral : 7.993 59.785 5340 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 12.06 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.10 (0.17), residues: 2325 helix: 0.56 (0.27), residues: 417 sheet: 0.49 (0.20), residues: 648 loop : -0.54 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 36 HIS 0.005 0.001 HIS F 100I PHE 0.021 0.002 PHE L 71 TYR 0.019 0.001 TYR D 92 ARG 0.009 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 227 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8619 (tpt) REVERT: A 207 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7708 (tptp) REVERT: A 387 THR cc_start: 0.9120 (p) cc_final: 0.8636 (t) REVERT: A 475 MET cc_start: 0.8531 (mmm) cc_final: 0.8233 (mmt) REVERT: A 650 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: H 35 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7143 (mmp) REVERT: H 67 LEU cc_start: 0.7276 (tp) cc_final: 0.6731 (mt) REVERT: H 81 MET cc_start: 0.6612 (mmm) cc_final: 0.6069 (tpt) REVERT: L 4 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5883 (mtp) REVERT: L 27 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5483 (mp0) REVERT: L 49 TYR cc_start: 0.7370 (m-80) cc_final: 0.6656 (m-80) REVERT: L 87 TYR cc_start: 0.5304 (m-80) cc_final: 0.4934 (m-80) REVERT: L 95 ASP cc_start: 0.7573 (t70) cc_final: 0.7269 (t0) REVERT: B 207 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7940 (tmtt) REVERT: B 530 MET cc_start: 0.8979 (mtm) cc_final: 0.8720 (mtm) REVERT: B 629 MET cc_start: 0.8694 (mmm) cc_final: 0.8487 (mmm) REVERT: D 27 GLU cc_start: 0.6108 (mp0) cc_final: 0.5814 (mp0) REVERT: D 63 LYS cc_start: 0.7678 (tptp) cc_final: 0.7288 (mptt) REVERT: D 70 GLN cc_start: 0.7701 (tp-100) cc_final: 0.6946 (pp30) REVERT: D 71 PHE cc_start: 0.8632 (m-80) cc_final: 0.8353 (m-80) REVERT: D 95 ASP cc_start: 0.7765 (t70) cc_final: 0.7387 (t0) REVERT: E 104 MET cc_start: 0.8993 (tpp) cc_final: 0.8754 (tpt) REVERT: E 207 LYS cc_start: 0.8546 (mmtt) cc_final: 0.7890 (tmtt) REVERT: E 387 THR cc_start: 0.8937 (p) cc_final: 0.8525 (t) REVERT: E 426 MET cc_start: 0.8093 (tpp) cc_final: 0.7690 (mmm) REVERT: E 629 MET cc_start: 0.8961 (mmm) cc_final: 0.8656 (mmm) REVERT: E 650 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: F 100 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: G 63 LYS cc_start: 0.7632 (tptp) cc_final: 0.7422 (mptt) outliers start: 59 outliers final: 40 residues processed: 264 average time/residue: 0.3272 time to fit residues: 131.7827 Evaluate side-chains 253 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.0040 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 153 optimal weight: 0.0270 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 177 optimal weight: 0.4980 chunk 205 optimal weight: 9.9990 overall best weight: 0.6252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 352 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 101 ASN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20703 Z= 0.168 Angle : 0.634 9.341 28104 Z= 0.313 Chirality : 0.046 0.237 3564 Planarity : 0.003 0.053 3372 Dihedral : 7.551 57.363 5340 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.89 % Allowed : 12.21 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.02 (0.18), residues: 2325 helix: 0.77 (0.27), residues: 399 sheet: 0.61 (0.20), residues: 663 loop : -0.53 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 571 HIS 0.007 0.001 HIS F 100I PHE 0.022 0.002 PHE L 71 TYR 0.019 0.001 TYR D 92 ARG 0.006 0.000 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 218 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8553 (tpt) REVERT: A 207 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7727 (tptp) REVERT: A 387 THR cc_start: 0.9127 (p) cc_final: 0.8636 (t) REVERT: A 475 MET cc_start: 0.8534 (mmm) cc_final: 0.8209 (mmt) REVERT: A 629 MET cc_start: 0.8883 (mmm) cc_final: 0.8190 (mmm) REVERT: H 33 ASP cc_start: 0.8292 (m-30) cc_final: 0.8022 (m-30) REVERT: H 35 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7039 (mmp) REVERT: H 