Starting phenix.real_space_refine on Mon Mar 18 10:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/03_2024/7rso_24676.pdb" } resolution = 4.1 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= 0.001 sd= 0.066 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 120 5.16 5 C 12888 2.51 5 N 3348 2.21 5 O 4212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: 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: 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" 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: "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: 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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.96, per 1000 atoms: 0.58 Number of scatterers: 20568 At special positions: 0 Unit cell: (146.72, 150.65, 121.83, 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 120 16.00 O 4212 8.00 N 3348 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 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 B 598 " - pdb=" SG CYS B 604 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.06 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.06 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN b 4 " - " MAN b 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA Q 3 " - " MAN Q 5 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 5 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG 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-ASN " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 230 " " NAG A 604 " - " ASN A 325 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 405 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 188 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 462 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 230 " " NAG C 604 " - " ASN C 325 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 289 " " NAG C 610 " - " ASN C 188 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 462 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 88 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 325 " " NAG D 605 " - " ASN D 355 " " NAG D 606 " - " ASN D 392 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 405 " " NAG D 609 " - " ASN D 289 " " NAG D 610 " - " ASN D 188 " " NAG D 611 " - " ASN D 160 " " NAG D 612 " - " ASN D 462 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 625 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 339 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 413 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 339 " " NAG f 1 " - " ASN C 386 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 413 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN D 156 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 241 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 448 " " NAG q 1 " - " ASN D 339 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 130 " " NAG t 1 " - " ASN D 295 " " NAG u 1 " - " ASN D 413 " " NAG v 1 " - " ASN D 332 " Time building additional restraints: 9.49 Conformation dependent library (CDL) restraints added in 3.5 seconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 23.3% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.787A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.342A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.659A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'I' and resid 25 through 30 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 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 67 through 68 removed outlier: 6.209A pdb=" N ASN A 67 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) 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 129 through 130 Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.210A pdb=" N ASN C 67 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN D 67 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'D' and resid 154 through 162 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE D 468 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.564A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 1926 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: 7.40 Time building geometry restraints manager: 10.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 6118 1.35 - 1.50: 7224 1.50 - 1.66: 7475 1.66 - 1.81: 108 1.81 - 1.97: 54 Bond restraints: 20979 Sorted by residual: bond pdb=" CB TYR G 100E" pdb=" CG TYR G 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB TYR I 100E" pdb=" CG TYR I 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.55e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.54e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 20974 not shown) Histogram of bond angle deviations from ideal: 98.76 - 111.21: 9015 111.21 - 123.65: 18065 123.65 - 136.09: 1372 136.09 - 148.53: 0 148.53 - 160.97: 6 Bond angle restraints: 28458 Sorted by residual: angle pdb=" C2 NAG C 609 " pdb=" N2 NAG C 609 " pdb=" C7 NAG C 609 " ideal model delta sigma weight residual 124.56 160.97 -36.41 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 609 " pdb=" N2 NAG D 609 " pdb=" C7 NAG D 609 " ideal model delta sigma weight residual 124.56 160.96 -36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG v 2 " pdb=" N2 NAG v 2 " pdb=" C7 NAG v 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C2 NAG j 2 " pdb=" N2 NAG j 2 " pdb=" C7 NAG j 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 ... (remaining 28453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 13737 21.14 - 42.27: 360 42.27 - 63.40: 114 63.40 - 84.54: 90 84.54 - 105.67: 60 Dihedral angle restraints: 14361 sinusoidal: 7605 harmonic: 6756 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 74 " pdb=" CB CYS D 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 14358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2096 0.100 - 0.200: 813 0.200 - 0.300: 358 0.300 - 0.399: 195 0.399 - 0.499: 120 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.13e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.12e+02 ... (remaining 3579 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG p 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG R 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.211 