Starting phenix.real_space_refine on Sun Feb 18 09:20:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opo_20151/02_2024/6opo_20151_updated.pdb" } resolution = 3.5 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= -0.002 sd= 0.090 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 114 5.16 5 C 13422 2.51 5 N 3588 2.21 5 O 4317 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 TYR 217": "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 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "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 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21441 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "D" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.10, per 1000 atoms: 0.52 Number of scatterers: 21441 At special positions: 0 Unit cell: (155.89, 157.2, 144.1, 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 114 16.00 O 4317 8.00 N 3588 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.11 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.18 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.11 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 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 D 501 " - pdb=" SG CYS F 605 " distance=2.18 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.11 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.04 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS M 605 " distance=2.18 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 617 " - " ASN A 339 " " NAG A 624 " - " ASN A 397 " " NAG A 628 " - " ASN A 448 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG D 601 " - " ASN D 88 " " NAG D 617 " - " ASN D 339 " " NAG D 624 " - " ASN D 397 " " NAG D 628 " - " ASN D 448 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 616 " " NAG J 601 " - " ASN J 88 " " NAG J 617 " - " ASN J 339 " " NAG J 624 " - " ASN J 397 " " NAG J 628 " - " ASN J 448 " " NAG M 702 " - " ASN M 611 " " NAG M 703 " - " ASN M 616 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 362 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN D 234 " " NAG a 1 " - " ASN D 241 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 276 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 332 " " NAG f 1 " - " ASN D 362 " " NAG g 1 " - " ASN D 386 " " NAG h 1 " - " ASN D 392 " " NAG i 1 " - " ASN D 413 " " NAG j 1 " - " ASN J 234 " " NAG k 1 " - " ASN J 241 " " NAG l 1 " - " ASN J 262 " " NAG m 1 " - " ASN J 276 " " NAG n 1 " - " ASN J 295 " " NAG o 1 " - " ASN J 332 " " NAG p 1 " - " ASN J 362 " " NAG q 1 " - " ASN J 386 " " NAG r 1 " - " ASN J 392 " " NAG s 1 " - " ASN J 413 " Time building additional restraints: 9.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 36 sheets defined 20.4% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.877A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.017A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 530 through 546 Processing helix chain 'B' and resid 566 through 596 removed outlier: 4.466A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 660 Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.225A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 100 through 100B No H-bonds generated for 'chain 'H' and resid 100 through 100B' Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.877A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 335 through 352 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 475 through 485 removed outlier: 4.017A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 530 through 546 Processing helix chain 'F' and resid 566 through 596 removed outlier: 4.466A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 660 Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.225A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 100 through 100B No H-bonds generated for 'chain 'I' and resid 100 through 100B' Processing helix chain 'J' and resid 65 through 72 removed outlier: 3.877A pdb=" N HIS J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 113 Processing helix chain 'J' and resid 335 through 352 Processing helix chain 'J' and resid 369 through 372 No H-bonds generated for 'chain 'J' and resid 369 through 372' Processing helix chain 'J' and resid 388 through 390 No H-bonds generated for 'chain 'J' and resid 388 through 390' Processing helix chain 'J' and resid 475 through 485 removed outlier: 4.017A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS J 485 " --> pdb=" O SER J 481 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing helix chain 'M' and resid 515 through 517 No H-bonds generated for 'chain 'M' and resid 515 