Starting phenix.real_space_refine on Tue Feb 20 03:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l56_23165/02_2024/7l56_23165_updated.pdb" } resolution = 3.6 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= 0.024 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 132 5.16 5 C 16951 2.51 5 N 4432 2.21 5 O 5068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26583 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7128 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 933} Chain breaks: 10 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 682 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'TYR:plan': 1, 'ASN:plan1': 13, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 6870 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 888 Unresolved non-hydrogen angles: 1115 Unresolved non-hydrogen dihedrals: 676 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 39, 'TYR:plan': 1, 'ASN:plan1': 26, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 464 Chain: "C" Number of atoms: 6947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 6947 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 10 Unresolved non-hydrogen bonds: 818 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 19, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 31, 'ASP:plan': 31} Unresolved non-hydrogen planarities: 421 Chain: "F" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 872 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 688 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 882 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "J" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 901 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 694 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 708 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 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: "I" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 15.10, per 1000 atoms: 0.57 Number of scatterers: 26583 At special positions: 0 Unit cell: (140.714, 136.482, 187.266, 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 132 16.00 O 5068 8.00 N 4432 7.00 C 16951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 100E" distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 100 " - pdb=" SG CYS J 100E" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " MAN I 7 " - " MAN I 8 " " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 7 " ALPHA1-6 " BMA I 3 " - " MAN I 7 " " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " BETA1-2 " MAN I 4 " - " NAG I 5 " " MAN M 4 " - " NAG M 5 " " MAN P 4 " - " NAG P 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG I 5 " - " GAL I 6 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG M 5 " - " GAL M 6 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG P 5 " - " GAL P 6 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 343 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 11.89 Conformation dependent library (CDL) restraints added in 5.4 seconds 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 50 sheets defined 19.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.23 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.899A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.207A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 756 removed outlier: 4.287A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.585A pdb=" N LEU A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 766 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 777 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 940 removed outlier: 4.175A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 967 removed outlier: 4.258A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 954 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 955 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.485A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.657A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.275A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.552A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 887 through 890 No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 940 removed outlier: 4.674A pdb=" N GLU B 918 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS B 921 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 924 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 928 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 936 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 938 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 939 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 967 removed outlier: 3.659A pdb=" N GLY B 946 " --> pdb=" O SER B 943 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 955 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 958 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 965 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 967 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.761A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.688A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1143 No H-bonds generated for 'chain 'B' and resid 1140 through 1143' Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.525A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 784 removed outlier: 3.614A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLN C 784 " --> pdb=" O GLU C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.789A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 913 through 938 removed outlier: 4.466A pdb=" N GLU C 918 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS C 921 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 924 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 928 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER C 937 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 967 removed outlier: 3.888A pdb=" N LEU C 945 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 955 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 959 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN C 965 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 removed outlier: 3.786A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.195A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1143 No H-bonds generated for 'chain 'C' and resid 1140 through 1143' Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.780A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= E, first strand: chain 'A' and resid 538 through 541 removed outlier: 5.986A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 642 through 645 removed outlier: 5.015A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.649A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= I, first strand: chain 'A' and resid 717 through 728 removed outlier: 5.888A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id= L, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= M, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.756A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.469A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= P, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.649A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 376 through 380 Processing sheet with id= R, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= S, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.080A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 