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG d 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7714 2.91 - 3.40: 18478 3.40 - 3.90: 34610 3.90 - 4.40: 39772 4.40 - 4.90: 61451 Nonbonded interactions: 162025 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.407 2.520 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.407 2.520 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 432 " model vdw 2.407 2.520 nonbonded pdb=" OE2 GLU A 290 " pdb=" NZ LYS A 337 " model vdw 2.429 2.520 nonbonded pdb=" OE2 GLU C 290 " pdb=" NZ LYS C 337 " model vdw 2.429 2.520 ... (remaining 162020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'W' selection = chain 'a' selection = chain 'i' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'c' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.570 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 57.110 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.440 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.164 20979 Z= 1.432 Angle : 1.853 36.410 28458 Z= 1.149 Chirality : 0.161 0.499 3582 Planarity : 0.009 0.133 3417 Dihedral : 14.246 105.674 9906 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % 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: 0.79 (0.16), residues: 2307 helix: 0.03 (0.22), residues: 444 sheet: 0.89 (0.18), residues: 738 loop : 0.67 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP K 35 HIS 0.008 0.003 HIS G 35A PHE 0.036 0.005 PHE G 76 TYR 0.047 0.009 TYR I 100E ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 899 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7636 (ptm) cc_final: 0.7160 (ptm) REVERT: A 98 ASN cc_start: 0.8542 (t0) cc_final: 0.7521 (m-40) REVERT: A 100 MET cc_start: 0.7323 (mtp) cc_final: 0.6819 (ttm) REVERT: A 110 SER cc_start: 0.9470 (m) cc_final: 0.9135 (t) REVERT: A 129 LEU cc_start: 0.9263 (mt) cc_final: 0.8768 (mp) REVERT: A 131 CYS cc_start: 0.5903 (p) cc_final: 0.5647 (p) REVERT: A 338 TRP cc_start: 0.9110 (t-100) cc_final: 0.8738 (t-100) REVERT: A 377 ASN cc_start: 0.8320 (t0) cc_final: 0.8065 (t0) REVERT: B 584 GLU cc_start: 0.8891 (tt0) cc_final: 0.8657 (tt0) REVERT: B 601 LYS cc_start: 0.8816 (mttt) cc_final: 0.8603 (mtmm) REVERT: B 634 GLU cc_start: 0.8132 (tt0) cc_final: 0.7638 (tp30) REVERT: H 9 SER cc_start: 0.8153 (m) cc_final: 0.7819 (p) REVERT: H 33 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7348 (mp0) REVERT: H 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.7901 (tt0) REVERT: H 100 TRP cc_start: 0.8294 (m-10) cc_final: 0.7919 (m-10) REVERT: H 108 LEU cc_start: 0.9201 (tp) cc_final: 0.8994 (tp) REVERT: L 78 MET cc_start: 0.8379 (mmm) cc_final: 0.8109 (mmm) REVERT: L 96 GLU cc_start: 0.8311 (pt0) cc_final: 0.7630 (pt0) REVERT: C 95 MET cc_start: 0.8138 (ptm) cc_final: 0.7368 (ptm) REVERT: C 98 ASN cc_start: 0.8340 (t0) cc_final: 0.7285 (m110) REVERT: C 100 MET cc_start: 0.7952 (mtp) cc_final: 0.7317 (ttm) REVERT: C 110 SER cc_start: 0.9462 (m) cc_final: 0.9186 (t) REVERT: C 297 THR cc_start: 0.9273 (m) cc_final: 0.9016 (p) REVERT: C 377 ASN cc_start: 0.8348 (t0) cc_final: 0.8062 (t0) REVERT: C 427 TRP cc_start: 0.8415 (m-90) cc_final: 0.8079 (m-90) REVERT: C 474 ASP cc_start: 0.7449 (t0) cc_final: 0.7204 (t0) REVERT: E 540 GLN cc_start: 0.8320 (mm110) cc_final: 0.7870 (mm-40) REVERT: E 590 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9043 (tp40) REVERT: E 592 LEU cc_start: 0.9399 (tp) cc_final: 0.9150 (mt) REVERT: E 593 LEU cc_start: 0.8957 (mt) cc_final: 0.8697 (mm) REVERT: E 601 LYS cc_start: 0.8919 (mttt) cc_final: 0.8660 (mtmm) REVERT: E 616 ASN cc_start: 0.8100 (p0) cc_final: 0.7802 (p0) REVERT: E 634 GLU cc_start: 0.7871 (tt0) cc_final: 0.7510 (tp30) REVERT: E 639 THR cc_start: 0.8550 (m) cc_final: 0.8266 (p) REVERT: D 95 MET cc_start: 0.7950 (ptm) cc_final: 0.7691 (ptm) REVERT: D 98 ASN cc_start: 0.8295 (t0) cc_final: 0.7315 (m110) REVERT: D 104 MET cc_start: 0.8444 (ttm) cc_final: 0.7828 (tpp) REVERT: D 110 SER cc_start: 0.9344 (m) cc_final: 0.9015 (t) REVERT: D 165 VAL cc_start: 0.7750 (t) cc_final: 0.7530 (t) REVERT: D 217 TYR cc_start: 0.8133 (m-80) cc_final: 0.7186 (m-80) REVERT: D 352 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8415 (mm-40) REVERT: D 371 ILE cc_start: 0.8501 (mm) cc_final: 0.8200 (mm) REVERT: D 377 ASN cc_start: 0.8574 (t0) cc_final: 0.8155 (t0) REVERT: F 540 GLN cc_start: 0.8257 (mm110) cc_final: 0.7705 (mm-40) REVERT: F 601 LYS cc_start: 0.8918 (mttt) cc_final: 0.8516 (mttm) REVERT: F 634 GLU cc_start: 0.8339 (tt0) cc_final: 0.7928 (tp30) REVERT: G 36 TRP cc_start: 0.9295 (m100) cc_final: 0.8620 (m100) REVERT: G 89 THR cc_start: 0.9350 (m) cc_final: 0.8927 (p) REVERT: G 99 THR cc_start: 0.6348 (p) cc_final: 0.6080 (p) REVERT: G 100 GLN cc_start: 0.8285 (tt0) cc_final: 0.7556 (tt0) REVERT: J 33 MET cc_start: 0.8009 (ttm) cc_final: 0.7443 (mpp) REVERT: I 33 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7308 (mp0) REVERT: I 57 ASN cc_start: 0.9064 (t0) cc_final: 0.8811 (t0) REVERT: I 89 THR cc_start: 0.9405 (m) cc_final: 0.8979 (p) REVERT: I 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.8111 (tt0) REVERT: K 96 GLU cc_start: 0.8508 (pt0) cc_final: 0.8291 (pt0) outliers start: 3 outliers final: 0 residues processed: 902 average time/residue: 0.3553 time to fit residues: 467.4055 Evaluate side-chains 461 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 57 ASN L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 302 ASN E 653 GLN D 103 GLN D 229 ASN J 6 GLN J 32 HIS ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 95 GLN K 6 GLN K 32 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20979 Z= 0.256 Angle : 0.773 9.482 28458 Z= 0.396 Chirality : 0.057 0.791 3582 Planarity : 0.005 0.056 3417 Dihedral : 11.684 81.374 5478 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 0.29 % Allowed : 2.66 % Favored : 97.04 % 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: 0.76 (0.17), residues: 2307 helix: 1.20 (0.23), residues: 432 sheet: 0.64 (0.18), residues: 765 loop : 0.27 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP I 103 HIS 0.006 0.001 HIS D 374 PHE 0.031 0.002 PHE I 58 TYR 0.034 0.002 TYR E 643 ARG 0.007 0.001 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 634 