through 517' Processing helix chain 'M' and resid 530 through 546 Processing helix chain 'M' and resid 566 through 596 removed outlier: 4.466A pdb=" N GLY M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE M 595 " --> pdb=" O GLN M 591 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TRP M 596 " --> pdb=" O LEU M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 625 Processing helix chain 'M' and resid 628 through 635 Processing helix chain 'M' and resid 639 through 660 Processing helix chain 'N' and resid 59 through 64 removed outlier: 4.225A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 78 No H-bonds generated for 'chain 'N' and resid 76 through 78' Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 100 through 100B No H-bonds generated for 'chain 'O' and resid 100 through 100B' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 197 through 202 Processing sheet with id= E, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.629A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 413 through 418 removed outlier: 3.864A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= H, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.213A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.542A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 37 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= K, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= N, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= P, first strand: chain 'D' and resid 197 through 202 Processing sheet with id= Q, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.629A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASN D 362 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 413 through 418 removed outlier: 3.865A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= T, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.213A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.542A pdb=" N PHE G 26 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 37 " --> pdb=" O TRP G 28 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 12 through 17 Processing sheet with id= W, first strand: chain 'I' and resid 3 through 6 Processing sheet with id= X, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.619A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 35 through 40 Processing sheet with id= Z, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 53 through 56 Processing sheet with id= AB, first strand: chain 'J' and resid 197 through 202 Processing sheet with id= AC, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.630A pdb=" N THR J 467 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASN J 362 " --> pdb=" O PRO J 470 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 413 through 418 removed outlier: 3.864A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'K' and resid 85 through 90 removed outlier: 6.213A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 2 through 5 removed outlier: 4.542A pdb=" N PHE N 26 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 37 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 12 through 17 Processing sheet with id= AI, first strand: chain 'O' and resid 3 through 6 Processing sheet with id= AJ, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.619A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 1950 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: 7.77 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3968 1.31 - 1.44: 6065 1.44 - 1.58: 11648 1.58 - 1.71: 30 1.71 - 1.84: 144 Bond restraints: 21855 Sorted by residual: bond pdb=" C1 NAG D 624 " pdb=" O5 NAG D 624 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 21850 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.46: 367 104.46 - 111.90: 10374 111.90 - 119.35: 8516 119.35 - 126.80: 10086 126.80 - 134.24: 306 Bond angle restraints: 29649 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.72e+01 angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.71e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 129.88 -9.96 1.07e+00 8.73e-01 8.66e+01 angle pdb=" C PHE D 353 " pdb=" N PRO D 354 " pdb=" CA PRO D 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C PHE J 353 " pdb=" N PRO J 354 " pdb=" CA PRO J 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.92e+01 ... (remaining 29644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 13810 21.79 - 43.57: 386 43.57 - 65.36: 132 65.36 - 87.14: 54 87.14 - 108.93: 27 Dihedral angle restraints: 14409 sinusoidal: 7047 harmonic: 7362 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.67 75.67 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 