Starting phenix.real_space_refine on Wed Jul 24 12:42:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/07_2024/8u29_41842.cif" } resolution = 2.8 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= 0.096 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 123 5.16 5 C 16434 2.51 5 N 4206 2.21 5 O 4963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 831": "OD1" <-> "OD2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 563": "OD1" <-> "OD2" Residue "B ASP 567": "OD1" <-> "OD2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 831": "OD1" <-> "OD2" Residue "B TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C ASP 567": "OD1" <-> "OD2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 831": "OD1" <-> "OD2" Residue "C TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25726 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8073 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 8075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8075 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8078 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 155 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.30, per 1000 atoms: 0.59 Number of scatterers: 25726 At special positions: 0 Unit cell: (156, 142, 170, 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 123 16.00 O 4963 8.00 N 4206 7.00 C 16434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.10 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.05 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.08 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.02 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.04 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.04 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.12 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.02 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.22 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.10 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.05 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 514 " distance=2.08 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.02 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.04 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.12 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.02 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.22 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 351 " distance=2.10 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.05 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 514 " distance=2.08 Simple disulfide: pdb=" SG CYS C 469 " - pdb=" SG CYS C 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.04 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.12 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.02 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.22 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 H 4 " - " MAN H 5 " " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " BMA R 3 " - " MAN R 6 " " BMA b 3 " - " MAN b 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A 24 " " NAG A1302 " - " ASN A 159 " " NAG A1303 " - " ASN A 272 " " NAG A1304 " - " ASN A 333 " " NAG A1305 " - " ASN A 360 " " NAG A1306 " - " ASN A 592 " " NAG A1307 " - " ASN A 605 " " NAG A1308 " - " ASN A 648 " " NAG A1309 " - " ASN A1117 " " NAG A1310 " - " ASN A 148 " " NAG A1311 " - " ASN A1057 " " NAG B1301 " - " ASN B 24 " " NAG B1302 " - " ASN B 159 " " NAG B1303 " - " ASN B 272 " " NAG B1304 " - " ASN B 333 " " NAG B1305 " - " ASN B 360 " " NAG B1306 " - " ASN B 592 " " NAG B1307 " - " ASN B 605 " " NAG B1308 " - " ASN B 648 " " NAG B1309 " - " ASN B1117 " " NAG B1310 " - " ASN B 148 " " NAG B1311 " - " ASN B1057 " " NAG C1301 " - " ASN C 24 " " NAG C1302 " - " ASN C 159 " " NAG C1303 " - " ASN C 272 " " NAG C1304 " - " ASN C 333 " " NAG C1305 " - " ASN C 360 " " NAG C1306 " - " ASN C 592 " " NAG C1307 " - " ASN C 605 " " NAG C1308 " - " ASN C 648 " " NAG C1309 " - " ASN C1117 " " NAG C1310 " - " ASN C 148 " " NAG C1311 " - " ASN C1057 " " NAG D 1 " - " ASN A 65 " " NAG E 1 " - " ASN A 115 " " NAG F 1 " - " ASN A 125 " " NAG G 1 " - " ASN A 162 " " NAG H 1 " - " ASN A 230 " " NAG I 1 " - " ASN A 321 " " NAG J 1 " - " ASN A 692 " " NAG K 1 " - " ASN A 700 " " NAG L 1 " - " ASN A 784 " " NAG M 1 " - " ASN A1081 " " NAG N 1 " - " ASN B 65 " " NAG O 1 " - " ASN B 115 " " NAG P 1 " - " ASN B 125 " " NAG Q 1 " - " ASN B 162 " " NAG R 1 " - " ASN B 230 " " NAG S 1 " - " ASN B 321 " " NAG T 1 " - " ASN B 692 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B1081 " " NAG X 1 " - " ASN C 65 " " NAG Y 1 " - " ASN C 115 " " NAG Z 1 " - " ASN C 125 " " NAG a 1 " - " ASN C 162 " " NAG b 1 " - " ASN C 230 " " NAG c 1 " - " ASN C 321 " " NAG d 1 " - " ASN C 692 " " NAG e 1 " - " ASN C 700 " " NAG f 1 " - " ASN C 784 " " NAG g 1 " - " ASN C1081 " Time building additional restraints: 10.75 Conformation dependent library (CDL) restraints added in 4.5 seconds 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 24.9% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.871A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.595A pdb=" N ILE A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 902 through 923 removed outlier: 3.681A pdb=" N ILE A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 918 " --> pdb=" O ILE A 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.871A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 622 through 627 Processing helix chain 'B' and resid 720 through 726 removed outlier: 3.594A pdb=" N ILE B 725 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 764 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 832 through 839 Processing helix chain 'B' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 902 through 923 removed outlier: 