36 TRP cc_start: 0.6447 (m100) cc_final: 0.6197 (m100) REVERT: H 67 LEU cc_start: 0.7360 (tp) cc_final: 0.6815 (mt) REVERT: H 81 MET cc_start: 0.6604 (mmm) cc_final: 0.6192 (tpt) REVERT: L 4 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6206 (mtp) REVERT: L 27 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5375 (mp0) REVERT: L 49 TYR cc_start: 0.7351 (m-80) cc_final: 0.6664 (m-80) REVERT: L 87 TYR cc_start: 0.5268 (m-80) cc_final: 0.4988 (m-80) REVERT: L 95 ASP cc_start: 0.7537 (t70) cc_final: 0.7173 (t0) REVERT: B 207 LYS cc_start: 0.8571 (mmtt) cc_final: 0.7949 (tmtt) REVERT: B 362 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.6242 (t) REVERT: D 63 LYS cc_start: 0.7600 (tptp) cc_final: 0.7106 (mptt) REVERT: D 70 GLN cc_start: 0.7695 (tp-100) cc_final: 0.6876 (pp30) REVERT: D 95 ASP cc_start: 0.7890 (t70) cc_final: 0.7498 (t0) REVERT: E 104 MET cc_start: 0.8976 (tpp) cc_final: 0.8721 (tpt) REVERT: E 207 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7904 (tmtt) REVERT: E 387 THR cc_start: 0.8924 (p) cc_final: 0.8504 (t) REVERT: E 426 MET cc_start: 0.8053 (tpp) cc_final: 0.7657 (mmm) REVERT: E 620 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6669 (t0) REVERT: E 629 MET cc_start: 0.8931 (mmm) cc_final: 0.8610 (mmm) REVERT: E 650 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: F 67 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6698 (mt) REVERT: F 100 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7815 (ttpp) outliers start: 59 outliers final: 40 residues processed: 257 average time/residue: 0.3234 time to fit residues: 128.0289 Evaluate side-chains 253 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN E 374 HIS ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20703 Z= 0.414 Angle : 0.778 10.250 28104 Z= 0.383 Chirality : 0.049 0.303 3564 Planarity : 0.005 0.082 3372 Dihedral : 8.131 55.059 5340 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.84 % Allowed : 13.04 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.53 (0.17), residues: 2325 helix: -0.08 (0.26), residues: 426 sheet: 0.39 (0.20), residues: 675 loop : -0.85 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 47 HIS 0.009 0.002 HIS B 105 PHE 0.024 0.003 PHE A 383 TYR 0.020 0.002 TYR D 92 ARG 0.008 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 220 time to evaluate : 2.206 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 42 VAL cc_start: 0.9349 (t) cc_final: 0.8897 (p) REVERT: A 104 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8722 (tpt) REVERT: A 111 LEU cc_start: 0.9114 (mt) cc_final: 0.8831 (tt) REVERT: A 207 LYS cc_start: 0.8549 (mmtt) cc_final: 0.7879 (tptp) REVERT: A 629 MET cc_start: 0.9046 (mmm) cc_final: 0.8305 (mmm) REVERT: A 650 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: H 35 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7129 (mmp) REVERT: H 67 LEU cc_start: 0.7411 (tp) cc_final: 0.7034 (mt) REVERT: L 4 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.6144 (mtp) REVERT: L 27 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5212 (mp0) REVERT: L 87 TYR cc_start: 0.5645 (m-80) cc_final: 0.5312 (m-80) REVERT: L 95 ASP cc_start: 0.7634 (t70) cc_final: 0.7430 (t0) REVERT: B 207 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8032 (tmtt) REVERT: B 320 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8936 (p) REVERT: D 4 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6487 (ttm) REVERT: D 53 LYS cc_start: 0.7827 (pttp) cc_final: 0.7580 (pttp) REVERT: D 63 LYS cc_start: 0.7720 (tptp) cc_final: 0.7473 (mppt) REVERT: D 70 GLN cc_start: 0.7851 (tp-100) cc_final: 0.6920 (pp30) REVERT: D 95 ASP cc_start: 0.7994 (t70) cc_final: 0.7504 (t0) REVERT: E 104 MET cc_start: 0.8923 (tpp) cc_final: 0.8674 (tpt) REVERT: E 207 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8071 (tmtt) REVERT: E 426 MET cc_start: 0.8148 (tpp) cc_final: 0.7940 (mmm) REVERT: E 629 MET cc_start: 0.9104 (mmm) cc_final: 0.8809 (mmm) REVERT: E 650 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: F 100 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7951 (ttpp) outliers start: 58 outliers final: 40 residues processed: 263 average time/residue: 0.3159 time to fit residues: 128.5154 Evaluate side-chains 251 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 185 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN B 195 ASN B 300 ASN B 374 HIS C 2 GLN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20703 Z= 0.213 Angle : 0.674 10.368 28104 Z= 0.332 Chirality : 0.046 0.244 3564 Planarity : 0.004 0.071 3372 Dihedral : 7.684 52.599 5340 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.30 % Allowed : 14.41 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.28 (0.17), residues: 2325 helix: 0.59 (0.27), residues: 399 sheet: 0.20 (0.19), residues: 741 loop : -0.66 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 47 HIS 0.005 0.001 HIS F 100I PHE 0.019 0.002 PHE A 361 TYR 0.021 0.001 TYR D 92 ARG 0.010 0.001 ARG F 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 2.323 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 104 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8608 (tpt) REVERT: A 207 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7733 (tptp) REVERT: A 629 MET cc_start: 0.8912 (mmm) cc_final: 0.8262 (mmm) REVERT: H 33 ASP cc_start: 0.8409 (m-30) cc_final: 0.8135 (m-30) REVERT: H 47 TRP cc_start: 0.6648 (t-100) cc_final: 0.6400 (t-100) REVERT: L 4 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6023 (ttm) REVERT: L 27 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.4957 (mp0) REVERT: L 49 TYR cc_start: 0.7438 (m-80) cc_final: 0.6844 (m-80) REVERT: L 87 TYR cc_start: 0.5538 (m-80) cc_final: 0.5164 (m-80) REVERT: B 207 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7929 (tmtt) REVERT: B 362 THR cc_start: 0.6576 (OUTLIER) cc_final: 0.6246 (t) REVERT: B 530 MET cc_start: 0.9020 (mtm) cc_final: 0.8755 (mtm) REVERT: D 4 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5955 (ttm) REVERT: D 53 LYS cc_start: 0.7725 (pttp) cc_final: 0.7478 (pttp) REVERT: D 63 LYS cc_start: 0.7763 (tptp) cc_final: 0.7452 (mppt) REVERT: D 70 GLN cc_start: 0.7799 (tp-100) cc_final: 0.6991 (pp30) REVERT: D 95 ASP cc_start: 0.7835 (t70) cc_final: 0.7568 (t0) REVERT: E 104 MET cc_start: 0.8979 (tpp) cc_final: 0.8689 (tpt) REVERT: E 207 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8003 (tmtt) REVERT: E 629 MET cc_start: 0.9001 (mmm) cc_final: 0.8716 (mmm) REVERT: E 650 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: F 20 LEU cc_start: 0.8628 (tp) cc_final: 0.8281 (tp) REVERT: F 100 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: G 87 TYR cc_start: 0.5462 (m-80) cc_final: 0.4925 (m-80) outliers start: 47 outliers final: 34 residues processed: 248 average time/residue: 0.3290 time to fit residues: 124.4208 Evaluate side-chains 248 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 207 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 171 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076989 restraints weight = 53508.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078302 restraints weight = 34223.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079149 restraints weight = 24275.990| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 20703 Z= 0.245 Angle : 0.825 59.200 28104 Z= 0.443 Chirality : 0.048 0.744 3564 Planarity : 0.004 0.068 3372 Dihedral : 7.674 52.560 5338 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.30 % Allowed : 14.31 % Favored : 83.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % 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: -0.27 (0.17), residues: 2325 helix: 0.62 (0.27), residues: 399 sheet: 0.20 (0.19), residues: 741 loop : -0.65 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP F 36 HIS 0.006 0.001 HIS F 100I PHE 0.019 0.002 PHE A 361 TYR 0.015 0.001 TYR L 92 ARG 0.008 0.000 ARG F 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.05 seconds wall clock time: 71 minutes 21.63 seconds (4281.63 seconds total)