14406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2811 0.118 - 0.235: 698 0.235 - 0.353: 68 0.353 - 0.470: 14 0.470 - 0.588: 6 Chirality restraints: 3597 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 BMA b 3 " pdb=" O4 NAG b 2 " pdb=" C2 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 3594 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.059 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" C7 NAG p 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.078 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.059 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" C7 NAG V 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.90e+01 pdb=" C7 NAG f 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 8898 2.89 - 3.39: 18700 3.39 - 3.90: 37070 3.90 - 4.40: 41870 4.40 - 4.90: 68179 Nonbonded interactions: 174717 Sorted by model distance: nonbonded pdb=" N ASN D 88 " pdb=" OD1 ASN D 88 " model vdw 2.392 2.520 nonbonded pdb=" N ASN J 88 " pdb=" OD1 ASN J 88 " model vdw 2.392 2.520 nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.393 2.520 nonbonded pdb=" O5 NAG b 1 " pdb=" O6 NAG b 1 " model vdw 2.425 2.432 nonbonded pdb=" O5 NAG l 1 " pdb=" O6 NAG l 1 " model vdw 2.426 2.432 ... (remaining 174712 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 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'Y' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 6.520 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 60.620 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.141 21855 Z= 1.420 Angle : 1.762 10.168 29649 Z= 1.137 Chirality : 0.103 0.588 3597 Planarity : 0.009 0.049 3660 Dihedral : 13.053 108.929 9546 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.79 % Favored : 97.97 % Rotamer: Outliers : 0.41 % Allowed : 0.27 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2517 helix: 0.82 (0.23), residues: 438 sheet: 1.47 (0.20), residues: 663 loop : 0.45 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.011 TRP D 479 HIS 0.011 0.003 HIS J 374 PHE 0.044 0.007 PHE E 98 TYR 0.036 0.008 TYR A 486 ARG 0.007 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 642 time to evaluate : 2.403 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 80 ASN cc_start: 0.7584 (t0) cc_final: 0.7292 (p0) REVERT: A 113 ASP cc_start: 0.7837 (m-30) cc_final: 0.7620 (m-30) REVERT: A 210 PHE cc_start: 0.8844 (t80) cc_final: 0.8620 (t80) REVERT: A 279 ASP cc_start: 0.7218 (p0) cc_final: 0.6613 (t0) REVERT: A 377 ASN cc_start: 0.8470 (t0) cc_final: 0.7678 (t0) REVERT: B 574 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8972 (mmtt) REVERT: C 81 THR cc_start: 0.8697 (m) cc_final: 0.8218 (p) REVERT: H 27 ASP cc_start: 0.8064 (t0) cc_final: 0.7745 (t0) REVERT: H 100 TYR cc_start: 0.7196 (t80) cc_final: 0.6635 (t80) REVERT: H 100 ASP cc_start: 0.6086 (m-30) cc_final: 0.5755 (m-30) REVERT: D 80 ASN cc_start: 0.7900 (t0) cc_final: 0.7617 (p0) REVERT: D 95 MET cc_start: 0.8588 (ptm) cc_final: 0.8273 (ptp) REVERT: D 279 ASP cc_start: 0.6918 (p0) cc_final: 0.6157 (t0) REVERT: D 475 MET cc_start: 0.8362 (mmt) cc_final: 0.8098 (mmt) REVERT: F 617 LYS cc_start: 0.8629 (mttm) cc_final: 0.8245 (mtmt) REVERT: F 634 GLU cc_start: 0.8128 (tp30) cc_final: 0.7780 (tp30) REVERT: I 12 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7771 (mtpt) REVERT: I 82 LEU cc_start: 0.7751 (tp) cc_final: 0.7533 (tp) REVERT: I 87 THR cc_start: 0.7866 (m) cc_final: 0.7634 (t) REVERT: I 100 TYR cc_start: 0.7485 (t80) cc_final: 0.6387 (t80) REVERT: I 100 ASP cc_start: 0.5980 (m-30) cc_final: 0.5467 (m-30) REVERT: I 100 ASN cc_start: 0.6613 (t0) cc_final: 0.6355 (t0) REVERT: J 279 ASP cc_start: 0.7098 (p0) cc_final: 0.6319 (t0) REVERT: M 620 ASN cc_start: 0.7993 (m-40) cc_final: 0.7720 (m-40) REVERT: N 5 LEU cc_start: 0.8486 (tt) cc_final: 0.8246 (tt) REVERT: O 12 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7670 (mtpt) REVERT: O 19 LYS cc_start: 0.7362 (tttt) cc_final: 0.7118 (mmtt) REVERT: O 27 ASP cc_start: 0.8128 (t0) cc_final: 0.7723 (t0) REVERT: O 82 LEU cc_start: 0.7798 (tp) cc_final: 0.7588 (tp) REVERT: O 100 TYR cc_start: 0.7244 (t80) cc_final: 0.6246 (t80) REVERT: O 100 ASN cc_start: 0.6568 (t0) cc_final: 0.6290 (t0) outliers start: 9 outliers final: 2 residues processed: 648 average time/residue: 0.3861 time to fit residues: 364.2001 Evaluate side-chains 342 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain J residue 88 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 607 ASN H 102 HIS D 72 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN I 1 GLN I 102 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 