Starting phenix.real_space_refine on Sun Feb 18 11:43:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opp_20152/02_2024/6opp_20152_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.074 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 115 5.16 5 C 13657 2.51 5 N 3604 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "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 "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "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 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "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 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21852 Number of models: 1 Model: "" Number of chains: 54 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: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1071 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 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: "I" 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: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Chain: "E" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 1 Chain: "G" 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: "O" 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: "K" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "J" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2998 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 3 Chain: "M" 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: "N" 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: "F" 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: "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: 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: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Unusual residues: {'LMT': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "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: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'LMT': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 9 Chain: "K" 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: "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 Time building chain proxies: 11.52, per 1000 atoms: 0.53 Number of scatterers: 21852 At special positions: 0 Unit cell: (161.13, 158.51, 145.41, 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 115 16.00 O 4476 8.00 N 3604 7.00 C 13657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS A 501 " distance=2.12 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 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=2.12 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " 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=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.12 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 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 E 605 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 605 " - pdb=" SG CYS J 501 " distance=2.08 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.07 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=2.03 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 M 16 " - pdb=" SG CYS M 84 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " 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 R 5 " - " MAN R 6 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA g 3 " - " MAN g 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " BMA c 3 " - " MAN c 7 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 621 " - " ASN A 339 " " NAG A 622 " - " ASN A 355 " " NAG A 632 " - " ASN A 397 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG B 704 " - " ASN B 625 " " NAG B 705 " - " ASN B 637 " " NAG D 601 " - " ASN D 88 " " NAG D 620 " - " ASN D 339 " " NAG D 621 " - " ASN D 355 " " NAG D 631 " - " ASN D 397 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 616 " " NAG E 703 " - " ASN E 625 " " NAG E 704 " - " ASN E 637 " " NAG J 601 " - " ASN J 88 " " NAG J 620 " - " ASN J 339 " " NAG J 621 " - " ASN J 355 " " NAG J 632 " - " ASN J 397 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 616 " " NAG K 703 " - " ASN K 625 " " NAG K 704 " - " ASN K 637 " " 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 A 448 " " NAG a 1 " - " ASN D 234 " " NAG b 1 " - " ASN D 241 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 332 " " NAG g 1 " - " ASN D 362 " " NAG h 1 " - " ASN D 386 " " NAG i 1 " - " ASN D 392 " " NAG j 1 " - " ASN D 413 " " NAG k 1 " - " ASN D 448 " " NAG l 1 " - " ASN J 234 " " NAG m 1 " - " ASN J 241 " " NAG n 1 " - " ASN J 262 " " NAG o 1 " - " ASN J 276 " " NAG p 1 " - " ASN J 295 " " NAG q 1 " - " ASN J 332 " " NAG r 1 " - " ASN J 362 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 392 " " NAG u 1 " - " ASN J 413 " " NAG v 1 " - " ASN J 448 " Time building additional restraints: 10.10 Conformation dependent library (CDL) restraints added in 3.6 seconds 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 41 sheets defined 20.1% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... 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 530 through 545 Processing helix chain 'B' and resid 568 through 596 removed outlier: 4.410A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 4.857A 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 634 Processing helix chain 'B' and resid 636 through 663 removed outlier: 5.084A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 643 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.025A 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 115 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.610A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) 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: 3.996A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.072A 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 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 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'D' and resid 65 through 73 removed outlier: 3.711A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.557A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) 