3.680A pdb=" N ILE B 917 " --> pdb=" O ALA B 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 919 " --> pdb=" O SER B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 959 through 967 Processing helix chain 'B' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.872A pdb=" N TRP C 343 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 720 through 726 removed outlier: 3.594A pdb=" N ILE C 725 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 764 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 832 through 839 Processing helix chain 'C' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 896 through 902 Processing helix chain 'C' and resid 902 through 923 removed outlier: 3.681A pdb=" N ILE C 917 " --> pdb=" O ALA C 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 918 " --> pdb=" O ILE C 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 919 " --> pdb=" O SER C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 959 through 967 Processing helix chain 'C' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN A 65 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A 259 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 184 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 183 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU A 197 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 199 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR A 203 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ARG A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE A 216 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG A 38 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU A 219 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE A 40 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP A 277 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE A 234 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE A 138 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL A 236 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN A 140 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N MET A 238 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 240 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 144 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 137 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 156 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N ASP A 141 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER A 154 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR A 152 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR A 145 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER A 150 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.452A pdb=" N THR A 239 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 104 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG A 105 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 165 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP A 563 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 564 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 348 removed outlier: 4.014A pdb=" N VAL A 386 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 385 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 352 removed outlier: 6.462A pdb=" N CYS A 351 " --> pdb=" O CYS A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR A 645 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR A 679 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU A 647 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A1059 " --> pdb=" O MET A1080 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 771 through 772 removed outlier: 5.749A pdb=" N ILE A 771 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN B 65 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 259 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B 184 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 183 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 197 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS B 224 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 199 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 203 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL B 218 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N ARG B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE B 216 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 38 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU B 219 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE B 40 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP B 277 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE B 234 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE B 138 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL B 236 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN B 140 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N MET B 238 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 240 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 144 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR B 137 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 156 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ASP B 141 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER B 154 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET B 143 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR B 152 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR B 145 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 150 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.453A pdb=" N THR B 239 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 104 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG B 105 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP B 563 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 564 " --> pdb=" O GLY