575 GLN M 607 ASN M 652 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21855 Z= 0.248 Angle : 0.711 10.516 29649 Z= 0.377 Chirality : 0.049 0.263 3597 Planarity : 0.005 0.043 3660 Dihedral : 9.085 59.755 4783 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.48 % Allowed : 8.53 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.60 (0.16), residues: 2517 helix: 1.46 (0.24), residues: 435 sheet: 1.05 (0.20), residues: 639 loop : -0.20 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 614 HIS 0.005 0.001 HIS J 374 PHE 0.018 0.002 PHE D 53 TYR 0.028 0.002 TYR L 49 ARG 0.008 0.001 ARG J 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 416 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6046 (m) cc_final: 0.5715 (m) REVERT: A 80 ASN cc_start: 0.7580 (t0) cc_final: 0.7309 (p0) REVERT: A 210 PHE cc_start: 0.8711 (t80) cc_final: 0.8325 (t80) REVERT: A 377 ASN cc_start: 0.8109 (t0) cc_final: 0.7608 (t0) REVERT: L 78 LEU cc_start: 0.7684 (tp) cc_final: 0.7159 (tt) REVERT: L 91 TYR cc_start: 0.5247 (m-80) cc_final: 0.4735 (m-10) REVERT: L 92 ASN cc_start: 0.8423 (t0) cc_final: 0.8093 (t0) REVERT: B 518 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6047 (t80) REVERT: D 74 CYS cc_start: 0.5822 (m) cc_final: 0.5521 (m) REVERT: D 95 MET cc_start: 0.8437 (ptm) cc_final: 0.8127 (ptp) REVERT: D 104 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: D 252 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8408 (mtt-85) REVERT: E 49 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.5245 (t80) REVERT: E 78 LEU cc_start: 0.7640 (tp) cc_final: 0.7434 (tt) REVERT: E 92 ASN cc_start: 0.8784 (t0) cc_final: 0.8508 (t0) REVERT: F 518 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.6435 (t80) REVERT: F 617 LYS cc_start: 0.8585 (mttm) cc_final: 0.8360 (mtmt) REVERT: F 659 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8035 (tm-30) REVERT: J 252 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8632 (mtp85) REVERT: J 368 ASP cc_start: 0.8185 (m-30) cc_final: 0.7949 (m-30) REVERT: K 24 ARG cc_start: 0.7242 (ttm110) cc_final: 0.7037 (ttm110) REVERT: K 91 TYR cc_start: 0.4553 (m-80) cc_final: 0.3756 (m-10) REVERT: K 92 ASN cc_start: 0.8538 (t0) cc_final: 0.8275 (t0) REVERT: M 518 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.6146 (t80) REVERT: M 542 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7177 (mtt90) REVERT: M 636 ASP cc_start: 0.8443 (t0) cc_final: 0.8199 (t0) REVERT: M 655 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8567 (ttmm) REVERT: O 10 GLU cc_start: 0.6886 (tt0) cc_final: 0.6280 (tt0) REVERT: O 12 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7114 (mmtt) REVERT: O 82 LEU cc_start: 0.7869 (tp) cc_final: 0.7575 (tp) REVERT: O 100 TYR cc_start: 0.6904 (t80) cc_final: 0.6017 (t80) outliers start: 55 outliers final: 28 residues processed: 447 average time/residue: 0.3726 time to fit residues: 244.5595 Evaluate side-chains 355 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 322 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain F residue 518 PHE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain O residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN B 607 ASN D 374 HIS E 79 GLN I 1 GLN K 100 GLN M 540 GLN M 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21855 Z= 0.209 Angle : 0.608 6.771 29649 Z= 0.323 Chirality : 0.046 0.318 3597 Planarity : 0.004 0.043 3660 Dihedral : 6.986 50.748 4783 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.80 % Allowed : 9.65 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.16), residues: 2517 helix: 1.61 (0.25), residues: 432 sheet: 0.69 (0.19), residues: 660 loop : -0.38 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.007 0.001 HIS H 62 PHE 0.016 0.002 PHE A 53 TYR 0.026 0.002 TYR E 49 ARG 0.009 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 368 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7581 (t0) cc_final: 0.7325 (p0) REVERT: A 104 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8141 (ttt) REVERT: A 210 PHE cc_start: 0.8666 (t80) cc_final: 0.8274 (t80) REVERT: A 279 ASP cc_start: 0.7170 (t0) cc_final: 0.6866 (t0) REVERT: A 368 ASP cc_start: 0.8297 (m-30) cc_final: 0.7837 (m-30) REVERT: A 377 ASN cc_start: 0.8133 (t0) cc_final: 0.7375 (t0) REVERT: L 78 LEU cc_start: 0.7681 (tp) cc_final: 0.7353 (tt) REVERT: L 92 ASN cc_start: 0.8361 (t0) cc_final: 0.7934 (t0) REVERT: H 1 GLN cc_start: 0.7521 (mp10) cc_final: 0.7178 (mp10) REVERT: H 28 THR cc_start: 0.8161 (p) cc_final: 0.7437 (p) REVERT: D 80 ASN cc_start: 0.8110 (p0) cc_final: 0.7894 (p0) REVERT: D 402 