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: 3.970A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 546 Processing helix chain 'E' and resid 566 through 596 removed outlier: 3.571A pdb=" N LEU E 581 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU E 593 " --> pdb=" O GLN E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 625 Processing helix chain 'E' and resid 628 through 634 Processing helix chain 'E' and resid 636 through 662 removed outlier: 4.926A pdb=" N GLN E 640 " --> pdb=" O ASN E 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 643 " --> pdb=" O GLN E 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 100 through 100B No H-bonds generated for 'chain 'G' and resid 100 through 100B' Processing helix chain 'O' and resid 80 through 82 No H-bonds generated for 'chain 'O' and resid 80 through 82' Processing helix chain 'K' and resid 530 through 546 Processing helix chain 'K' and resid 566 through 596 removed outlier: 3.640A pdb=" N TRP K 571 " --> pdb=" O LEU K 568 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU K 593 " --> pdb=" O GLN K 590 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 625 Processing helix chain 'K' and resid 628 through 634 removed outlier: 3.888A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 639 through 662 Processing helix chain 'J' and resid 65 through 73 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 114 Processing helix chain 'J' and resid 335 through 352 removed outlier: 3.836A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) 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 475 through 485 removed outlier: 4.287A pdb=" N SER J 481 " --> pdb=" O ASN J 478 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TYR J 484 " --> pdb=" O SER J 481 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS J 485 " --> pdb=" O GLU J 482 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.163A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 78 No H-bonds generated for 'chain 'M' and resid 76 through 78' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 84 through 86 No H-bonds generated for 'chain 'N' and resid 84 through 86' Processing helix chain 'N' and resid 100 through 100B No H-bonds generated for 'chain 'N' and resid 100 through 100B' Processing helix chain 'F' and resid 59 through 64 removed outlier: 4.408A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing sheet with id= A, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.520A pdb=" N ARG L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL L 13 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU L 105 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.875A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= E, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= H, first strand: chain 'A' and resid 196 through 202 Processing sheet with id= I, first strand: chain 'A' and resid 271 through 273 removed outlier: 5.934A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.451A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= M, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= N, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.528A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= P, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.902A pdb=" N ARG I 103 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL I 13 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLU I 105 " --> pdb=" O VAL I 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.250A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= S, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= T, first strand: chain 'D' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'D' and resid 91 through 94 Processing sheet with id= V, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= W, first strand: chain 'D' and resid 271 through 274 removed outlier: 3.507A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASN D 362 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 443 through 449 removed outlier: 3.623A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= Z, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.799A pdb=" N SER G 33 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 4 through 6 Processing sheet with id= AB, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.348A pdb=" N ARG O 103 " --> pdb=" O LEU O 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'O' and resid 85 through 90 removed outlier: 6.248A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 35 through 39 Processing sheet with id= AE, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= AG, first strand: chain 'J' and resid 197 through 202 Processing sheet with id= AH, first strand: chain 'J' and resid 271 through 274 removed outlier: 5.935A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASN J 362 " --> pdb=" O PRO J 470 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 374 through 378 removed outlier: 4.154A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.337A pdb=" N ASN M 30 " --> pdb=" O LYS M 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS M 35 " --> pdb=" O ASN M 30 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 12 through 17 Processing sheet with id= AL, first strand: chain 'N' and resid 3 through 5 Processing sheet with id= AM, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.122A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 2 through 5 removed outlier: 4.335A pdb=" N PHE F 26 " --> pdb=" O ASN F 39 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 12 through 17 777 hydrogen bonds defined for protein. 