B 555 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 344 through 348 removed outlier: 4.013A pdb=" N VAL B 386 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 385 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 351 through 352 removed outlier: 6.462A pdb=" N CYS B 351 " --> pdb=" O CYS B 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AD3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AD4, first strand: chain 'B' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR B 645 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 679 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU B 647 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AD6, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B1059 " --> pdb=" O MET B1080 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 867 through 868 Processing sheet with id=AE1, first strand: chain 'B' and resid 1103 through 1105 Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN C 65 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS C 259 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS C 184 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 183 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU C 197 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS C 224 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 199 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR C 203 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL C 218 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ARG C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE C 216 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG C 38 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU C 219 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE C 40 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AE4, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.068A pdb=" N ASP C 277 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE C 234 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE C 138 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL C 236 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN C 140 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N MET C 238 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 240 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 144 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR C 137 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL C 156 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ASP C 141 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER C 154 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET C 143 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR C 152 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR C 145 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER C 150 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.453A pdb=" N THR C 239 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 104 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG C 105 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 165 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP C 563 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 564 " --> pdb=" O GLY C 555 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 344 through 348 removed outlier: 4.014A pdb=" N VAL C 386 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 385 " --> pdb=" O GLU C 505 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.463A pdb=" N CYS C 351 " --> pdb=" O CYS C 514 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 441 through 443 Processing sheet with id=AF3, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AF4, first strand: chain 'C' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR C 645 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR C 679 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU C 647 " --> pdb=" O THR C 679 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C1059 " --> pdb=" O MET C1080 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 867 through 868 Processing sheet with id=AF9, first strand: chain 'C' and resid 1103 through 1105 1058 hydrogen bonds defined for protein. 2904 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: 11.92 Time building geometry restraints manager: 11.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.50: 15841 1.50 - 1.84: 10464 1.84 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.87: 3 Bond restraints: 26308 Sorted by residual: bond pdb=" C PRO A 285 " pdb=" N LEU A 286 " ideal model delta sigma weight residual 1.335 2.866 -1.531 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO B 285 " pdb=" N LEU B 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO C 285 " pdb=" N LEU C 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C ASN A 148 " pdb=" O ASN A 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.29e+01 bond pdb=" C ASN C 148 " pdb=" O ASN C 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.27e+01 ... (remaining 26303 not shown) Histogram of bond angle deviations from ideal: 87.79 - 97.33: 3 97.33 - 106.87: 785 106.87 - 116.41: 17699 116.41 - 125.95: 17181 125.95 - 135.49: 243 Bond angle restraints: 35911 Sorted by residual: angle pdb=" C PRO B 285 " pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 120.72 87.79 32.93 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO A 285 " pdb=" N LEU A 286 " pdb=" CA LEU A 286 " ideal model delta sigma weight residual 120.72 87.80 32.92 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO C 285 " pdb=" N LEU C 286 " pdb=" CA LEU C 286 " ideal model delta sigma weight residual 120.72 87.82 32.90 1.67e+00 3.59e-01 3.88e+02 angle pdb=" N HIS C 614 " pdb=" CA HIS C 614 " pdb=" CB HIS C 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 angle pdb=" N