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6649 (p0) REVERT: E 24 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7855 (ttm110) REVERT: E 49 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4674 (t80) REVERT: E 78 LEU cc_start: 0.7796 (tp) cc_final: 0.7166 (tt) REVERT: F 659 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7967 (tm-30) REVERT: J 80 ASN cc_start: 0.7710 (p0) cc_final: 0.7476 (p0) REVERT: K 92 ASN cc_start: 0.8409 (t0) cc_final: 0.7962 (t0) REVERT: M 542 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7365 (mtt90) REVERT: M 636 ASP cc_start: 0.8529 (t0) cc_final: 0.8242 (t0) REVERT: O 100 TYR cc_start: 0.7249 (t80) cc_final: 0.6595 (t80) outliers start: 62 outliers final: 37 residues processed: 407 average time/residue: 0.3728 time to fit residues: 224.7803 Evaluate side-chains 352 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 312 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN M 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21855 Z= 0.252 Angle : 0.595 6.999 29649 Z= 0.314 Chirality : 0.046 0.338 3597 Planarity : 0.004 0.050 3660 Dihedral : 6.156 51.866 4783 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.89 % Allowed : 10.87 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2517 helix: 1.53 (0.25), residues: 429 sheet: 0.45 (0.19), residues: 660 loop : -0.51 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 35 HIS 0.006 0.001 HIS J 374 PHE 0.018 0.002 PHE J 53 TYR 0.027 0.002 TYR E 49 ARG 0.005 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 354 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7551 (t0) cc_final: 0.7322 (p0) REVERT: A 104 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8184 (ttm) REVERT: A 279 ASP cc_start: 0.7246 (t0) cc_final: 0.6908 (t0) REVERT: A 462 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6147 (mm110) REVERT: A 475 MET cc_start: 0.7794 (mmt) cc_final: 0.7494 (mmt) REVERT: L 78 LEU cc_start: 0.7717 (tp) cc_final: 0.7397 (tt) REVERT: L 92 ASN cc_start: 0.8376 (t0) cc_final: 0.8160 (t0) REVERT: D 80 ASN cc_start: 0.7952 (p0) cc_final: 0.7662 (p0) REVERT: E 78 LEU cc_start: 0.7740 (tp) cc_final: 0.7258 (tt) REVERT: F 659 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7991 (tm-30) REVERT: G 77 GLU cc_start: 0.8244 (pm20) cc_final: 0.8002 (pm20) REVERT: I 12 LYS cc_start: 0.8073 (mmpt) cc_final: 0.7300 (mmpt) REVERT: I 66 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6666 (ttm170) REVERT: J 80 ASN cc_start: 0.7864 (p0) cc_final: 0.7552 (p0) REVERT: K 92 ASN cc_start: 0.8430 (t0) cc_final: 0.8163 (t0) REVERT: M 542 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7328 (mtt90) REVERT: M 636 ASP cc_start: 0.8496 (t0) cc_final: 0.8111 (t0) REVERT: O 1 GLN cc_start: 0.7604 (mp10) cc_final: 0.7198 (mp10) outliers start: 64 outliers final: 46 residues processed: 391 average time/residue: 0.3610 time to fit residues: 208.9978 Evaluate side-chains 359 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 312 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 205 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 HIS M 652 GLN M 656 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21855 Z= 0.345 Angle : 0.643 12.303 29649 Z= 0.337 Chirality : 0.047 0.324 3597 Planarity : 0.004 0.048 3660 Dihedral : 6.346 58.533 4783 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.61 % Allowed : 11.19 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.16), residues: 2517 helix: 1.36 (0.26), residues: 429 sheet: 0.23 (0.19), residues: 660 loop : -0.76 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.009 0.001 HIS J 374 PHE 0.017 0.002 PHE A 382 TYR 0.025 0.002 TYR E 49 ARG 0.010 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 357 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8315 (ttm) REVERT: A 279 ASP cc_start: 0.7585 (t0) cc_final: 0.7091 (t0) REVERT: A 475 MET cc_start: 0.7888 (mmt) cc_final: 0.7520 (mmt) REVERT: L 78 LEU cc_start: 0.7749 (tp) cc_final: 0.7490 (tt) REVERT: L 79 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6584 (mt0) REVERT: L 92 ASN cc_start: 0.8628 (t0) cc_final: 0.8174 (t0) REVERT: H 12 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7958 (mmmt) REVERT: D 80 ASN cc_start: 0.8032 (p0) cc_final: 0.7737 (p0) REVERT: D 104 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8184 (ttm) REVERT: E 49 TYR cc_start: 0.5403 (OUTLIER) cc_final: 0.4844 (t80) REVERT: F 659 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7971 (tm-30) REVERT: I 10 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5763 (tt0) REVERT: I 66 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6957 (ttm170) REVERT: I 100 TYR cc_start: 0.7553 (t80) cc_final: 0.7353 (t80) REVERT: J 80 ASN cc_start: 0.7988 (p0) cc_final: 0.7623 (p0) REVERT: K 92 ASN cc_start: 0.8468 (t0) cc_final: 0.7942 (t0) REVERT: M 542 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7347 (mtt90) REVERT: N 77 GLU cc_start: 0.8356 (pm20) cc_final: 0.8053 (pm20) REVERT: O 1 GLN cc_start: 0.7692 (mp10) cc_final: 0.7245 (mp10) outliers start: 80 outliers final: 59 residues processed: 406 average time/residue: 0.3751 time to fit residues: 226.3793 Evaluate side-chains 386 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 323 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 21855 Z= 0.364 Angle : 0.670 9.764 29649 Z= 0.349 Chirality : 0.048 0.327 3597 Planarity : 0.005 0.049 3660 Dihedral : 6.614 58.986 4783 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.56 % Allowed : 12.63 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.34 (0.16), residues: 2517 helix: 1.31 (0.26), residues: 429 sheet: 0.26 (0.19), residues: 651 loop : -0.95 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 35 HIS 0.010 0.001 HIS J 374 PHE 0.019 0.002 PHE J 376 TYR 0.035 0.002 TYR L 91 ARG 0.011 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 349 time to evaluate : 2.396 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: A 104 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8311 (ttm) REVERT: A 475 MET cc_start: 0.7700 (mmt) cc_final: 0.7375 (mmt) REVERT: L 79 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6375 (mt0) REVERT: L 92 ASN cc_start: 0.8632 (t0) cc_final: 0.8298 (t0) REVERT: L 100 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7603 (mm110) REVERT: H 12 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7897 (mmmt) REVERT: D 80 ASN cc_start: 0.7774 (p0) cc_final: 0.7502 (p0) REVERT: D 104 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8337 (ttm) REVERT: E 49 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4789 (t80) REVERT: F 659 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8102 (tm-30) REVERT: I 12 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7796 (mmpt) REVERT: I 66 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7420 (ttm170) REVERT: J 80 ASN cc_start: 0.7780 (p0) cc_final: 0.7548 (p0) REVERT: K 92 ASN cc_start: 0.8607 (t0) cc_final: 0.8185 (t0) REVERT: M 655 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8496 (ttmm) REVERT: N 77 GLU cc_start: 0.8364 (pm20) cc_final: 0.8032 (pm20) REVERT: O 1 GLN cc_start: 0.7479 (mp10) cc_final: 0.7079 (mp10) outliers start: 79 outliers final: 61 residues processed: 398 average time/residue: 0.3890 time to fit residues: 227.0144 Evaluate side-chains 387 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 323 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 175 optimal weight: 0.0370 chunk 136 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN F 656 ASN ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21855 Z= 0.281 Angle : 0.628 9.069 29649 Z= 0.328 Chirality : 0.046 0.265 3597 Planarity : 0.004 0.049 3660 Dihedral : 6.437 58.999 4783 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.07 % Allowed : 13.49 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.16), residues: 2517 helix: 1.46 (0.26), residues: 426 sheet: 0.29 (0.20), residues: 651 loop : -1.04 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 35 HIS 0.006 0.001 HIS J 374 PHE 0.033 0.002 PHE I 29 TYR 0.027 0.002 TYR L 91 ARG 0.016 0.001 ARG O 82A *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 347 time to evaluate : 2.453 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: A 104 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8302 (ttm) REVERT: A 279 ASP cc_start: 0.7756 (t0) cc_final: 0.7544 (t0) REVERT: A 475 MET cc_start: 0.7786 (mmt) cc_final: 0.7317 (mmt) REVERT: L 30 SER cc_start: 0.8909 (m) cc_final: 0.8650 (p) REVERT: L 79 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6469 (mt0) REVERT: B 626 MET cc_start: 0.8201 (mtp) cc_final: 0.7841 (ttm) REVERT: H 12 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7917 (mmmt) REVERT: D 104 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: E 30 SER cc_start: 0.8862 (m) cc_final: 0.8639 (p) REVERT: E 79 GLN cc_start: 0.7510 (mp10) cc_final: 0.6368 (mp10) REVERT: F 647 GLU cc_start: 0.7945 (tt0) cc_final: 0.7176 (tt0) REVERT: I 66 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7428 (ttm170) REVERT: J 80 ASN cc_start: 0.7822 (p0) cc_final: 0.7568 (p0) REVERT: K 2 LEU cc_start: 0.6896 (mt) cc_final: 0.6569 (mp) REVERT: K 78 LEU cc_start: 0.7732 (tp) cc_final: 0.7183 (tt) REVERT: K 79 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6805 (mt0) REVERT: K 92 ASN cc_start: 0.8698 (t0) cc_final: 0.8391 (t0) REVERT: M 542 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7296 (mtt90) REVERT: M 655 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8477 (ttmm) REVERT: M 659 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8033 (tm-30) REVERT: N 77 GLU cc_start: 0.8487 (pm20) cc_final: 0.8232 (pm20) REVERT: O 1 GLN cc_start: 0.7343 (mp10) cc_final: 0.6964 (mp10) outliers start: 68 outliers final: 57 residues processed: 389 average time/residue: 0.3834 time to fit residues: 220.3879 Evaluate side-chains 388 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21855 Z= 0.267 Angle : 0.621 8.513 29649 Z= 0.323 Chirality : 0.046 0.328 3597 Planarity : 0.004 0.062 3660 Dihedral : 6.343 57.040 4783 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.02 % Allowed : 14.25 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.41 (0.16), residues: 2517 helix: 1.47 (0.26), residues: 426 sheet: 0.28 (0.20), residues: 651 loop : -1.11 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.006 0.001 HIS J 374 PHE 0.025 0.002 PHE I 29 TYR 0.027 0.002 TYR L 91 ARG 0.013 0.001 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 348 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8333 (ttm) REVERT: A 279 ASP cc_start: 0.7873 (t0) cc_final: 0.7666 (t0) REVERT: A 305 LYS cc_start: 0.6373 (mmtt) cc_final: 0.6155 (mmtm) REVERT: A 475 MET cc_start: 0.7782 (mmt) cc_final: 0.7325 (mmt) REVERT: L 30 SER cc_start: 0.8963 (m) cc_final: 0.8740 (p) REVERT: L 79 GLN cc_start: 0.7076 (mm-40) cc_final: 0.6502 (mt0) REVERT: B 626 MET cc_start: 0.8223 (mtp) cc_final: 0.7830 (ttm) REVERT: H 39 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 104 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8306 (ttm) REVERT: E 79 GLN cc_start: 0.7491 (mp10) cc_final: 0.6937 (mm-40) REVERT: F 647 GLU cc_start: 0.7938 (tt0) cc_final: 0.7167 (tt0) REVERT: G 77 GLU cc_start: 0.8178 (pm20) cc_final: 0.7920 (pm20) REVERT: G 94 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7411 (tt0) REVERT: I 43 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6936 (mp10) REVERT: I 66 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7125 (ttm170) REVERT: J 80 ASN cc_start: 0.7861 (p0) cc_final: 0.7587 (p0) REVERT: K 78 LEU cc_start: 0.7803 (tp) cc_final: 0.7101 (tt) REVERT: K 92 ASN cc_start: 0.9097 (t0) cc_final: 0.8890 (t0) REVERT: M 542 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7285 (mtt90) REVERT: M 655 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8468 (ttmm) REVERT: N 77 GLU cc_start: 0.8455 (pm20) cc_final: 0.8217 (pm20) REVERT: O 1 GLN cc_start: 0.7363 (mp10) cc_final: 0.6979 (mp10) outliers start: 67 outliers final: 56 residues processed: 388 average time/residue: 0.3733 time to fit residues: 213.7300 Evaluate side-chains 387 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 329 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 0.0370 chunk 229 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 222 optimal weight: 0.4980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 100 GLN J 67 ASN ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21855 Z= 0.243 Angle : 0.622 8.479 29649 Z= 0.324 Chirality : 0.046 0.328 3597 Planarity : 0.004 0.045 3660 Dihedral : 6.261 57.489 4783 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.66 % Allowed : 14.98 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.40 (0.16), residues: 2517 helix: 1.46 (0.26), residues: 429 sheet: 0.32 (0.20), residues: 651 loop : -1.12 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 35 HIS 0.008 0.001 HIS I 62 PHE 0.025 0.002 PHE I 29 TYR 0.030 0.002 TYR E 49 ARG 0.008 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 341 time to evaluate : 2.379 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 104 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8336 (ttm) REVERT: A 279 ASP cc_start: 0.7829 (t0) cc_final: 0.7627 (t0) REVERT: A 475 MET cc_start: 0.7750 (mmt) cc_final: 0.7277 (mmt) REVERT: L 79 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6513 (mt0) REVERT: L 100 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7614 (mm110) REVERT: B 626 MET cc_start: 0.8201 (mtp) cc_final: 0.7834 (ttm) REVERT: H 39 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 104 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8135 (ttm) REVERT: E 54 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: E 79 GLN cc_start: 0.7523 (mp10) cc_final: 0.6415 (mp10) REVERT: G 56 ASP cc_start: 0.8032 (t0) cc_final: 0.7751 (t70) REVERT: G 77 GLU cc_start: 0.8167 (pm20) cc_final: 