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.7823 (m-80) cc_final: 0.7211 (m-80) REVERT: A 460 ASN cc_start: 0.8766 (m-40) cc_final: 0.8015 (m-40) REVERT: B 634 GLU cc_start: 0.8120 (tt0) cc_final: 0.7584 (tp30) REVERT: B 651 ASN cc_start: 0.7785 (t0) cc_final: 0.7573 (t0) REVERT: H 9 SER cc_start: 0.8439 (m) cc_final: 0.7911 (p) REVERT: H 33 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7102 (mp0) REVERT: H 39 GLN cc_start: 0.8923 (tp40) cc_final: 0.8708 (tp40) REVERT: H 89 THR cc_start: 0.9075 (m) cc_final: 0.8730 (p) REVERT: H 108 LEU cc_start: 0.9356 (tp) cc_final: 0.9142 (tp) REVERT: L 5 THR cc_start: 0.7960 (m) cc_final: 0.7275 (p) REVERT: L 78 MET cc_start: 0.8432 (mmm) cc_final: 0.8216 (mmm) REVERT: L 81 GLU cc_start: 0.8581 (tt0) cc_final: 0.8372 (tt0) REVERT: L 96 GLU cc_start: 0.8029 (pt0) cc_final: 0.7448 (pt0) REVERT: C 95 MET cc_start: 0.8003 (ptm) cc_final: 0.7802 (ptm) REVERT: C 377 ASN cc_start: 0.8131 (t0) cc_final: 0.7722 (t0) REVERT: C 430 VAL cc_start: 0.8877 (t) cc_final: 0.8654 (m) REVERT: E 601 LYS cc_start: 0.8873 (mttt) cc_final: 0.8538 (mtmm) REVERT: E 616 ASN cc_start: 0.8048 (p0) cc_final: 0.7648 (p0) REVERT: E 634 GLU cc_start: 0.8258 (tt0) cc_final: 0.7728 (tp30) REVERT: E 639 THR cc_start: 0.8900 (m) cc_final: 0.8101 (p) REVERT: E 653 GLN cc_start: 0.8423 (tm130) cc_final: 0.7984 (tm-30) REVERT: D 69 TRP cc_start: 0.6488 (p-90) cc_final: 0.5744 (p-90) REVERT: D 102 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8054 (tm-30) REVERT: D 111 LEU cc_start: 0.9023 (tp) cc_final: 0.8586 (tp) REVERT: D 217 TYR cc_start: 0.8082 (m-80) cc_final: 0.7363 (m-80) REVERT: F 539 VAL cc_start: 0.9255 (t) cc_final: 0.9032 (p) REVERT: F 584 GLU cc_start: 0.8905 (tt0) cc_final: 0.8664 (tt0) REVERT: F 601 LYS cc_start: 0.8919 (mttt) cc_final: 0.8511 (mttm) REVERT: F 633 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8090 (mtmt) REVERT: F 644 ASN cc_start: 0.8000 (m110) cc_final: 0.7654 (m110) REVERT: F 648 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7728 (tm-30) REVERT: F 651 ASN cc_start: 0.7661 (t0) cc_final: 0.7377 (t0) REVERT: G 26 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7834 (tm-30) REVERT: G 33 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7076 (mp0) REVERT: G 36 TRP cc_start: 0.9216 (m100) cc_final: 0.8578 (m100) REVERT: G 39 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8507 (tm-30) REVERT: G 50 TRP cc_start: 0.9210 (p-90) cc_final: 0.8679 (p-90) REVERT: G 89 THR cc_start: 0.9109 (m) cc_final: 0.8739 (p) REVERT: G 99 THR cc_start: 0.6433 (p) cc_final: 0.6168 (p) REVERT: G 108 LEU cc_start: 0.9390 (tp) cc_final: 0.9072 (tp) REVERT: J 17 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8012 (mt-10) REVERT: J 77 ARG cc_start: 0.9178 (mtm110) cc_final: 0.8884 (ptp90) REVERT: J 81 GLU cc_start: 0.9057 (tt0) cc_final: 0.8714 (tm-30) REVERT: I 9 SER cc_start: 0.8648 (m) cc_final: 0.8369 (p) REVERT: I 33 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7411 (mp0) REVERT: I 50 TRP cc_start: 0.9224 (p-90) cc_final: 0.8861 (p-90) REVERT: I 89 THR cc_start: 0.9158 (m) cc_final: 0.8731 (p) REVERT: I 94 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7262 (ptm-80) REVERT: I 99 THR cc_start: 0.6386 (p) cc_final: 0.6091 (t) REVERT: I 100 GLN cc_start: 0.8216 (tt0) cc_final: 0.7946 (tt0) REVERT: I 100 TYR cc_start: 0.6178 (m-80) cc_final: 0.5436 (m-10) REVERT: I 108 LEU cc_start: 0.9422 (tp) cc_final: 0.9135 (tp) REVERT: K 5 THR cc_start: 0.7569 (m) cc_final: 0.6919 (p) REVERT: K 81 GLU cc_start: 0.8923 (tt0) cc_final: 0.8566 (tm-30) REVERT: K 82 ASP cc_start: 0.8692 (m-30) cc_final: 0.8457 (m-30) outliers start: 6 outliers final: 3 residues processed: 639 average time/residue: 0.3165 time to fit residues: 308.5796 Evaluate side-chains 459 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 456 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 328 GLN A 330 HIS A 352 GLN A 460 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN C 99 ASN C 229 ASN C 287 GLN C 328 GLN C 330 HIS C 352 GLN C 460 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 644 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 328 GLN D 330 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN J 6 GLN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 20979 Z= 0.420 Angle : 0.793 9.242 28458 Z= 0.412 Chirality : 0.055 0.646 3582 Planarity : 0.006 0.069 3417 Dihedral : 10.173 71.405 5478 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.24 % Allowed : 3.15 % Favored : 96.61 % 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: 0.36 (0.17), residues: 2307 helix: 0.86 (0.24), residues: 453 sheet: 0.71 (0.19), residues: 687 loop : -0.22 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 628 HIS 0.010 0.002 HIS A 374 PHE 0.021 0.003 PHE A 233 TYR 0.042 0.003 TYR E 643 ARG 0.009 0.001 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 553 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7087 (p-90) cc_final: 0.5803 (p-90) REVERT: A 78 ASP cc_start: 0.8325 (m-30) cc_final: 0.7742 (p0) REVERT: A 111 LEU cc_start: 0.9069 (mt) cc_final: 0.8830 (mt) REVERT: A 460 ASN cc_start: 0.8788 (m110) cc_final: 0.8279 (t0) REVERT: B 584 GLU cc_start: 0.9190 (tt0) cc_final: 0.8905 (tt0) REVERT: B 634 GLU cc_start: 0.8565 (tt0) cc_final: 0.8185 (tt0) REVERT: B 651 ASN cc_start: 0.7674 (t0) cc_final: 0.7437 (t0) REVERT: H 33 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7500 (mp0) REVERT: H 89 THR cc_start: 0.9248 (m) cc_final: 0.8845 (p) REVERT: H 101 ASP cc_start: 0.8594 (t0) cc_final: 0.8295 (t0) REVERT: L 75 ILE cc_start: 0.7377 (tp) cc_final: 0.7123 (tp) REVERT: C 69 TRP cc_start: 0.6551 (p-90) cc_final: 0.6085 (p-90) REVERT: C 111 LEU cc_start: 0.8941 (tt) cc_final: 0.8538 (tt) REVERT: C 287 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: C 430 VAL cc_start: 0.8837 (t) cc_final: 0.8607 (m) REVERT: E 601 LYS cc_start: 0.9009 (mttt) cc_final: 0.8702 (mtmm) REVERT: E 634 GLU cc_start: 0.8307 (tt0) cc_final: 0.7825 (tp30) REVERT: E 639 THR cc_start: 0.9044 (m) cc_final: 0.8498 (p) REVERT: E 643 TYR cc_start: 0.8826 (m-80) cc_final: 0.8566 (m-80) REVERT: E 650 GLN cc_start: 0.8498 (tt0) cc_final: 0.7794 (tt0) REVERT: D 53 PHE cc_start: 0.8819 (p90) cc_final: 