HIS B 614 " pdb=" CA HIS B 614 " pdb=" CB HIS B 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 ... (remaining 35906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 16286 21.62 - 43.25: 488 43.25 - 64.87: 105 64.87 - 86.49: 54 86.49 - 108.12: 30 Dihedral angle restraints: 16963 sinusoidal: 7501 harmonic: 9462 Sorted by residual: dihedral pdb=" C LEU A 613 " pdb=" N LEU A 613 " pdb=" CA LEU A 613 " pdb=" CB LEU A 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU C 613 " pdb=" N LEU C 613 " pdb=" CA LEU C 613 " pdb=" CB LEU C 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU B 613 " pdb=" N LEU B 613 " pdb=" CA LEU B 613 " pdb=" CB LEU B 613 " ideal model delta harmonic sigma weight residual -122.60 -161.92 39.32 0 2.50e+00 1.60e-01 2.47e+02 ... (remaining 16960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4391 0.340 - 0.680: 18 0.680 - 1.020: 0 1.020 - 1.360: 0 1.360 - 1.700: 9 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 148 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 ... (remaining 4415 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO B 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO B 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU B 286 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO A 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO A 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU A 286 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO C 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO C 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU C 286 " -0.032 2.00e-02 2.50e+03 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12786 2.97 - 3.46: 22373 3.46 - 3.94: 42075 3.94 - 4.42: 47191 4.42 - 4.90: 77853 Nonbonded interactions: 202278 Sorted by model distance: nonbonded pdb=" O GLY B 891 " pdb=" NZ LYS B1021 " model vdw 2.492 2.520 nonbonded pdb=" O GLY C 891 " pdb=" NZ LYS C1021 " model vdw 2.492 2.520 nonbonded pdb=" O GLY A 891 " pdb=" NZ LYS A1021 " model vdw 2.492 2.520 nonbonded pdb=" OD1 ASP C 44 " pdb=" N ASP C 45 " model vdw 2.528 2.520 nonbonded pdb=" OD1 ASP A 44 " pdb=" N ASP A 45 " model vdw 2.528 2.520 ... (remaining 202273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 1125 or resid 1301 thr \ ough 1311)) selection = (chain 'C' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 559 or (resid 560 and \ (name N or name CA or name C or name O or name CB )) or resid 561 through 1125 o \ r resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'b' } 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 individual isotropic 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: 13.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 72.240 Find NCS groups from input model: 4.570 Set up NCS constraints: 0.190 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.020 1.531 26308 Z= 1.632 Angle : 1.411 32.925 35911 Z= 0.921 Chirality : 0.117 1.700 4418 Planarity : 0.006 0.103 4525 Dihedral : 12.485 108.116 10765 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.44 % Rotamer: Outliers : 1.13 % Allowed : 1.38 % Favored : 97.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3222 helix: -0.11 (0.18), residues: 729 sheet: 1.20 (0.18), residues: 702 loop : -0.36 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP B1085 HIS 0.005 0.001 HIS B 128 PHE 0.021 0.003 PHE A 234 TYR 0.035 0.004 TYR B 203 ARG 0.005 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 385 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1084 HIS cc_start: 0.7971 (m90) cc_final: 0.7724 (m90) REVERT: A 1102 ASN cc_start: 0.6093 (m-40) cc_final: 0.5721 (m-40) REVERT: B 166 ASN cc_start: 0.7638 (t0) cc_final: 0.7336 (t0) REVERT: B 952 ASN cc_start: 0.7475 (m-40) cc_final: 0.7226 (m-40) REVERT: B 976 ILE cc_start: 0.8452 (mt) cc_final: 0.8236 (mp) outliers start: 27 outliers final: 6 residues processed: 405 average time/residue: 1.3891 time to fit residues: 647.9260 Evaluate side-chains 198 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 905 GLN Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.8980 chunk 245 optimal weight: 0.3980 chunk 136 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 253 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 233 GLN A 304 GLN A 474 GLN A 602 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN B 135 ASN B 436 GLN B 602 GLN B 787 GLN B 918 GLN C 602 GLN C 787 GLN C 878 GLN C 918 GLN C 988 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26308 Z= 0.197 Angle : 0.610 8.085 35911 Z= 0.322 Chirality : 0.050 0.971 4418 Planarity : 0.004 0.036 4525 Dihedral : 9.778 93.114 5800 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.04 % Allowed : 8.39 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.14), residues: 3228 helix: 1.29 (0.20), residues: 753 sheet: 1.46 (0.20), residues: 630 loop : -0.38 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 622 HIS 0.011 0.001 HIS A 184 PHE 0.017 0.001 PHE C 123 TYR 0.020 0.001 TYR B1050 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7671 (ttp-110) REVERT: A 1084 HIS cc_start: 0.7956 (m90) cc_final: 0.7699 (m90) REVERT: A 1102 ASN cc_start: 0.6289 (m-40) cc_final: 0.5918 (m-40) REVERT: B 1033 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8094 (ptp) REVERT: C 723 MET cc_start: 0.8853 (ttt) cc_final: 0.8632 (ttm) REVERT: C 916 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7175 (mppt) outliers start: 49 outliers final: 14 residues processed: 264 average time/residue: 1.2259 time to fit residues: 382.4558 Evaluate side-chains 206 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 916 LYS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 318 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 236 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 233 GLN A 304 