0.7919 (pm20) REVERT: G 94 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7431 (tt0) REVERT: I 66 ARG cc_start: 0.7901 (ttp-170) cc_final: 0.7187 (ttm170) REVERT: J 80 ASN cc_start: 0.7889 (p0) cc_final: 0.7600 (p0) REVERT: J 400 ARG cc_start: 0.7592 (ttt180) cc_final: 0.7100 (tpp-160) REVERT: K 78 LEU cc_start: 0.7758 (tp) cc_final: 0.7052 (tt) REVERT: K 79 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6811 (mt0) REVERT: K 92 ASN cc_start: 0.8959 (t0) cc_final: 0.8679 (t0) REVERT: M 655 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8461 (ttmm) REVERT: N 77 GLU cc_start: 0.8397 (pm20) cc_final: 0.8152 (pm20) REVERT: O 1 GLN cc_start: 0.7367 (mp10) cc_final: 0.6985 (mp10) outliers start: 59 outliers final: 53 residues processed: 374 average time/residue: 0.3826 time to fit residues: 211.1347 Evaluate side-chains 384 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 329 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21855 Z= 0.237 Angle : 0.613 8.437 29649 Z= 0.321 Chirality : 0.045 0.322 3597 Planarity : 0.004 0.064 3660 Dihedral : 6.207 58.267 4781 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.57 % Allowed : 15.07 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.41 (0.17), residues: 2517 helix: 1.50 (0.26), residues: 429 sheet: 0.27 (0.20), residues: 669 loop : -1.14 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 35 HIS 0.007 0.001 HIS I 62 PHE 0.024 0.002 PHE I 29 TYR 0.026 0.002 TYR E 49 ARG 0.015 0.001 ARG E 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 344 time to evaluate : 2.277 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 104 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: A 279 ASP cc_start: 0.7916 (t0) cc_final: 0.7680 (t0) REVERT: A 475 MET cc_start: 0.7726 (mmt) cc_final: 0.7260 (mmt) REVERT: L 79 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6523 (mt0) REVERT: B 626 MET cc_start: 0.8176 (mtp) cc_final: 0.7795 (ttm) REVERT: H 81 GLU cc_start: 0.6518 (tm-30) cc_final: 0.6129 (tm-30) REVERT: D 80 ASN cc_start: 0.8083 (p0) cc_final: 0.7640 (p0) REVERT: D 104 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8355 (ttm) REVERT: E 54 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8121 (mtm-85) REVERT: E 79 GLN cc_start: 0.7703 (mp10) cc_final: 0.7301 (mp10) REVERT: F 647 GLU cc_start: 0.7929 (tt0) cc_final: 0.7172 (tt0) REVERT: G 53 ASP cc_start: 0.8366 (p0) cc_final: 0.8072 (p0) REVERT: G 56 ASP cc_start: 0.8030 (t0) cc_final: 0.7727 (t70) REVERT: G 77 GLU cc_start: 0.8111 (pm20) cc_final: 0.7854 (pm20) REVERT: G 94 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7483 (tt0) REVERT: J 80 ASN cc_start: 0.7834 (p0) cc_final: 0.7522 (p0) REVERT: J 400 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6877 (tpp-160) REVERT: K 45 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6801 (ttp80) REVERT: K 78 LEU cc_start: 0.7661 (tp) cc_final: 0.7125 (tt) REVERT: K 79 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6896 (mt0) REVERT: K 92 ASN cc_start: 0.8974 (t0) cc_final: 0.8729 (t0) REVERT: M 542 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7244 (mtt90) REVERT: M 655 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8467 (ttmm) REVERT: O 1 GLN cc_start: 0.7287 (mp10) cc_final: 0.6991 (mp10) REVERT: O 29 PHE cc_start: 0.8976 (t80) cc_final: 0.8694 (t80) REVERT: O 39 GLN cc_start: 0.7201 (tp40) cc_final: 0.6891 (tm-30) outliers start: 57 outliers final: 52 residues processed: 375 average time/residue: 0.3755 time to fit residues: 206.0089 Evaluate side-chains 383 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 328 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** M 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102029 restraints weight = 35190.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102476 restraints weight = 29579.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103576 restraints weight = 27254.998| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21855 Z= 0.207 Angle : 0.596 8.395 29649 Z= 0.313 Chirality : 0.045 0.320 3597 Planarity : 0.004 0.045 3660 Dihedral : 6.032 59.571 4781 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.53 % Allowed : 15.29 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.40 (0.17), residues: 2517 helix: 1.46 (0.26), residues: 432 sheet: 0.31 (0.20), residues: 669 loop : -1.13 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 35 HIS 0.007 0.001 HIS I 62 PHE 0.024 0.002 PHE I 29 TYR 0.030 0.001 TYR E 49 ARG 0.011 0.001 ARG H 82A Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.52 seconds wall clock time: 86 minutes 32.95 seconds (5192.95 seconds total)