0.8582 (p90) REVERT: D 106 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 545 LEU cc_start: 0.8126 (tt) cc_final: 0.7905 (tp) REVERT: F 584 GLU cc_start: 0.9020 (tt0) cc_final: 0.8796 (tp30) REVERT: F 592 LEU cc_start: 0.9613 (tp) cc_final: 0.9398 (mt) REVERT: F 601 LYS cc_start: 0.8879 (mttt) cc_final: 0.8437 (mttm) REVERT: F 621 ASN cc_start: 0.8670 (t0) cc_final: 0.8315 (t0) REVERT: F 648 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7773 (tm-30) REVERT: G 36 TRP cc_start: 0.9230 (m100) cc_final: 0.8485 (m100) REVERT: G 39 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8542 (tm-30) REVERT: G 50 TRP cc_start: 0.9347 (p-90) cc_final: 0.8880 (p-90) REVERT: G 72 ASP cc_start: 0.8461 (t0) cc_final: 0.8099 (t0) REVERT: G 89 THR cc_start: 0.9156 (m) cc_final: 0.8716 (p) REVERT: G 98 TYR cc_start: 0.5233 (t80) cc_final: 0.4742 (t80) REVERT: G 108 LEU cc_start: 0.9425 (tp) cc_final: 0.9204 (tp) REVERT: J 3 VAL cc_start: 0.8858 (t) cc_final: 0.8506 (t) REVERT: J 77 ARG cc_start: 0.9260 (mtm110) cc_final: 0.9005 (ptp90) REVERT: I 9 SER cc_start: 0.9163 (m) cc_final: 0.8840 (p) REVERT: I 26 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8066 (tm-30) REVERT: I 31 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8366 (ttm-80) REVERT: I 89 THR cc_start: 0.9216 (m) cc_final: 0.8820 (p) REVERT: I 98 TYR cc_start: 0.5978 (t80) cc_final: 0.5407 (t80) REVERT: I 99 THR cc_start: 0.6480 (p) cc_final: 0.5796 (p) REVERT: I 100 TYR cc_start: 0.6572 (m-80) cc_final: 0.5273 (m-80) REVERT: I 108 LEU cc_start: 0.9539 (tp) cc_final: 0.9285 (tp) REVERT: K 5 THR cc_start: 0.7746 (m) cc_final: 0.7025 (p) REVERT: K 42 GLN cc_start: 0.8509 (tp40) cc_final: 0.8289 (tp-100) REVERT: K 66 GLN cc_start: 0.6600 (tt0) cc_final: 0.6049 (pt0) REVERT: K 81 GLU cc_start: 0.9036 (tt0) cc_final: 0.8640 (tm-30) REVERT: K 82 ASP cc_start: 0.8894 (m-30) cc_final: 0.8499 (m-30) outliers start: 5 outliers final: 0 residues processed: 556 average time/residue: 0.3170 time to fit residues: 268.1653 Evaluate side-chains 416 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 653 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 70 GLN C 287 GLN C 330 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 653 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 651 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 32 HIS J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20979 Z= 0.267 Angle : 0.670 6.869 28458 Z= 0.345 Chirality : 0.051 0.577 3582 Planarity : 0.005 0.059 3417 Dihedral : 9.156 64.439 5478 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.29 % Allowed : 1.89 % Favored : 97.82 % 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: 0.29 (0.17), residues: 2307 helix: 1.06 (0.24), residues: 447 sheet: 0.89 (0.19), residues: 660 loop : -0.51 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 610 HIS 0.008 0.001 HIS D 374 PHE 0.023 0.002 PHE H 58 TYR 0.028 0.002 TYR E 643 ARG 0.012 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 525 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8349 (m-30) cc_final: 0.7775 (p0) REVERT: A 460 ASN cc_start: 0.8455 (m110) cc_final: 0.7917 (t0) REVERT: B 584 GLU cc_start: 0.9150 (tt0) cc_final: 0.8897 (tt0) REVERT: B 634 GLU cc_start: 0.8769 (tt0) cc_final: 0.8142 (tp30) REVERT: H 33 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7602 (mp0) REVERT: H 39 GLN cc_start: 0.8799 (tp40) cc_final: 0.8531 (tp40) REVERT: H 89 THR cc_start: 0.9190 (m) cc_final: 0.8775 (p) REVERT: L 46 LEU cc_start: 0.8204 (pt) cc_final: 0.7921 (pp) REVERT: L 60 ASP cc_start: 0.8393 (t0) cc_final: 0.8145 (m-30) REVERT: L 61 ARG cc_start: 0.6242 (mtp85) cc_final: 0.6025 (mtt-85) REVERT: C 111 LEU cc_start: 0.8924 (tt) cc_final: 0.8639 (tt) REVERT: C 348 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8162 (tptt) REVERT: C 373 MET cc_start: 0.8861 (mtm) cc_final: 0.8653 (mtm) REVERT: E 601 LYS cc_start: 0.8900 (mttt) cc_final: 0.8568 (mtmm) REVERT: E 634 GLU cc_start: 0.8480 (tt0) cc_final: 0.7939 (tp30) REVERT: E 639 THR cc_start: 0.9171 (m) cc_final: 0.8567 (p) REVERT: E 653 GLN cc_start: 0.8917 (tm130) cc_final: 0.8680 (tm-30) REVERT: D 460 ASN cc_start: 0.8472 (m-40) cc_final: 0.8212 (m-40) REVERT: F 540 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8408 (mm-40) REVERT: F 543 GLN cc_start: 0.8717 (mt0) cc_final: 0.8430 (mt0) REVERT: F 584 GLU cc_start: 0.9048 (tt0) cc_final: 0.8551 (tp30) REVERT: F 592 LEU cc_start: 0.9562 (tp) cc_final: 0.9333 (mt) REVERT: F 601 LYS cc_start: 0.8960 (mttt) cc_final: 0.8721 (mtpt) REVERT: F 621 ASN cc_start: 0.8541 (t0) cc_final: 0.8273 (t0) REVERT: F 643 TYR cc_start: 0.8910 (m-80) cc_final: 0.8540 (m-10) REVERT: F 648 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7814 (tm-30) REVERT: G 31 ARG cc_start: 0.9030 (mtt-85) cc_final: 0.8747 (ttm-80) REVERT: G 36 TRP cc_start: 0.9228 (m100) cc_final: 0.8532 (m100) REVERT: G 39 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8455 (tm-30) REVERT: G 72 ASP cc_start: 0.8574 (t0) cc_final: 0.8178 (t0) REVERT: G 75 LEU cc_start: 0.8046 (mp) cc_final: 0.7825 (mp) REVERT: G 89 THR cc_start: 0.9046 (m) cc_final: 0.8650 (p) REVERT: G 99 THR cc_start: 0.6284 (p) cc_final: 0.6075 (p) REVERT: G 108 LEU cc_start: 0.9362 (tp) cc_final: 0.9118 (tp) REVERT: J 5 THR cc_start: 0.7924 (m) cc_final: 0.7277 (p) REVERT: J 77 ARG cc_start: 0.9308 (mtm110) cc_final: 0.9050 (ptp90) REVERT: I 9 SER cc_start: 0.9180 (m) cc_final: 0.8925 (p) REVERT: I 26 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7978 (tm-30) REVERT: I 89 THR cc_start: 0.9205 (m) cc_final: 0.8747 (p) REVERT: I 100 TYR cc_start: 0.6442 (m-80) cc_final: 0.5740 (m-80) REVERT: I 107 THR cc_start: 0.9548 (t) cc_final: 0.9241 (t) REVERT: I 108 LEU cc_start: 0.9566 (tp) cc_final: 0.9352 (tp) REVERT: K 5 THR cc_start: 0.7624 (m) cc_final: 0.6931 (p) REVERT: K 17 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8477 (mt-10) REVERT: K 65 SER cc_start: 0.9089 (t) cc_final: 0.8509 (t) REVERT: K 81 GLU cc_start: 0.9141 (tt0) cc_final: 0.8713 (tm-30) REVERT: K 82 ASP cc_start: 0.8902 (m-30) cc_final: 0.8388 (m-30) outliers start: 6 outliers final: 0 residues processed: 526 average time/residue: 0.2931 time to fit residues: 239.6552 Evaluate