1791 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: 7.76 Time building geometry restraints manager: 10.42 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: 4013 1.31 - 1.45: 6630 1.45 - 1.58: 11450 1.58 - 1.71: 23 1.71 - 1.85: 144 Bond restraints: 22260 Sorted by residual: bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.385 0.112 1.40e-02 5.10e+03 6.42e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 22255 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.44: 551 105.44 - 112.66: 11909 112.66 - 119.88: 8377 119.88 - 127.09: 9069 127.09 - 134.31: 295 Bond angle restraints: 30201 Sorted by residual: angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 120.03 128.37 -8.34 9.90e-01 1.02e+00 7.10e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 128.85 -8.93 1.07e+00 8.73e-01 6.96e+01 angle pdb=" N ARG A 440 " pdb=" CA ARG A 440 " pdb=" C ARG A 440 " ideal model delta sigma weight residual 111.28 120.31 -9.03 1.09e+00 8.42e-01 6.86e+01 angle pdb=" C ALA H 60 " pdb=" N PRO H 61 " pdb=" CA PRO H 61 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.03e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.89e+01 ... (remaining 30196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.47: 14345 26.47 - 52.93: 416 52.93 - 79.40: 108 79.40 - 105.87: 118 105.87 - 132.33: 50 Dihedral angle restraints: 15037 sinusoidal: 7662 harmonic: 7375 Sorted by residual: 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 93.00 154.83 -61.83 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 150.63 -57.63 1 1.00e+01 1.00e-02 4.46e+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 93.00 149.72 -56.72 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 15034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2900 0.115 - 0.230: 738 0.230 - 0.345: 96 0.345 - 0.460: 21 0.460 - 0.575: 15 Chirality restraints: 3770 Sorted by residual: chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.73e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.55e+01 ... (remaining 3767 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.093 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" CG ASN D 234 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.162 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 234 " -0.063 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN J 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN J 234 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN J 234 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 1 " 0.082 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" C7 NAG q 1 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG q 1 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG q 1 " -0.108 2.00e-02 2.50e+03 pdb=" O7 NAG q 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5848 2.80 - 3.32: 19591 3.32 - 3.85: 37507 3.85 - 4.37: 43970 4.37 - 4.90: 71531 Nonbonded interactions: 178447 Sorted by model distance: nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.271 2.520 nonbonded pdb=" O4 NAG q 2 " pdb=" O6 NAG q 2 " model vdw 2.346 2.440 nonbonded pdb=" OG1 THR D 37 " pdb=" OG1 THR D 499 " model vdw 2.385 2.440 nonbonded pdb=" N ASP N 100A" pdb=" OD1 ASP N 100A" model vdw 2.398 2.520 nonbonded pdb=" O5 NAG W 1 " pdb=" O6 NAG W 1 " model vdw 2.404 2.432 ... (remaining 178442 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' and (resid 32 through 127 or resid 196 through 505 or resid 601 throu \ gh 632)) selection = (chain 'D' and (resid 32 through 127 or resid 196 through 505 or resid 601 throu \ gh 631)) selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) selection = (chain 'E' and (resid 518 through 547 or resid 563 or resid 568 through 664 or r \ esid 702 through 704)) selection = (chain 'K' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'X' selection = chain 'Y' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'R' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'n' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'o' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.030 Extract box with map and model: 6.250 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 58.620 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.430 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.144 22260 Z= 1.444 Angle : 1.795 11.280 30201 Z= 1.139 Chirality : 0.107 0.575 3770 Planarity : 0.009 0.068 3672 Dihedral : 17.095 132.332 10158 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.94 % 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: 0.77 (0.16), residues: 2511 helix: 0.78 (0.23), residues: 429 sheet: 0.69 (0.18), residues: 752 loop : 0.47 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.010 TRP J 479 HIS 0.016 0.002 HIS H 102 PHE 0.044 0.007 PHE H 29 TYR 0.083 0.009 TYR E 638 ARG 0.007 0.001 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 601 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLN cc_start: 0.8861 (tp40) cc_final: 0.8338 (tm-30) REVERT: A 368 ASP cc_start: 0.7830 (m-30) cc_final: 0.7448 (m-30) REVERT: H 100 TYR cc_start: 0.7061 (t80) cc_final: 0.6533 (t80) REVERT: I 79 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7542 (mp10) REVERT: E 530 MET cc_start: 0.9031 (mtm) cc_final: 0.8743 (mtp) REVERT: E 662 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7820 (mt-10) REVERT: O 33 LEU cc_start: 0.7624 (tp) cc_final: 0.7183 (tp) REVERT: O 36 TYR cc_start: 0.6914 (m-80) cc_final: 0.6489 (m-80) REVERT: O 38 GLN cc_start: 0.5532 (tt0) cc_final: 0.4954 (tm-30) REVERT: O 42 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7799 (mm110) REVERT: K 629 MET cc_start: 0.8349 (mtm) cc_final: 0.7508 (ttm) REVERT: K 635 ILE cc_start: 0.9300 (pt) cc_final: 0.9100 (pt) REVERT: J 61 TYR cc_start: 0.8237 (p90) cc_final: 0.7521 (p90) REVERT: J 95 MET cc_start: 0.8239 (ptm) cc_final: 0.8023 (ptm) REVERT: J 100 MET cc_start: 0.8986 (mtp) cc_final: 0.8653 (mtm) REVERT: J 215 ILE cc_start: 0.9489 (mm) cc_final: 0.9129 (pt) REVERT: J 435 TYR cc_start: 0.8267 (m-80) cc_final: 0.8023 (m-80) REVERT: J 486 TYR cc_start: 0.8973 (m-80) cc_final: 0.8476 (m-10) REVERT: M 85 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7507 (tm-30) REVERT: N 6 GLU cc_start: 0.6063 (pm20) cc_final: 0.5644 (pm20) REVERT: N 23 LYS cc_start: 0.7260 (tptt) cc_final: 0.7006 (tptt) REVERT: N 32 TYR cc_start: 0.7844 (p90) cc_final: 0.7320 (p90) REVERT: N 62 HIS cc_start: 0.8410 (p-80) cc_final: 0.8207 (p90) REVERT: N 63 LEU cc_start: 0.9062 (mt) cc_final: 0.8794 (mt) REVERT: N 81 GLU cc_start: 0.8976 (tt0) cc_final: 0.8757 (tm-30) REVERT: N 82 ASN cc_start: 0.8974 (m-40) cc_final: 0.8548 (m-40) REVERT: F 39 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: F 78 ASP cc_start: 0.7629 (m-30) cc_final: 0.7323 (m-30) REVERT: F 97 VAL cc_start: 0.4379 (t) cc_final: 0.3088 (t) outliers start: 13 outliers final: 9 residues processed: 612 average time/residue: 0.3928 time to fit residues: 348.2831 Evaluate side-chains 279 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 270 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain K residue 611 ASN Chi-restraints excluded: chain K residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 102 HIS O 93 ASN K 652 GLN J 308 HIS J 442 GLN F 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22260 Z= 0.255 Angle : 0.759 8.869 30201 Z= 0.394 Chirality : 0.049 0.266 3770 Planarity : 0.005 0.045 3672 Dihedral : 13.897 113.133 5398 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 2.69 % Allowed : 8.21 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.18 (0.16), residues: 2511 helix: 0.95 (0.24), residues: 420 sheet: 0.31 (0.18), residues: 726 loop : -0.17 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 96 HIS 0.007 0.001 HIS D 249 PHE 0.023 0.002 PHE N 100J TYR 0.026 0.002 TYR N 32 ARG 0.005 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 356 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 92 ASN cc_start: 0.8498 (t0) cc_final: 0.7791 (t0) REVERT: A 368 ASP cc_start: 0.7832 (m-30) cc_final: 0.7505 (m-30) REVERT: A 400 ARG cc_start: 0.6900 (ttt180) cc_final: 0.6537 (ttt90) REVERT: A 482 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8013 (tp30) REVERT: C 88 ASP cc_start: 0.8909 (p0) cc_final: 0.8338 (p0) REVERT: C 89 GLN cc_start: 0.8241 (mp10) cc_final: 0.7858 (tm-30) REVERT: H 97 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6495 (mm-30) REVERT: H 100 TYR cc_start: 0.7553 (t80) cc_final: 0.6359 (t80) REVERT: I 36 TYR cc_start: 0.7522 (m-80) cc_final: 0.7210 (m-80) REVERT: D 368 ASP cc_start: 0.7461 (m-30) cc_final: 0.7244 (m-30) REVERT: E 633 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8871 (mtmm) REVERT: E 638 TYR cc_start: 0.8186 (m-80) cc_final: 0.7891 (m-10) REVERT: E 662 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7573 (mt-10) REVERT: G 12 LYS cc_start: 0.8245 (mmmm) cc_final: 0.8001 (mmmt) REVERT: G 31 ARG cc_start: 0.8455 (tpp80) cc_final: 0.8081 (mtt-85) REVERT: G 101 LYS cc_start: 0.8677 (tptt) cc_final: 0.8456 (tptp) REVERT: O 36 TYR cc_start: 0.6766 (m-80) cc_final: 0.5762 (m-80) REVERT: O 37 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.4059 (tm-30) REVERT: O 38 GLN cc_start: 0.5723 (tt0) cc_final: 0.5181 (tm-30) REVERT: K 629 MET cc_start: 0.8281 (mtm) cc_final: 0.6916 (mtp) REVERT: J 100 MET cc_start: 0.8551 (mtp) cc_final: 0.8252 (mtm) REVERT: J 215 ILE cc_start: 0.9372 (mm) cc_final: 0.9103 (pt) REVERT: J 280 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.6567 (t0) REVERT: J 333 ILE cc_start: 0.8607 (mt) cc_final: 0.8362 (tt) REVERT: J 475 MET cc_start: 0.8146 (mmt) cc_final: 0.7756 (mmt) REVERT: M 85 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7515 (tm-30) REVERT: N 19 LYS cc_start: 0.8821 (tttt) cc_final: 0.8077 (tptp) REVERT: N 63 LEU cc_start: 0.8871 (mt) cc_final: 0.8435 (mt) REVERT: N 82 LEU cc_start: 0.8249 (tp) cc_final: 0.8000 (mt) REVERT: F 73 ASN cc_start: 0.8233 (t0) cc_final: 0.7881 (p0) REVERT: F 74 LEU cc_start: 0.8544 (mt) cc_final: 0.8331 (tp) REVERT: F 87 GLU cc_start: 0.7205 (mp0) cc_final: 0.6929 (mp0) REVERT: F 89 GLN cc_start: 0.8461 (mp10) cc_final: 0.8202 (mp10) outliers start: 60 outliers final: 32 residues processed: 396 average time/residue: 0.3492 time to fit residues: 210.6050 Evaluate side-chains 309 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 275 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 73 LYS Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 201 optimal weight: 0.0060 chunk 224 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN C 20 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN K 652 GLN J 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22260 Z= 0.234 Angle : 0.673 11.463 30201 Z= 0.342 Chirality : 0.049 0.663 3770 Planarity : 0.005 0.051 3672 Dihedral : 10.126 97.961 5387 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.29 % Allowed : 10.14 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2511 helix: 0.74 (0.26), residues: 423 sheet: 0.21 (0.19), residues: 731 loop : -0.40 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 96 HIS 0.005 0.001 HIS J 105 PHE 0.036 0.002 PHE H 29 TYR 0.024 0.002 TYR N 32 ARG 0.009 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 304 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: L 92 ASN cc_start: 0.8420 (t0) cc_final: 0.7728 (t0) REVERT: A 368 ASP cc_start: 0.7886 (m-30) cc_final: 0.7601 (m-30) REVERT: A 479 TRP cc_start: 0.7993 (m-10) cc_final: 0.7489 (m-90) REVERT: A 482 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7965 (tp30) REVERT: C 88 ASP cc_start: 0.8963 (p0) cc_final: 0.8667 (p0) REVERT: C 89 GLN cc_start: 0.8209 (mp10) cc_final: 0.7963 (tm-30) REVERT: H 39 GLN cc_start: 0.8372 (tp40) cc_final: 0.7678 (tm-30) REVERT: I 11 LEU cc_start: 0.8105 (tp) cc_final: 0.7895 (mp) REVERT: I 36 TYR cc_start: 0.7717 (m-80) cc_final: 0.7460 (m-80) REVERT: I 42 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7560 (mp10) REVERT: E 662 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7543 (mt-10) REVERT: G 48 MET cc_start: 0.7303 (mtp) cc_final: 0.6966 (ttm) REVERT: O 36 TYR cc_start: 0.6858 (m-80) cc_final: 0.5888 (m-80) REVERT: O 37 GLN cc_start: 0.4361 (OUTLIER) cc_final: 0.4133 (tm-30) REVERT: O 38 GLN cc_start: 0.5900 (tt0) cc_final: 0.4913 (tm-30) REVERT: O 42 GLN cc_start: 0.7776 (mm110) cc_final: 0.7294 (mp10) REVERT: K 621 GLU cc_start: 0.7984 (tp30) cc_final: 0.7764 (tp30) REVERT: K 629 MET cc_start: 0.7976 (mtm) cc_final: 0.7104 (mtp) REVERT: J 95 MET cc_start: 0.7667 (ptm) cc_final: 