GLN A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 324 ASN B 436 GLN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 201 HIS C 324 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26308 Z= 0.206 Angle : 0.581 11.116 35911 Z= 0.301 Chirality : 0.052 1.229 4418 Planarity : 0.004 0.035 4525 Dihedral : 8.592 89.147 5793 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.79 % Allowed : 9.18 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.14), residues: 3228 helix: 1.39 (0.20), residues: 756 sheet: 1.12 (0.19), residues: 684 loop : -0.58 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.005 0.001 HIS C 151 PHE 0.018 0.002 PHE B1104 TYR 0.020 0.001 TYR C 484 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7718 (ttp-110) REVERT: A 952 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7189 (m110) REVERT: A 1084 HIS cc_start: 0.7920 (m90) cc_final: 0.7697 (m90) REVERT: A 1102 ASN cc_start: 0.6533 (m-40) cc_final: 0.6253 (m-40) REVERT: B 123 PHE cc_start: 0.8375 (p90) cc_final: 0.8121 (p90) REVERT: B 937 GLN cc_start: 0.8228 (mt0) cc_final: 0.7944 (pt0) REVERT: C 723 MET cc_start: 0.8936 (ttt) cc_final: 0.8658 (ttm) REVERT: C 1102 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6250 (m110) outliers start: 43 outliers final: 14 residues processed: 233 average time/residue: 1.1971 time to fit residues: 330.1312 Evaluate side-chains 206 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.0000 chunk 221 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 304 GLN A 324 ASN A 602 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 324 ASN B 602 GLN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26308 Z= 0.220 Angle : 0.572 12.594 35911 Z= 0.294 Chirality : 0.049 0.644 4418 Planarity : 0.004 0.035 4525 Dihedral : 7.956 85.927 5793 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.67 % Allowed : 9.97 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.14), residues: 3228 helix: 1.57 (0.20), residues: 732 sheet: 1.12 (0.19), residues: 708 loop : -0.63 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 427 HIS 0.006 0.002 HIS C 151 PHE 0.015 0.002 PHE B 665 TYR 0.020 0.001 TYR C 484 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7823 (ttp-110) REVERT: A 952 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: A 1084 HIS cc_start: 0.7932 (m90) cc_final: 0.7697 (m90) REVERT: B 123 PHE cc_start: 0.8388 (p90) cc_final: 0.8157 (p90) REVERT: B 937 GLN cc_start: 0.8229 (mt0) cc_final: 0.7951 (pt0) REVERT: C 233 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: C 723 MET cc_start: 0.8942 (ttt) cc_final: 0.8675 (ttm) REVERT: C 1102 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6700 (m110) outliers start: 40 outliers final: 17 residues processed: 222 average time/residue: 1.1663 time to fit residues: 307.7801 Evaluate side-chains 212 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 216 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 602 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26308 Z= 0.294 Angle : 0.605 6.694 35911 Z= 0.313 Chirality : 0.050 0.476 4418 Planarity : 0.005 0.038 4525 Dihedral : 7.788 84.969 5793 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.25 % Allowed : 9.55 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.14), residues: 3228 helix: 1.36 (0.19), residues: 735 sheet: 0.99 (0.19), residues: 738 loop : -0.86 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 427 HIS 0.008 0.002 HIS C 201 PHE 0.015 0.002 PHE A 665 TYR 0.026 0.002 TYR C 484 ARG 0.006 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 762 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7850 (ttp-110) REVERT: A 952 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (m110) REVERT: A 1002 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7708 (tpm170) REVERT: A 1084 HIS cc_start: 0.7953 (m90) cc_final: 0.7722 (m90) REVERT: B 595 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7621 (mmtt) REVERT: B 937 GLN cc_start: 0.8244 (mt0) cc_final: 0.7959 (pt0) REVERT: C 347 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7558 (ttt-90) outliers start: 54 outliers final: 27 residues processed: 240 average time/residue: 1.2029 time to fit residues: 341.9985 Evaluate side-chains 223 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 981 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 313 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 164 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 324 ASN B 602 GLN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN C 324 ASN C 602 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26308 Z= 0.168 Angle : 0.532 8.155 35911 Z= 0.276 Chirality : 0.047 0.433 4418 Planarity : 0.004 0.041 4525 Dihedral : 7.471 81.570 5793 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.04 % Allowed : 10.51 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3228 helix: 1.73 (0.20), residues: 732 sheet: 0.95 (0.19), residues: 744 loop : -0.84 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 622 HIS 0.003 0.001 HIS A 201 PHE 0.016 0.001 PHE B1104 TYR 0.019 0.001 TYR B1050 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 208 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7832 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7663 (tpm170) REVERT: A 1084 HIS cc_start: 0.7860 (m90) cc_final: 0.7642 (m90) REVERT: B 165 TYR cc_start: 0.7234 (t80) cc_final: 0.6928 (t80) REVERT: B 595 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7556 (mmtt) REVERT: B 937 GLN cc_start: 0.8255 (mt0) cc_final: 0.7998 (pt0) outliers start: 49 outliers final: 23 residues processed: 232 average time/residue: 1.1472 time to fit residues: 316.7871 Evaluate side-chains 220 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 263 optimal weight: 0.0670 