side-chains 400 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 0.0270 chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 200 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** H 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 653 GLN D 203 GLN ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 651 ASN F 653 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20979 Z= 0.245 Angle : 0.642 8.174 28458 Z= 0.330 Chirality : 0.048 0.310 3582 Planarity : 0.005 0.062 3417 Dihedral : 8.259 58.597 5478 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.29 % Allowed : 1.94 % Favored : 97.77 % 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: 2307 helix: 1.32 (0.25), residues: 423 sheet: 0.53 (0.19), residues: 723 loop : -0.54 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 36 HIS 0.006 0.001 HIS D 374 PHE 0.029 0.002 PHE G 58 TYR 0.024 0.002 TYR E 643 ARG 0.010 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 498 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8487 (m-30) cc_final: 0.7817 (p0) REVERT: A 460 ASN cc_start: 0.8567 (m110) cc_final: 0.7993 (t0) REVERT: B 584 GLU cc_start: 0.9196 (tt0) cc_final: 0.8625 (tp30) REVERT: B 634 GLU cc_start: 0.8838 (tt0) cc_final: 0.8498 (tt0) REVERT: B 648 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 651 ASN cc_start: 0.7684 (t0) cc_final: 0.7446 (t0) REVERT: H 31 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.8246 (ttp-110) REVERT: H 39 GLN cc_start: 0.8761 (tp40) cc_final: 0.8489 (tp40) REVERT: H 89 THR cc_start: 0.9201 (m) cc_final: 0.8769 (p) REVERT: H 99 THR cc_start: 0.6530 (t) cc_final: 0.5972 (t) REVERT: H 108 LEU cc_start: 0.9434 (tp) cc_final: 0.9224 (tp) REVERT: L 46 LEU cc_start: 0.8075 (pt) cc_final: 0.7863 (pp) REVERT: L 60 ASP cc_start: 0.8515 (t0) cc_final: 0.8203 (t70) REVERT: L 61 ARG cc_start: 0.6262 (mtp85) cc_final: 0.5986 (mtt-85) REVERT: C 348 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8924 (tptt) REVERT: C 373 MET cc_start: 0.8864 (mtm) cc_final: 0.8654 (mtm) REVERT: E 543 GLN cc_start: 0.8804 (mt0) cc_final: 0.8352 (mt0) REVERT: E 584 GLU cc_start: 0.9238 (tt0) cc_final: 0.8687 (tp30) REVERT: E 601 LYS cc_start: 0.8897 (mttt) cc_final: 0.8598 (mtmm) REVERT: E 616 ASN cc_start: 0.8136 (p0) cc_final: 0.7624 (p0) REVERT: E 629 MET cc_start: 0.7911 (ttm) cc_final: 0.7680 (ttt) REVERT: E 634 GLU cc_start: 0.8568 (tt0) cc_final: 0.8114 (tp30) REVERT: D 460 ASN cc_start: 0.8525 (m-40) cc_final: 0.8069 (m-40) REVERT: F 543 GLN cc_start: 0.8767 (mt0) cc_final: 0.8458 (mt0) REVERT: F 584 GLU cc_start: 0.9041 (tt0) cc_final: 0.8532 (tp30) REVERT: F 621 ASN cc_start: 0.8448 (t0) cc_final: 0.8169 (t0) REVERT: F 626 MET cc_start: 0.7474 (ttm) cc_final: 0.6450 (ttm) REVERT: F 648 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 651 ASN cc_start: 0.7729 (t0) cc_final: 0.7510 (t0) REVERT: G 36 TRP cc_start: 0.9235 (m100) cc_final: 0.8557 (m100) REVERT: G 39 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8534 (tm-30) REVERT: G 65 GLN cc_start: 0.8932 (tt0) cc_final: 0.8721 (mt0) REVERT: G 72 ASP cc_start: 0.8555 (t0) cc_final: 0.7978 (t0) REVERT: G 75 LEU cc_start: 0.8140 (mp) cc_final: 0.7718 (mt) REVERT: G 89 THR cc_start: 0.8991 (m) cc_final: 0.8578 (p) REVERT: G 98 TYR cc_start: 0.5739 (t80) cc_final: 0.5146 (t80) REVERT: G 99 THR cc_start: 0.6397 (p) cc_final: 0.6046 (p) REVERT: G 108 LEU cc_start: 0.9334 (tp) cc_final: 0.9106 (tp) REVERT: J 5 THR cc_start: 0.7925 (m) cc_final: 0.7355 (p) REVERT: J 46 LEU cc_start: 0.8441 (pt) cc_final: 0.8195 (pp) REVERT: J 77 ARG cc_start: 0.9302 (mtm110) cc_final: 0.9050 (ptp90) REVERT: I 9 SER cc_start: 0.9230 (m) cc_final: 0.8854 (p) REVERT: I 26 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8086 (tm-30) REVERT: I 108 LEU cc_start: 0.9498 (tp) cc_final: 0.9279 (tp) REVERT: K 5 THR cc_start: 0.7602 (m) cc_final: 0.6916 (p) REVERT: K 17 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8621 (mt-10) REVERT: K 37 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7705 (tm-30) REVERT: K 54 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8272 (ttt-90) REVERT: K 65 SER cc_start: 0.9073 (t) cc_final: 0.8490 (t) REVERT: K 66 GLN cc_start: 0.8227 (pt0) cc_final: 0.7959 (pt0) REVERT: K 82 ASP cc_start: 0.8845 (m-30) cc_final: 0.8294 (m-30) outliers start: 6 outliers final: 0 residues processed: 500 average time/residue: 0.2917 time to fit residues: 228.7767 Evaluate side-chains 395 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN B 653 GLN ** H 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN I 100BGLN K 6 GLN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20979 Z= 0.454 Angle : 0.784 8.684 28458 Z= 0.406 Chirality : 0.051 0.337 3582 Planarity : 0.006 0.074 3417 Dihedral : 8.514 59.339 5478 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.82 % 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: -0.30 (0.17), residues: 2307 helix: 0.77 (0.24), residues: 441 sheet: 0.28 (0.19), residues: 747 loop : -0.89 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP I 36 HIS 0.007 0.002 HIS D 374 PHE 0.026 0.003 PHE H 58 TYR 0.022 0.003 TYR G 100E ARG 0.011 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 465 time to evaluate : 2.340 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 78 ASP cc_start: 0.8527 (m-30) cc_final: 0.7849 (p0) REVERT: A 95 MET cc_start: 0.8337 (ptm) cc_final: 0.8045 (ppp) REVERT: A 425 ASN cc_start: 0.8487 (t0) cc_final: 0.8258 (t0) REVERT: A 460 ASN cc_start: 0.8420 (m110) cc_final: 0.8112 (t0) REVERT: B 530 MET cc_start: 0.8998 (mmm) cc_final: 0.8650 (mmm) REVERT: B 584 GLU cc_start: 0.9357 (tt0) cc_final: 0.8881 (tp30) REVERT: B 626 MET cc_start: 0.7074 (ttm) cc_final: 0.6452 (mtp) REVERT: B 634 GLU cc_start: 0.8851 (tt0) cc_final: 0.8478 (tt0) REVERT: B 648 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 651 ASN cc_start: 0.7602 (t0) cc_final: 0.7390 (t0) REVERT: H 31 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8630 (ttp-110) REVERT: H 89 THR cc_start: 0.9281 (m) cc_final: 0.8838 (p) REVERT: H 95 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7991 (tm-30) REVERT: H 107 THR cc_start: 0.9312 (t) cc_final: 0.9055 (t) REVERT: H 108 LEU cc_start: 0.9495 (tp) cc_final: 