0.7337 (ptt) REVERT: J 100 MET cc_start: 0.8514 (mtp) cc_final: 0.8062 (mtm) REVERT: J 280 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.6757 (t0) REVERT: J 333 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8487 (tt) REVERT: J 475 MET cc_start: 0.8101 (mmt) cc_final: 0.7746 (mmt) REVERT: J 486 TYR cc_start: 0.9060 (m-80) cc_final: 0.8702 (m-10) REVERT: M 85 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7511 (tm-30) REVERT: N 63 LEU cc_start: 0.9098 (mt) cc_final: 0.8710 (mt) REVERT: N 82 LEU cc_start: 0.8454 (tp) cc_final: 0.8128 (mt) REVERT: N 99 GLU cc_start: 0.8466 (tt0) cc_final: 0.8128 (tp30) REVERT: N 100 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7342 (mm-30) REVERT: F 73 ASN cc_start: 0.8416 (t0) cc_final: 0.8093 (t0) REVERT: F 74 LEU cc_start: 0.8629 (mt) cc_final: 0.8284 (tp) REVERT: F 87 GLU cc_start: 0.7618 (mp0) cc_final: 0.7145 (mp0) REVERT: F 89 GLN cc_start: 0.8495 (mp10) cc_final: 0.8093 (mp10) outliers start: 51 outliers final: 26 residues processed: 335 average time/residue: 0.3372 time to fit residues: 173.6317 Evaluate side-chains 296 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain F residue 78 ASP 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: 3.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 227 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN J 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22260 Z= 0.224 Angle : 0.634 11.632 30201 Z= 0.322 Chirality : 0.046 0.420 3770 Planarity : 0.005 0.049 3672 Dihedral : 8.332 73.408 5385 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 11.09 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.14 (0.16), residues: 2511 helix: 0.72 (0.26), residues: 425 sheet: 0.24 (0.19), residues: 750 loop : -0.50 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 45 HIS 0.005 0.001 HIS D 374 PHE 0.027 0.002 PHE H 29 TYR 0.022 0.002 TYR L 91 ARG 0.012 0.001 ARG O 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 291 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7171 (mmm-85) REVERT: L 92 ASN cc_start: 0.8385 (t0) cc_final: 0.7747 (t0) REVERT: B 647 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 368 ASP cc_start: 0.7913 (m-30) cc_final: 0.7630 (m-30) REVERT: A 479 TRP cc_start: 0.8081 (m-10) cc_final: 0.7576 (m-90) REVERT: A 482 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7961 (tp30) REVERT: C 88 ASP cc_start: 0.8989 (p0) cc_final: 0.8665 (p0) REVERT: C 89 GLN cc_start: 0.8216 (mp10) cc_final: 0.7950 (tm-30) REVERT: H 80 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8452 (tt) REVERT: I 36 TYR cc_start: 0.7682 (m-80) cc_final: 0.7442 (m-10) REVERT: D 80 ASN cc_start: 0.8894 (t0) cc_final: 0.8682 (t0) REVERT: D 479 TRP cc_start: 0.8211 (m-10) cc_final: 0.7670 (m-90) REVERT: E 662 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7514 (mt-10) REVERT: G 48 MET cc_start: 0.7232 (mtp) cc_final: 0.6969 (ttm) REVERT: O 36 TYR cc_start: 0.6895 (m-80) cc_final: 0.5914 (m-80) REVERT: O 37 GLN cc_start: 0.4368 (OUTLIER) cc_final: 0.4133 (tm-30) REVERT: O 42 GLN cc_start: 0.7811 (mm110) cc_final: 0.7425 (mp10) REVERT: K 584 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8220 (tm-30) REVERT: K 621 GLU cc_start: 0.7870 (tp30) cc_final: 0.7593 (tp30) REVERT: J 100 MET cc_start: 0.8615 (mtp) cc_final: 0.8222 (mtm) REVERT: J 280 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.6771 (t0) REVERT: J 333 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8455 (tt) REVERT: J 475 MET cc_start: 0.8035 (mmt) cc_final: 0.7628 (mmt) REVERT: J 486 TYR cc_start: 0.9067 (m-80) cc_final: 0.8695 (m-10) REVERT: M 24 ILE cc_start: 0.8497 (mt) cc_final: 0.8216 (pt) REVERT: M 66 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8630 (t0) REVERT: M 85 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7380 (tm-30) REVERT: N 59 TYR cc_start: 0.7294 (m-80) cc_final: 0.7087 (m-80) REVERT: N 82 LEU cc_start: 0.8456 (tp) cc_final: 0.8153 (mt) REVERT: N 99 GLU cc_start: 0.8414 (tt0) cc_final: 0.8187 (tp30) REVERT: N 100 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7568 (mm-30) REVERT: F 73 ASN cc_start: 0.8469 (t0) cc_final: 0.8111 (t0) REVERT: F 74 LEU cc_start: 0.8641 (mt) cc_final: 0.8339 (tp) REVERT: F 87 GLU cc_start: 0.7693 (mp0) cc_final: 0.7384 (mp0) outliers start: 56 outliers final: 35 residues processed: 328 average time/residue: 0.3277 time to fit residues: 167.7401 Evaluate side-chains 300 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 0.0020 chunk 166 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN O 38 GLN J 302 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22260 Z= 0.257 Angle : 0.618 10.277 30201 Z= 0.315 Chirality : 0.047 0.536 3770 Planarity : 0.005 0.050 3672 Dihedral : 7.671 69.302 5383 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.10 % Allowed : 11.27 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2511 helix: 0.81 (0.26), residues: 425 sheet: 0.25 (0.19), residues: 755 loop : -0.58 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 96 HIS 0.006 0.001 HIS D 374 PHE 0.029 0.002 PHE H 29 TYR 0.022 0.002 TYR L 91 ARG 0.007 0.001 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 283 time to evaluate : 2.186 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: L 18 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7245 (mmm-85) REVERT: L 92 ASN cc_start: 0.8428 (t0) cc_final: 0.7734 (t0) REVERT: B 629 MET cc_start: 0.8180 (mtp) cc_final: 0.7384 (mtt) REVERT: A 479 TRP cc_start: 0.8141 (m-10) cc_final: 0.7599 (m-90) REVERT: C 88 ASP cc_start: 0.9014 (p0) cc_final: 0.8669 (p0) REVERT: H 39 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: H 100 ASP cc_start: 0.8467 (t0) cc_final: 0.8216 (t0) REVERT: I 36 TYR cc_start: 0.7844 (m-80) cc_final: 0.7606 (m-80) REVERT: I 39 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7074 (mtmm) REVERT: D 80 ASN cc_start: 0.8921 (t0) cc_final: 0.8689 (t0) REVERT: D 479 TRP cc_start: 0.8210 (m-10) cc_final: 0.7598 (m-90) REVERT: E 632 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7910 (tm-30) REVERT: E 662 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7385 (mt-10) REVERT: G 48 MET cc_start: 0.7105 (mtp) cc_final: 0.6872 (ttm) REVERT: O 33 LEU cc_start: 0.7351 (tp) cc_final: 0.7085 (tp) REVERT: O 36 TYR cc_start: 0.7016 (m-80) cc_final: 0.6136 (m-80) REVERT: O 42 GLN cc_start: 0.7922 (mm110) cc_final: 0.7579 (mp10) REVERT: O 70 GLU cc_start: 0.8467 (pp20) cc_final: 0.8174 (pm20) REVERT: K 584 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8275 (tm-30) REVERT: K 621 GLU cc_start: 0.8015 (tp30) cc_final: 0.7682 (tp30) REVERT: K 629 MET cc_start: 0.8153 (mtp) cc_final: 0.7721 (mtm) REVERT: J 100 MET cc_start: 0.8672 (mtp) cc_final: 0.8313 (mtm) REVERT: J 280 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.6836 (t0) REVERT: J 333 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (tt) REVERT: J 475 MET cc_start: 0.8086 (mmt) cc_final: 0.7626 (mmt) REVERT: J 486 TYR cc_start: 0.9089 (m-80) cc_final: 0.8682 (m-10) REVERT: M 24 ILE cc_start: 0.8592 (mt) cc_final: 0.8333 (pt) REVERT: M 66 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8624 (t0) REVERT: M 85 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7625 (tm-30) REVERT: M 88 ASP cc_start: 0.8064 (t0) cc_final: 0.7765 (t0) REVERT: N 82 LEU cc_start: 0.8456 (tp) cc_final: 0.8162 (mt) REVERT: N 99 GLU cc_start: 0.8491 (tt0) cc_final: 0.8207 (tp30) REVERT: F 74 LEU cc_start: 0.8687 (mt) cc_final: 0.8381 (tp) REVERT: F 87 GLU cc_start: 0.7698 (mp0) cc_final: 0.7389 (mp0) outliers start: 69 outliers final: 42 residues processed: 324 average time/residue: 0.3318 time to fit residues: 167.5469 Evaluate side-chains 297 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 462 GLN C 20 GLN H 39 GLN I 6 GLN D 105 HIS D 249 HIS E 563 GLN O 37 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22260 Z= 0.362 Angle : 0.675 9.901 30201 Z= 0.345 Chirality : 0.048 0.596 3770 Planarity : 0.005 0.050 3672 Dihedral : 7.626 63.472 5383 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 2.96 % Allowed : 12.25 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.43 (0.17), residues: 2511 helix: 0.54 (0.25), residues: 438 sheet: 0.11 (0.19), residues: 766 loop : -0.77 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 45 HIS 0.009 0.001 HIS D 374 PHE 0.028 0.002 PHE H 29 TYR 0.019 0.002 TYR N 32 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.472 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: L 18 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: L 92 ASN cc_start: 0.8453 (t0) cc_final: 0.7820 (t0) REVERT: A 479 TRP cc_start: 0.8231 (m-10) cc_final: 0.7612 (m-90) REVERT: H 82 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7948 (mm) REVERT: H 100 ASP cc_start: 0.8558 (t0) cc_final: 0.8031 (t0) REVERT: I 36 TYR cc_start: 0.7760 (m-80) cc_final: 0.7544 (m-80) REVERT: I 39 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6545 (mtmm) REVERT: I 42 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7895 (mp10) REVERT: D 80 ASN cc_start: 0.8961 (t0) cc_final: 0.8720 (t0) REVERT: D 479 TRP cc_start: 0.8275 (m-10) cc_final: 0.7415 (m-90) REVERT: G 12 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7935 (mmmm) REVERT: O 33 LEU cc_start: 0.7629 (tp) cc_final: 0.7382 (tp) REVERT: O 36 TYR cc_start: 0.6910 (m-80) cc_final: 0.6408 (m-80) REVERT: O 70 GLU cc_start: 0.8521 (pp20) cc_final: 0.8198 (pm20) REVERT: O 95 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7254 (mmp80) REVERT: K 621 GLU cc_start: 0.8154 (tp30) cc_final: 0.7805 (tp30) REVERT: K 634 GLU cc_start: 0.8651 (tp30) cc_final: 0.8219 (tm-30) REVERT: J 100 MET cc_start: 0.8685 (mtp) cc_final: 0.8442 (mtm) REVERT: J 280 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.6970 (t0) REVERT: J 333 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8462 (tt) REVERT: J 486 TYR cc_start: 0.9118 (m-80) cc_final: 0.8700 (m-10) REVERT: M 24 ILE cc_start: 0.8775 (mt) cc_final: 0.8537 (pt) REVERT: M 66 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (t0) REVERT: M 85 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7730 (tm-30) REVERT: N 99 GLU cc_start: 0.8647 (tt0) cc_final: 0.8183 (tp30) REVERT: F 74 LEU cc_start: 0.8744 (mt) cc_final: 0.8454 (tp) REVERT: F 87 GLU cc_start: 0.7589 (mp0) cc_final: 0.7314 (mp0) outliers start: 66 outliers final: 49 residues processed: 303 average time/residue: 0.3314 time to fit residues: 156.3198 Evaluate side-chains 295 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 241 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 239 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22260 Z= 0.158 Angle : 0.577 10.372 30201 Z= 0.293 Chirality : 0.045 0.383 3770 Planarity : 0.004 0.045 3672 Dihedral : 7.049 60.021 5383 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.97 % Allowed : 13.55 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.24 (0.17), residues: 2511 helix: 0.86 (0.27), residues: 425 sheet: 0.28 (0.20), residues: 741 loop : -0.71 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 45 HIS 0.004 0.001 HIS D 249 PHE 0.026 0.001 PHE H 29 TYR 0.020 0.001 TYR O 49 ARG 0.006 0.000 ARG L 95B *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.185 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: L 18 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7571 (mmm-85) REVERT: L 92 ASN cc_start: 0.8331 (t0) cc_final: 0.7682 (t0) REVERT: A 400 ARG cc_start: 0.6726 (ttt180) cc_final: 0.6513 (ttt180) REVERT: A 479 TRP cc_start: 0.8072 (m-10) cc_final: 0.7660 (m-90) REVERT: H 27 ASP cc_start: 0.8077 (t0) cc_final: 0.7035 (p0) REVERT: H 48 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: H 100 ASP cc_start: 0.8402 (t0) cc_final: 0.8108 (t0) REVERT: H 100 LEU cc_start: 0.8501 (mt) cc_final: 0.7899 (mp) REVERT: I 36 TYR cc_start: 0.7748 (m-80) cc_final: 0.7435 (m-80) REVERT: I 42 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7900 (mp10) REVERT: D 80 ASN cc_start: 0.8911 (t0) cc_final: 0.8685 (t0) REVERT: D 479 TRP cc_start: 0.8206 (m-10) cc_final: 0.7556 (m-90) REVERT: G 12 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7827 (mmmm) REVERT: G 81 GLU cc_start: 0.7209 (tp30) cc_final: 0.6911 (tm-30) REVERT: O 36 TYR cc_start: 0.7029 (m-80) cc_final: 0.6584 (m-80) REVERT: O 40 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: O 42 GLN cc_start: 0.8779 (mm110) cc_final: 0.8241 (mp10) REVERT: O 70 GLU cc_start: 0.8460 (pp20) cc_final: 0.8131 (pm20) REVERT: K 634 GLU cc_start: 0.8388 (tp30) cc_final: 0.8107 (tm-30) REVERT: J 100 MET cc_start: 0.8653 (mtp) cc_final: 0.8258 (mtm) REVERT: J 280 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.6862 (t0) REVERT: J 333 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8476 (tt) REVERT: J 475 MET cc_start: 0.7998 (tpp) cc_final: 0.7486 (mmt) REVERT: J 486 TYR cc_start: 0.9066 (m-80) cc_final: 0.8725 (m-10) REVERT: M 24 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (pt) REVERT: M 66 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8624 (t0) REVERT: M 85 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7649 (tm-30) REVERT: M 88 ASP cc_start: 0.7919 (t0) cc_final: 0.7717 (t0) REVERT: N 59 TYR cc_start: 0.7490 (m-80) cc_final: 0.7080 (m-80) REVERT: N 86 ASP cc_start: 0.7620 (m-30) cc_final: 0.7287 (m-30) REVERT: N 99 GLU cc_start: 0.8681 (tt0) cc_final: 0.8137 (tp30) REVERT: F 73 ASN cc_start: 0.8562 (t0) cc_final: 0.8315 (t0) REVERT: F 87 GLU cc_start: 0.7603 (mp0) cc_final: 0.7347 (mp0) outliers start: 44 outliers final: 29 residues processed: 309 average time/residue: 0.3229 time to fit residues: 155.8734 Evaluate side-chains 291 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 257 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 152 optimal weight: 0.2980 chunk 163 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22260 Z= 0.162 Angle : 0.573 10.574 30201 Z= 0.290 Chirality : 0.045 0.640 3770 Planarity : 0.004 0.044 3672 Dihedral : 6.569 59.050 5383 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.66 % Allowed : 13.82 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.22 (0.17), residues: 2511 helix: 0.87 (0.26), residues: 430 sheet: 0.40 (0.20), residues: 724 loop : -0.76 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 45 HIS 0.004 0.001 HIS D 249 PHE 0.026 0.001 PHE H 29 TYR 0.021 0.001 TYR O 49 ARG 0.005 0.000 ARG L 95B *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 275 time to evaluate : 2.721 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: L 92 ASN cc_start: 0.8338 (t0) cc_final: 0.7683 (t0) REVERT: B 519 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 400 ARG cc_start: 0.6675 (ttt180) cc_final: 0.6431 (ttt180) REVERT: A 479 TRP cc_start: 0.8084 (m-10) cc_final: 0.7579 (m-90) REVERT: H 27 ASP cc_start: 0.8160 (t0) cc_final: 0.7085 (p0) REVERT: H 29 PHE cc_start: 0.9001 (t80) cc_final: 0.8517 (t80) REVERT: H 48 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7418 (mpp) REVERT: H 100 LEU cc_start: 0.8523 (mt) cc_final: 0.7919 (mp) REVERT: I 36 TYR cc_start: 0.7725 (m-80) cc_final: 0.7389 (m-10) REVERT: I 42 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7861 (mp10) REVERT: D 80 ASN cc_start: 0.8916 (t0) cc_final: 0.8695 (t0) REVERT: D 479 TRP cc_start: 0.8291 (m-10) cc_final: 0.7557 (m-90) REVERT: E 662 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6477 (mp0) REVERT: G 12 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7940 (mmmm) REVERT: O 36 TYR cc_start: 0.6909 (m-80) cc_final: 0.5518 (m-80) REVERT: O 40 PRO cc_start: 0.8754 (Cg_exo) cc_final: 0.8412 (Cg_endo) REVERT: O 42 GLN cc_start: 0.8773 (mm110) cc_final: 0.8252 (mp10) REVERT: O 70 GLU cc_start: 0.8390 (pp20) cc_final: 0.7908 (pm20) REVERT: O 95 ARG cc_start: 0.8512 (mmp-170) cc_final: 0.8106 (mmp80) REVERT: K 632 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7113 (tm-30) REVERT: K 634 GLU cc_start: 0.8443 (tp30) cc_final: 0.8032 (tm-30) REVERT: K 636 ASP cc_start: 0.8015 (t0) cc_final: 0.7694 (t0) REVERT: J 100 MET cc_start: 0.8679 (mtp) cc_final: 0.8260 (mtm) REVERT: J 280 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.6849 (t0) REVERT: J 333 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (tt) REVERT: J 475 MET cc_start: 0.7945 (tpp) cc_final: 0.7475 (mmt) REVERT: J 486 TYR cc_start: 0.9042 (m-80) cc_final: 0.8720 (m-10) REVERT: M 24 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8450 (pt) REVERT: M 66 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8599 (t0) REVERT: M 85 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7408 (tm-30) REVERT: N 59 TYR cc_start: 0.7634 (m-80) cc_final: 0.7177 (m-80) REVERT: N 86 ASP cc_start: 0.7556 (m-30) cc_final: 0.7292 (m-30) REVERT: N 99 GLU cc_start: 0.8760 (tt0) cc_final: 0.8079 (tp30) REVERT: F 87 GLU cc_start: 0.7829 (mp0) cc_final: 0.7515 (mp0) outliers start: 37 outliers final: 25 residues processed: 298 average time/residue: 0.3388 time to fit residues: 157.6566 Evaluate side-chains 290 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 0.0070 chunk 229 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 175 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22260 Z= 0.162 Angle : 0.577 10.687 30201 Z= 0.293 Chirality : 0.044 0.470 3770 Planarity : 0.004 0.046 3672 Dihedral : 6.331 59.917 5383 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.71 % Allowed : 13.91 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.17), residues: 2511 helix: 0.93 (0.26), residues: 430 sheet: 0.45 (0.20), residues: 727 loop : -0.77 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 45 HIS 0.004 0.001 HIS D 249 PHE 0.026 0.001 PHE H 29 TYR 0.021 0.001 TYR O 49 ARG 0.011 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 272 time to evaluate : 2.395 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: L 92 ASN cc_start: 0.8274 (t0) cc_final: 0.7636 (t0) REVERT: B 519 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 612 ASP cc_start: 0.8240 (t0) cc_final: 0.8023 (t0) REVERT: B 629 MET cc_start: 0.8171 (mtt) cc_final: 0.7859 (mtp) REVERT: A 400 ARG cc_start: 0.6631 (ttt180) cc_final: 0.6368 (ttt180) REVERT: A 479 TRP cc_start: 0.8056 (m-10) cc_final: 0.7603 (m-90) REVERT: H 27 ASP cc_start: 0.8288 (t0) cc_final: 0.7394 (p0) REVERT: H 48 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7420 (mpp) REVERT: H 100 ASP cc_start: 0.8460 (t0) cc_final: 0.8161 (t0) REVERT: H 100 LEU cc_start: 0.8552 (mt) cc_final: 0.7943 (mp) REVERT: I 36 TYR cc_start: 0.7763 (m-80) cc_final: 0.7437 (m-10) REVERT: D 80 ASN cc_start: 0.8849 (t0) cc_final: 0.8633 (t0) REVERT: D 475 MET cc_start: 0.8381 (mmt) cc_final: 0.7295 (mmp) REVERT: D 479 TRP cc_start: 0.8292 (m-10) cc_final: 0.7877 (m-90) REVERT: G 12 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7947 (mmmm) REVERT: G 81 GLU cc_start: 0.7061 (tp30) cc_final: 0.6826 (tm-30) REVERT: O 36 TYR cc_start: 0.5891 (m-80) cc_final: 0.5278 (m-80) REVERT: O 40 PRO cc_start: 0.8803 (Cg_exo) cc_final: 0.8469 (Cg_endo) REVERT: O 42 GLN cc_start: 0.8756 (mm110) cc_final: 0.8251 (mp10) REVERT: O 70 GLU cc_start: 0.8413 (pp20) cc_final: 0.7923 (pm20) REVERT: K 565 MET cc_start: 0.6383 (mmp) cc_final: 0.4456 (mtm) REVERT: K 632 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7080 (tm-30) REVERT: K 634 GLU cc_start: 0.8488 (tp30) cc_final: 0.8079 (tm-30) REVERT: K 636 ASP cc_start: 0.7995 (t0) cc_final: 0.7663 (t0) REVERT: J 100 MET cc_start: 0.8673 (mtp) cc_final: 0.8247 (mtm) REVERT: J 280 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.6862 (t0) REVERT: J 333 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8465 (tt) REVERT: J 475 MET cc_start: 0.7905 (tpp) cc_final: 0.7438 (mmt) REVERT: J 486 TYR cc_start: 0.9019 (m-80) cc_final: 0.8649 (m-10) REVERT: M 24 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8447 (pt) REVERT: M 66 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8601 (t0) REVERT: M 85 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7333 (tm-30) REVERT: N 59 TYR cc_start: 0.7642 (m-80) cc_final: 0.7240 (m-80) REVERT: N 86 ASP cc_start: 0.7594 (m-30) cc_final: 0.7329 (m-30) REVERT: N 99 GLU cc_start: 0.8768 (tt0) cc_final: 0.8110 (tp30) REVERT: F 87 GLU cc_start: 0.7817 (mp0) cc_final: 0.7557 (mp0) outliers start: 38 outliers final: 30 residues processed: 297 average time/residue: 0.3343 time to fit residues: 156.4536 Evaluate side-chains 293 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22260 Z= 0.229 Angle : 0.607 11.020 30201 Z= 0.308 Chirality : 0.045 0.444 3770 Planarity : 0.004 0.046 3672 Dihedral : 6.351 59.818 5383 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.62 % Allowed : 14.77 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.23 (0.17), residues: 2511 helix: 0.92 (0.26), residues: 429 sheet: 0.40 (0.20), residues: 725 loop : -0.80 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 45 HIS 0.005 0.001 HIS D 374 PHE 0.032 0.002 PHE O 83 TYR 0.021 0.001 TYR O 49 ARG 0.007 0.000 ARG O 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.440 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: L 92 ASN cc_start: 0.8314 (t0) cc_final: 0.7698 (t0) REVERT: B 519 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 629 MET cc_start: 0.8328 (mtt) cc_final: 0.8127 (mtp) REVERT: A 40 TYR cc_start: 0.9145 (t80) cc_final: 0.8931 (t80) REVERT: A 479 TRP cc_start: 0.8104 (m-10) cc_final: 0.7568 (m-90) REVERT: H 27 ASP cc_start: 0.8350 (t0) cc_final: 0.7487 (p0) REVERT: H 48 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: H 100 ASP cc_start: 0.8430 (t0) cc_final: 0.8140 (t0) REVERT: H 100 LEU cc_start: 0.8596 (mt) cc_final: 0.8139 (mp) REVERT: I 36 TYR cc_start: 0.7766 (m-80) cc_final: 0.7471 (m-80) REVERT: D 80 ASN cc_start: 0.8851 (t0) cc_final: 0.8609 (t0) REVERT: D 479 TRP cc_start: 0.8245 (m-10) cc_final: 0.7504 (m-90) REVERT: G 12 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8004 (mmmm) REVERT: G 19 LYS cc_start: 0.7100 (mmmm) cc_final: 0.6866 (mmmm) REVERT: O 36 TYR cc_start: 0.6231 (m-80) cc_final: 0.5741 (m-80) REVERT: O 40 PRO cc_start: 0.8758 (Cg_exo) cc_final: 0.8361 (Cg_endo) REVERT: O 42 GLN cc_start: 0.8806 (mm110) cc_final: 0.8258 (mp10) REVERT: O 46 LEU cc_start: 0.8374 (tp) cc_final: 0.8155 (tp) REVERT: O 70 GLU cc_start: 0.8418 (pp20) cc_final: 0.7922 (pm20) REVERT: K 565 MET cc_start: 0.6470 (mmp) cc_final: 0.4503 (mtm) REVERT: K 634 GLU cc_start: 0.8508 (tp30) cc_final: 0.8094 (tm-30) REVERT: J 100 MET cc_start: 0.8748 (mtp) cc_final: 0.8395 (mtm) REVERT: J 280 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.6800 (t0) REVERT: J 333 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8518 (tt) REVERT: J 475 MET cc_start: 0.8014 (tpp) cc_final: 0.7509 (mmt) REVERT: J 486 TYR cc_start: 0.9040 (m-80) cc_final: 0.8728 (m-10) REVERT: M 24 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8508 (pt) REVERT: M 66 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (t0) REVERT: M 85 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7604 (tm-30) REVERT: N 86 ASP cc_start: 0.7500 (m-30) cc_final: 0.7175 (m-30) outliers start: 36 outliers final: 28 residues processed: 284 average time/residue: 0.3221 time to fit residues: 143.4036 Evaluate side-chains 284 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 203 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078615 restraints weight = 64523.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081373 restraints weight = 32732.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083088 restraints weight = 22152.559| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22260 Z= 0.167 Angle : 0.597 11.125 30201 Z= 0.303 Chirality : 0.045 0.410 3770 Planarity : 0.004 0.043 3672 Dihedral : 6.157 59.067 5383 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.62 % Allowed : 14.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.22 (0.17), residues: 2511 helix: 0.94 (0.26), residues: 430 sheet: 0.43 (0.20), residues: 725 loop : -0.81 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 45 HIS 0.004 0.001 HIS D 249 PHE 0.035 0.001 PHE O 83 TYR 0.021 0.001 TYR O 49 ARG 0.015 0.000 ARG I 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.65 seconds wall clock time: 78 minutes 53.22 seconds (4733.22 seconds total)