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN A 896 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 ASN B 324 ASN B 602 GLN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 602 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26308 Z= 0.140 Angle : 0.508 7.517 35911 Z= 0.262 Chirality : 0.046 0.393 4418 Planarity : 0.004 0.038 4525 Dihedral : 7.212 78.381 5793 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 10.97 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3228 helix: 1.99 (0.20), residues: 732 sheet: 0.98 (0.19), residues: 741 loop : -0.82 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.003 0.001 HIS A1066 PHE 0.019 0.001 PHE B 665 TYR 0.019 0.001 TYR B1050 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7612 (tpm170) REVERT: A 1084 HIS cc_start: 0.7849 (m90) cc_final: 0.7634 (m90) REVERT: B 165 TYR cc_start: 0.7240 (t80) cc_final: 0.6921 (t80) REVERT: B 937 GLN cc_start: 0.8205 (mt0) cc_final: 0.7976 (pt0) outliers start: 44 outliers final: 23 residues processed: 234 average time/residue: 1.2211 time to fit residues: 341.4341 Evaluate side-chains 216 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 154 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 245 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 602 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26308 Z= 0.186 Angle : 0.525 9.491 35911 Z= 0.272 Chirality : 0.047 0.460 4418 Planarity : 0.004 0.050 4525 Dihedral : 7.158 77.630 5793 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.79 % Allowed : 11.35 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3228 helix: 1.92 (0.20), residues: 735 sheet: 1.01 (0.19), residues: 738 loop : -0.86 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.004 0.001 HIS A 201 PHE 0.029 0.001 PHE B 665 TYR 0.018 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7694 (tpm170) REVERT: A 1084 HIS cc_start: 0.7836 (m90) cc_final: 0.7617 (m90) REVERT: B 165 TYR cc_start: 0.7230 (t80) cc_final: 0.6932 (t80) REVERT: B 937 GLN cc_start: 0.8219 (mt0) cc_final: 0.7991 (pt0) outliers start: 43 outliers final: 30 residues processed: 225 average time/residue: 1.1302 time to fit residues: 304.2029 Evaluate side-chains 225 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.1980 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 ASN B 324 ASN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 602 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26308 Z= 0.182 Angle : 0.528 12.377 35911 Z= 0.272 Chirality : 0.047 0.409 4418 Planarity : 0.004 0.043 4525 Dihedral : 7.199 76.582 5793 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.67 % Allowed : 11.35 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3228 helix: 1.92 (0.20), residues: 738 sheet: 1.00 (0.19), residues: 738 loop : -0.89 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.004 0.001 HIS A 201 PHE 0.020 0.001 PHE A1104 TYR 0.018 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7720 (tpm170) REVERT: A 1084 HIS cc_start: 0.7831 (m90) cc_final: 0.7605 (m90) REVERT: B 165 TYR cc_start: 0.7236 (t80) cc_final: 0.6955 (t80) REVERT: B 937 GLN cc_start: 0.8212 (mt0) cc_final: 0.7992 (pt0) outliers start: 40 outliers final: 30 residues processed: 227 average time/residue: 1.1051 time to fit residues: 300.9586 Evaluate side-chains 229 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 187 optimal weight: 0.3980 chunk 145 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 322 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 257 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 198 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 ASN B 324 ASN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 602 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26308 Z= 0.166 Angle : 0.526 10.603 35911 Z= 0.272 Chirality : 0.047 0.386 4418 Planarity : 0.004 0.052 4525 Dihedral : 7.247 92.174 5793 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.34 % Allowed : 11.89 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3228 helix: 1.96 (0.20), residues: 738 sheet: 0.98 (0.19), residues: 738 loop : -0.88 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 622 HIS 0.004 0.001 HIS A 201 PHE 0.022 0.001 PHE C1104 TYR 0.018 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7691 (tpm170) REVERT: A 1084 HIS cc_start: 0.7803 (m90) cc_final: 0.7576 (m90) REVERT: B 165 TYR cc_start: 0.7234 (t80) cc_final: 0.6951 (t80) REVERT: B 937 GLN cc_start: 0.8172 (mt0) cc_final: 0.7956 (pt0) REVERT: B 1033 MET cc_start: 0.8492 (ptm) cc_final: 0.8265 (ptp) outliers start: 32 outliers final: 27 residues processed: 216 average time/residue: 1.1283 time to fit residues: 291.1233 Evaluate side-chains 222 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 47 optimal weight: 0.0870 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 ASN B 324 ASN B 734 ASN ** B 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 ASN C 324 ASN C 602 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118790 restraints weight = 29325.955| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.28 r_work: 0.3158 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26308 Z= 0.239 Angle : 0.561 9.256 35911 Z= 0.289 Chirality : 0.048 0.394 4418 Planarity : 0.004 0.055 4525 Dihedral : 7.596 97.987 5793 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.79 % Allowed : 11.60 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3228 helix: 1.80 (0.20), residues: 738 sheet: 1.02 (0.19), residues: 717 loop : -0.98 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 427 HIS 0.006 0.001 HIS A 201 PHE 0.022 0.002 PHE C1104 TYR 0.020 0.001 TYR C 484 ARG 0.007 0.001 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7487.10 seconds wall clock time: 132 minutes 29.13 seconds (7949.13 seconds total)