0.9288 (tp) REVERT: L 30 TYR cc_start: 0.7600 (m-10) cc_final: 0.7286 (m-10) REVERT: L 82 ASP cc_start: 0.8638 (m-30) cc_final: 0.7779 (m-30) REVERT: E 530 MET cc_start: 0.8121 (tpt) cc_final: 0.7898 (tpp) REVERT: E 601 LYS cc_start: 0.8975 (mttt) cc_final: 0.8672 (mtmm) REVERT: F 584 GLU cc_start: 0.9227 (tt0) cc_final: 0.8749 (tp30) REVERT: F 617 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7802 (ttmt) REVERT: F 648 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7731 (tm-30) REVERT: G 39 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8466 (tm-30) REVERT: G 72 ASP cc_start: 0.8832 (t0) cc_final: 0.8308 (t0) REVERT: G 75 LEU cc_start: 0.8375 (mp) cc_final: 0.8029 (mt) REVERT: G 89 THR cc_start: 0.9095 (m) cc_final: 0.8727 (p) REVERT: G 99 THR cc_start: 0.6700 (p) cc_final: 0.6262 (p) REVERT: G 108 LEU cc_start: 0.9459 (tp) cc_final: 0.9258 (tp) REVERT: J 17 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8335 (mt-10) REVERT: J 77 ARG cc_start: 0.9323 (mtm110) cc_final: 0.9085 (ptp90) REVERT: I 26 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8125 (tm-30) REVERT: I 72 ASP cc_start: 0.8772 (t0) cc_final: 0.8119 (t0) REVERT: I 75 LEU cc_start: 0.8290 (mt) cc_final: 0.7901 (mt) REVERT: I 89 THR cc_start: 0.9219 (m) cc_final: 0.8748 (p) REVERT: I 107 THR cc_start: 0.9560 (t) cc_final: 0.9334 (t) REVERT: K 17 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8655 (mt-10) REVERT: K 37 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7657 (tm-30) REVERT: K 72 THR cc_start: 0.8331 (m) cc_final: 0.8114 (m) outliers start: 2 outliers final: 0 residues processed: 465 average time/residue: 0.3078 time to fit residues: 223.8733 Evaluate side-chains 370 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.0270 chunk 25 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 135 optimal weight: 0.0060 chunk 102 optimal weight: 0.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN E 540 GLN E 575 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100BGLN K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20979 Z= 0.189 Angle : 0.643 8.175 28458 Z= 0.335 Chirality : 0.051 0.714 3582 Planarity : 0.005 0.061 3417 Dihedral : 7.829 58.736 5478 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.19 % Allowed : 1.07 % Favored : 98.74 % 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: -0.09 (0.17), residues: 2307 helix: 1.22 (0.25), residues: 420 sheet: 0.38 (0.18), residues: 810 loop : -0.90 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 36 HIS 0.005 0.001 HIS C 105 PHE 0.022 0.002 PHE G 58 TYR 0.028 0.002 TYR L 30 ARG 0.012 0.001 ARG K 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 503 time to evaluate : 2.244 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 69 TRP cc_start: 0.7024 (p-90) cc_final: 0.6786 (p-90) REVERT: A 78 ASP cc_start: 0.8492 (m-30) cc_final: 0.7839 (p0) REVERT: A 104 MET cc_start: 0.8425 (tpp) cc_final: 0.8216 (ttm) REVERT: A 119 CYS cc_start: 0.7414 (m) cc_final: 0.7142 (m) REVERT: A 205 CYS cc_start: 0.7594 (m) cc_final: 0.7046 (m) REVERT: A 460 ASN cc_start: 0.8477 (m110) cc_final: 0.7853 (t0) REVERT: B 584 GLU cc_start: 0.9226 (tt0) cc_final: 0.8660 (tp30) REVERT: B 626 MET cc_start: 0.7266 (ttm) cc_final: 0.6546 (mtp) REVERT: B 634 GLU cc_start: 0.8867 (tt0) cc_final: 0.8559 (tt0) REVERT: B 648 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7802 (tm-30) REVERT: H 39 GLN cc_start: 0.8809 (tp40) cc_final: 0.8598 (tm-30) REVERT: H 99 THR cc_start: 0.7115 (t) cc_final: 0.6828 (t) REVERT: L 42 GLN cc_start: 0.8456 (tp40) cc_final: 0.8215 (tp-100) REVERT: L 46 LEU cc_start: 0.7875 (pt) cc_final: 0.7626 (pp) REVERT: L 60 ASP cc_start: 0.8423 (t0) cc_final: 0.7990 (m-30) REVERT: L 61 ARG cc_start: 0.6160 (ttm-80) cc_final: 0.5959 (mtp180) REVERT: L 77 ARG cc_start: 0.8257 (pmt170) cc_final: 0.7863 (ptt-90) REVERT: C 114 GLN cc_start: 0.9293 (tp40) cc_final: 0.9090 (tp40) REVERT: E 543 GLN cc_start: 0.8775 (mt0) cc_final: 0.8335 (mt0) REVERT: E 545 LEU cc_start: 0.8359 (tp) cc_final: 0.8019 (tp) REVERT: E 601 LYS cc_start: 0.8912 (mttt) cc_final: 0.8535 (mtmm) REVERT: E 616 ASN cc_start: 0.8110 (p0) cc_final: 0.7642 (p0) REVERT: E 643 TYR cc_start: 0.8606 (m-80) cc_final: 0.8245 (m-10) REVERT: D 104 MET cc_start: 0.8773 (ttm) cc_final: 0.8226 (ttm) REVERT: D 373 MET cc_start: 0.8428 (mtm) cc_final: 0.8139 (ptp) REVERT: D 377 ASN cc_start: 0.8436 (t0) cc_final: 0.8175 (t0) REVERT: F 584 GLU cc_start: 0.9104 (tt0) cc_final: 0.8556 (tp30) REVERT: F 648 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 36 TRP cc_start: 0.9181 (m100) cc_final: 0.8613 (m100) REVERT: G 39 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8431 (tm-30) REVERT: G 47 TRP cc_start: 0.8967 (t60) cc_final: 0.8731 (t60) REVERT: G 65 GLN cc_start: 0.8903 (tt0) cc_final: 0.8684 (mt0) REVERT: G 72 ASP cc_start: 0.8630 (t0) cc_final: 0.8024 (t0) REVERT: G 75 LEU cc_start: 0.8246 (mp) cc_final: 0.7838 (mt) REVERT: G 89 THR cc_start: 0.8956 (m) cc_final: 0.8592 (p) REVERT: G 108 LEU cc_start: 0.9341 (tp) cc_final: 0.9120 (tp) REVERT: J 5 THR cc_start: 0.7850 (m) cc_final: 0.7290 (p) REVERT: J 17 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8212 (mt-10) REVERT: J 60 ASP cc_start: 0.8148 (t0) cc_final: 0.7592 (t0) REVERT: J 72 THR cc_start: 0.8222 (m) cc_final: 0.7881 (m) REVERT: J 77 ARG cc_start: 0.9262 (mtm110) cc_final: 0.9030 (ptp90) REVERT: J 96 GLU cc_start: 0.8534 (pt0) cc_final: 0.8316 (pt0) REVERT: I 26 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8010 (tm-30) REVERT: I 65 GLN cc_start: 0.8764 (tt0) cc_final: 0.8523 (mt0) REVERT: I 89 THR cc_start: 0.9089 (m) cc_final: 0.8596 (p) REVERT: I 105 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8379 (mtm110) REVERT: K 5 THR cc_start: 0.7710 (m) cc_final: 0.7071 (p) REVERT: K 30 TYR cc_start: 0.7825 (m-10) cc_final: 0.7592 (m-80) REVERT: K 37 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7528 (tm-30) REVERT: K 72 THR cc_start: 0.8239 (m) cc_final: 0.7924 (m) outliers start: 4 outliers final: 0 residues processed: 504 average time/residue: 0.2884 time to fit residues: 228.2120 Evaluate side-chains 386 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 141 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 653 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN C 99 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 640 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 460 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20979 Z= 0.197 Angle : 0.626 7.518 28458 Z= 0.325 Chirality : 0.050 0.653 3582 Planarity : 0.005 0.060 3417 Dihedral : 7.386 55.601 5478 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.24 % Allowed : 1.07 % Favored : 98.69 % 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: -0.06 (0.17), residues: 2307 helix: 1.25 (0.26), residues: 423 sheet: 0.45 (0.18), residues: 798 loop : -0.92 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 614 HIS 0.005 0.001 HIS C 105 PHE 0.017 0.002 PHE A 233 TYR 0.029 0.002 TYR F 643 ARG 0.011 0.001 ARG K 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 485 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7018 (p-90) cc_final: 0.6749 (p-90) REVERT: A 78 ASP cc_start: 0.8512 (m-30) cc_final: 0.7831 (p0) REVERT: A 119 CYS cc_start: 0.7444 (m) cc_final: 0.7103 (m) REVERT: A 205 CYS cc_start: 0.7758 (m) cc_final: 0.7171 (m) REVERT: A 460 ASN cc_start: 0.8466 (m110) cc_final: 0.7860 (t0) REVERT: B 584 GLU cc_start: 0.9231 (tt0) cc_final: 0.8653 (tp30) REVERT: B 621 ASN cc_start: 0.8162 (p0) cc_final: 0.7802 (t0) REVERT: B 626 MET cc_start: 0.7318 (ttm) cc_final: 0.6842 (mtp) REVERT: B 634 GLU cc_start: 0.8798 (tt0) cc_final: 0.8523 (tt0) REVERT: B 648 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 89 THR cc_start: 0.9208 (m) cc_final: 0.8811 (p) REVERT: L 42 GLN cc_start: 0.8397 (tp40) cc_final: 0.8149 (tp-100) REVERT: L 60 ASP cc_start: 0.8332 (t0) cc_final: 0.8060 (m-30) REVERT: C 78 ASP cc_start: 0.8463 (m-30) cc_final: 0.7846 (p0) REVERT: E 545 LEU cc_start: 0.8312 (tp) cc_final: 0.8080 (tp) REVERT: E 601 LYS cc_start: 0.8903 (mttt) cc_final: 0.8564 (mtmm) REVERT: E 616 ASN cc_start: 0.8003 (p0) cc_final: 0.7659 (p0) REVERT: E 643 TYR cc_start: 0.8563 (m-80) cc_final: 0.8130 (m-10) REVERT: D 104 MET cc_start: 0.8788 (ttm) cc_final: 0.8213 (ttm) REVERT: D 460 ASN cc_start: 0.8456 (m110) cc_final: 0.8243 (t0) REVERT: F 540 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8214 (mt0) REVERT: F 584 GLU cc_start: 0.9065 (tt0) cc_final: 0.8598 (tp30) REVERT: F 648 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7678 (tm-30) REVERT: F 651 ASN cc_start: 0.7629 (t0) cc_final: 0.7334 (t0) REVERT: G 36 TRP cc_start: 0.9132 (m100) cc_final: 0.8573 (m100) REVERT: G 39 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8116 (tm-30) REVERT: G 47 TRP cc_start: 0.8991 (t60) cc_final: 0.8770 (t60) REVERT: G 65 GLN cc_start: 0.8970 (tt0) cc_final: 0.8732 (mt0) REVERT: G 72 ASP cc_start: 0.8611 (t0) cc_final: 0.8124 (t0) REVERT: G 89 THR cc_start: 0.8940 (m) cc_final: 0.8530 (p) REVERT: J 5 THR cc_start: 0.7812 (m) cc_final: 0.7271 (p) REVERT: J 17 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8159 (mt-10) REVERT: J 33 MET cc_start: 0.7116 (pmm) cc_final: 0.6557 (pmm) REVERT: J 82 ASP cc_start: 0.8993 (m-30) cc_final: 0.8676 (m-30) REVERT: I 26 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7954 (tm-30) REVERT: I 65 GLN cc_start: 0.8776 (tt0) cc_final: 0.8548 (mt0) REVERT: I 89 THR cc_start: 0.9067 (m) cc_final: 0.8591 (p) REVERT: K 37 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7575 (tm-30) REVERT: K 65 SER cc_start: 0.9063 (t) cc_final: 0.8634 (t) REVERT: K 72 THR cc_start: 0.8192 (m) cc_final: 0.7850 (m) outliers start: 5 outliers final: 1 residues processed: 487 average time/residue: 0.2985 time to fit residues: 229.0506 Evaluate side-chains 375 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 136 optimal weight: 0.0010 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 653 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20979 Z= 0.206 Angle : 0.631 7.068 28458 Z= 0.326 Chirality : 0.049 0.614 3582 Planarity : 0.004 0.059 3417 Dihedral : 7.196 58.641 5478 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.42 % 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: 2307 helix: 1.17 (0.25), residues: 423 sheet: 0.46 (0.18), residues: 801 loop : -0.96 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 36 HIS 0.006 0.001 HIS C 105 PHE 0.023 0.002 PHE I 58 TYR 0.026 0.002 TYR E 643 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 489 time to evaluate : 2.115 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 69 TRP cc_start: 0.6875 (p-90) cc_final: 0.6465 (p-90) REVERT: A 78 ASP cc_start: 0.8519 (m-30) cc_final: 0.7809 (p0) REVERT: A 95 MET cc_start: 0.7884 (ptm) cc_final: 0.7629 (ppp) REVERT: A 119 CYS cc_start: 0.7465 (m) cc_final: 0.7150 (m) REVERT: A 205 CYS cc_start: 0.7511 (m) cc_final: 0.7011 (m) REVERT: A 371 ILE cc_start: 0.9280 (tp) cc_final: 0.9064 (tp) REVERT: A 425 ASN cc_start: 0.8014 (t0) cc_final: 0.7794 (t0) REVERT: B 584 GLU cc_start: 0.9262 (tt0) cc_final: 0.8682 (tp30) REVERT: B 626 MET cc_start: 0.7216 (ttm) cc_final: 0.6978 (mtp) REVERT: B 634 GLU cc_start: 0.8810 (tt0) cc_final: 0.8519 (tt0) REVERT: B 648 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 89 THR cc_start: 0.9211 (m) cc_final: 0.8826 (p) REVERT: H 99 THR cc_start: 0.7378 (t) cc_final: 0.6720 (t) REVERT: H 108 LEU cc_start: 0.9466 (tp) cc_final: 0.9260 (tp) REVERT: L 42 GLN cc_start: 0.8373 (tp40) cc_final: 0.8123 (tp-100) REVERT: C 78 ASP cc_start: 0.8442 (m-30) cc_final: 0.7843 (p0) REVERT: C 474 ASP cc_start: 0.8244 (t0) cc_final: 0.7889 (p0) REVERT: E 601 LYS cc_start: 0.8932 (mttt) cc_final: 0.8538 (mtmm) REVERT: E 616 ASN cc_start: 0.7970 (p0) cc_final: 0.7633 (p0) REVERT: E 643 TYR cc_start: 0.8475 (m-80) cc_final: 0.8047 (m-10) REVERT: D 69 TRP cc_start: 0.6520 (p-90) cc_final: 0.6056 (p-90) REVERT: D 460 ASN cc_start: 0.8383 (m110) cc_final: 0.8153 (m-40) REVERT: D 466 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8137 (mm-30) REVERT: F 584 GLU cc_start: 0.9082 (tt0) cc_final: 0.8599 (tp30) REVERT: F 643 TYR cc_start: 0.8740 (m-80) cc_final: 0.8433 (m-10) REVERT: F 648 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 36 TRP cc_start: 0.9156 (m100) cc_final: 0.8588 (m100) REVERT: G 39 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8101 (tm-30) REVERT: G 47 TRP cc_start: 0.9019 (t60) cc_final: 0.8794 (t60) REVERT: G 65 GLN cc_start: 0.8952 (tt0) cc_final: 0.8721 (mt0) REVERT: G 72 ASP cc_start: 0.8644 (t0) cc_final: 0.8192 (t0) REVERT: G 89 THR cc_start: 0.8976 (m) cc_final: 0.8599 (p) REVERT: G 108 LEU cc_start: 0.9328 (tp) cc_final: 0.9126 (tp) REVERT: J 5 THR cc_start: 0.7829 (m) cc_final: 0.7267 (p) REVERT: J 17 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8059 (mt-10) REVERT: J 33 MET cc_start: 0.7186 (pmm) cc_final: 0.6466 (pmm) REVERT: I 26 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7989 (tm-30) REVERT: I 65 GLN cc_start: 0.8715 (tt0) cc_final: 0.8505 (mt0) REVERT: I 89 THR cc_start: 0.9099 (m) cc_final: 0.8609 (p) REVERT: I 108 LEU cc_start: 0.9422 (tp) cc_final: 0.9162 (tp) REVERT: K 30 TYR cc_start: 0.7881 (m-10) cc_final: 0.7622 (m-10) REVERT: K 65 SER cc_start: 0.9078 (t) cc_final: 0.8646 (t) REVERT: K 72 THR cc_start: 0.8139 (m) cc_final: 0.7776 (m) outliers start: 3 outliers final: 0 residues processed: 489 average time/residue: 0.2879 time to fit residues: 221.2474 Evaluate side-chains 380 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 145 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 621 ASN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20979 Z= 0.196 Angle : 0.630 7.977 28458 Z= 0.328 Chirality : 0.049 0.591 3582 Planarity : 0.005 0.069 3417 Dihedral : 6.949 57.069 5478 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % 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: -0.06 (0.17), residues: 2307 helix: 1.31 (0.26), residues: 405 sheet: 0.48 (0.18), residues: 777 loop : -0.91 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 36 HIS 0.005 0.001 HIS C 105 PHE 0.028 0.002 PHE I 58 TYR 0.019 0.001 TYR A 217 ARG 0.013 0.001 ARG J 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 489 time to evaluate : 2.451 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 78 ASP cc_start: 0.8526 (m-30) cc_final: 0.7810 (p0) REVERT: A 95 MET cc_start: 0.7832 (ptm) cc_final: 0.7620 (ppp) REVERT: A 119 CYS cc_start: 0.7717 (m) cc_final: 0.7346 (m) REVERT: A 205 CYS cc_start: 0.7741 (m) cc_final: 0.7206 (m) REVERT: A 425 ASN cc_start: 0.7946 (t0) cc_final: 0.7735 (t0) REVERT: B 584 GLU cc_start: 0.9177 (tt0) cc_final: 0.8649 (tp30) REVERT: B 621 ASN cc_start: 0.8347 (t0) cc_final: 0.8116 (t0) REVERT: B 626 MET cc_start: 0.7498 (ttm) cc_final: 0.6631 (mtp) REVERT: B 634 GLU cc_start: 0.8800 (tt0) cc_final: 0.8425 (tt0) REVERT: B 648 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7768 (tm-30) REVERT: H 62 ASP cc_start: 0.8908 (t70) cc_final: 0.8569 (t70) REVERT: H 89 THR cc_start: 0.9178 (m) cc_final: 0.8802 (p) REVERT: H 108 LEU cc_start: 0.9444 (tp) cc_final: 0.9241 (tp) REVERT: L 42 GLN cc_start: 0.8319 (tp40) cc_final: 0.8054 (tp-100) REVERT: L 46 LEU cc_start: 0.8132 (pt) cc_final: 0.7854 (pp) REVERT: L 65 SER cc_start: 0.9180 (t) cc_final: 0.8664 (m) REVERT: L 70 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7469 (pp30) REVERT: L 72 THR cc_start: 0.7935 (m) cc_final: 0.7472 (m) REVERT: C 78 ASP cc_start: 0.8466 (m-30) cc_final: 0.7835 (p0) REVERT: C 370 GLU cc_start: 0.7792 (mp0) cc_final: 0.7271 (pt0) REVERT: C 474 ASP cc_start: 0.8276 (t0) cc_final: 0.7931 (t0) REVERT: E 601 LYS cc_start: 0.8913 (mttt) cc_final: 0.8557 (mtmm) REVERT: E 621 ASN cc_start: 0.8635 (t0) cc_final: 0.8370 (p0) REVERT: E 643 TYR cc_start: 0.8388 (m-80) cc_final: 0.7982 (m-10) REVERT: D 69 TRP cc_start: 0.6622 (p-90) cc_final: 0.6030 (p-90) REVERT: D 78 ASP cc_start: 0.8514 (m-30) cc_final: 0.7722 (p0) REVERT: D 370 GLU cc_start: 0.7932 (mp0) cc_final: 0.7680 (pt0) REVERT: F 584 GLU cc_start: 0.9058 (tt0) cc_final: 0.8600 (tp30) REVERT: F 643 TYR cc_start: 0.8672 (m-80) cc_final: 0.8385 (m-10) REVERT: F 648 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7815 (tm-30) REVERT: F 651 ASN cc_start: 0.7577 (t0) cc_final: 0.7342 (t0) REVERT: G 36 TRP cc_start: 0.9097 (m100) cc_final: 0.8513 (m100) REVERT: G 39 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8221 (tm-30) REVERT: G 47 TRP cc_start: 0.9009 (t60) cc_final: 0.8765 (t60) REVERT: G 65 GLN cc_start: 0.8987 (tt0) cc_final: 0.8760 (mt0) REVERT: G 72 ASP cc_start: 0.8669 (t0) cc_final: 0.8186 (t0) REVERT: G 89 THR cc_start: 0.8965 (m) cc_final: 0.8558 (p) REVERT: J 5 THR cc_start: 0.7875 (m) cc_final: 0.7293 (p) REVERT: J 17 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8054 (mt-10) REVERT: J 33 MET cc_start: 0.7040 (pmm) cc_final: 0.6622 (pmm) REVERT: J 54 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7837 (ttt-90) REVERT: J 66 GLN cc_start: 0.8402 (pp30) cc_final: 0.7234 (tp-100) REVERT: I 26 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7965 (tm-30) REVERT: I 65 GLN cc_start: 0.8771 (tt0) cc_final: 0.8554 (mt0) REVERT: I 89 THR cc_start: 0.9084 (m) cc_final: 0.8588 (p) REVERT: I 108 LEU cc_start: 0.9419 (tp) cc_final: 0.9137 (tp) REVERT: K 30 TYR cc_start: 0.7880 (m-10) cc_final: 0.7605 (m-10) REVERT: K 65 SER cc_start: 0.9072 (t) cc_final: 0.8543 (t) REVERT: K 72 THR cc_start: 0.8111 (m) cc_final: 0.7661 (m) outliers start: 3 outliers final: 0 residues processed: 489 average time/residue: 0.2992 time to fit residues: 229.9178 Evaluate side-chains 377 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092147 restraints weight = 43977.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095049 restraints weight = 28173.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096980 restraints weight = 21346.120| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20979 Z= 0.187 Angle : 0.620 7.847 28458 Z= 0.324 Chirality : 0.048 0.571 3582 Planarity : 0.004 0.058 3417 Dihedral : 6.699 56.543 5478 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.15 % Allowed : 0.24 % Favored : 99.61 % 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: -0.09 (0.17), residues: 2307 helix: 1.01 (0.25), residues: 429 sheet: 0.50 (0.18), residues: 765 loop : -0.86 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 614 HIS 0.005 0.001 HIS C 105 PHE 0.021 0.002 PHE H 58 TYR 0.023 0.001 TYR A 217 ARG 0.009 0.001 ARG A 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.57 seconds wall clock time: 90 minutes 40.63 seconds (5440.63 seconds total)