642 through 645 removed outlier: 4.784A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 691 through 696 removed outlier: 5.744A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= W, first strand: chain 'B' and resid 721 through 728 removed outlier: 5.604A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 3.681A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AA, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.767A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.750A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 118 through 120 Processing sheet with id= AD, first strand: chain 'C' and resid 325 through 328 removed outlier: 8.132A pdb=" N ILE C 326 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.809A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AG, first strand: chain 'C' and resid 642 through 645 removed outlier: 5.539A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.830A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AJ, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.584A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id= AM, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id= AN, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.782A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 107 through 109 removed outlier: 6.729A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 34 through 38 Processing sheet with id= AQ, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.673A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.899A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.998A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 90 through 94 removed outlier: 3.509A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'K' and resid 34 through 38 removed outlier: 3.735A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 63 through 65 Processing sheet with id= AW, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.966A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'L' and resid 34 through 37 964 hydrogen bonds defined for protein. 2310 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: 11.05 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 8803 1.36 - 1.50: 8694 1.50 - 1.65: 9547 1.65 - 1.79: 84 1.79 - 1.94: 83 Bond restraints: 27211 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 NAG I 5 " pdb=" O5 NAG I 5 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.936 -0.128 3.30e-02 9.18e+02 1.51e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.692 0.116 3.30e-02 9.18e+02 1.23e+01 ... (remaining 27206 not shown) Histogram of bond angle deviations from ideal: 96.82 - 106.02: 746 106.02 - 115.21: 15864 115.21 - 124.40: 20147 124.40 - 133.60: 523 133.60 - 142.79: 37 Bond angle restraints: 37317 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 142.79 -28.39 2.30e+00 1.89e-01 1.52e+02 angle pdb=" C ASN F 52 " pdb=" CA ASN F 52 " pdb=" CB ASN F 52 " ideal model delta sigma weight residual 110.33 105.11 5.22 1.02e+00 9.61e-01 2.62e+01 angle pdb=" N ASP J 100H" pdb=" CA ASP J 100H" pdb=" C ASP J 100H" ideal model delta sigma weight residual 111.02 116.72 -5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PHE C 565 " pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " ideal model delta sigma weight residual 111.55 103.44 8.11 1.74e+00 3.30e-01 2.17e+01 angle pdb=" NE ARG A 328 " pdb=" CZ ARG A 328 " pdb=" NH2 ARG A 328 " ideal model delta sigma weight residual 119.20 115.13 4.07 9.00e-01 1.23e+00 2.05e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 15798 23.28 - 46.56: 601 46.56 - 69.83: 109 69.83 - 93.11: 45 93.11 - 116.39: 22 Dihedral angle restraints: 16575 sinusoidal: 5927 harmonic: 10648 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.04 -61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.36 55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA ASP J 100H" pdb=" C ASP J 100H" pdb=" N TYR J 100I" pdb=" CA TYR J 100I" ideal model delta harmonic sigma weight residual -180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 16572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 4471 0.331 - 0.663: 7 0.663 - 0.994: 1 0.994 - 1.326: 0 1.326 - 1.657: 2 Chirality restraints: 4481 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-01 2.50e+01 6.87e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-01 2.50e+01 5.21e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4478 not shown) Planarity restraints: 4850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " 0.124 9.50e-02 1.11e+02 8.16e-02 4.67e+01 pdb=" NE ARG A 328 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " 0.114 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.051 2.00e-02 2.50e+03 4.75e-02 2.82e+01 pdb=" CG ASN C 343 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.051 2.00e-02 2.50e+03 4.72e-02 2.79e+01 pdb=" CG ASN B 343 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.051 2.00e-02 2.50e+03 ... (remaining 4847 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 265 2.63 - 3.20: 25695 3.20 - 3.77: 38540 3.77 - 4.33: 52168 4.33 - 4.90: 88122 Nonbonded interactions: 204790 Sorted by model distance: nonbonded pdb=" OH TYR J 100F" pdb=" O4 BMA I 3 " model vdw 2.063 2.440 nonbonded pdb=" OE1 GLN B 784 " pdb=" OG SER B1030 " model vdw 2.114 2.440 nonbonded pdb=" O3 MAN P 4 " pdb=" O6 NAG P 5 " model vdw 2.180 2.440 nonbonded pdb=" O GLN A 675 " pdb=" N GLN A 690 " model vdw 2.227 2.520 nonbonded pdb=" O3 NAG D 1 " pdb=" O7 NAG D 1 " model vdw 2.227 2.440 ... (remaining 204785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 68 or resid 81 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 110 or (resid 115 through 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 or (resid 132 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 172 or resid 187 through 206 or \ (resid 207 and (name N or name CA or name C or name O or name CB )) or resid 208 \ through 215 or (resid 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 273 or (resid 274 and (name N or name CA or name C or n \ ame O or name CB )) or resid 275 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB )) or resid 285 through 288 or (resid 289 throu \ gh 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thr \ ough 292 or (resid 293 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 323 or (resid 324 through 325 and (name N or na \ me CA or name C or name O or name CB )) or resid 326 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 334 \ or (resid 335 and (name N or name CA or name C or name O or name CB )) or resid \ 336 through 339 or (resid 340 and (name N or name CA or name C or name O or nam \ e CB )) or resid 341 through 344 or (resid 345 through 346 and (name N or name C \ A or name C or name O or name CB )) or resid 347 through 353 or (resid 354 and ( \ name N or name CA or name C or name O or name CB )) or resid 355 or (resid 356 t \ hrough 357 and (name N or name CA or name C or name O or name CB )) or resid 358 \ or (resid 359 and (name N or name CA or name C or name O or name CB )) or resid \ 360 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB )) or resid 369 through 372 or (resid 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 or (resid 375 through 376 a \ nd (name N or name CA or name C or name O or name CB )) or resid 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 386 and (name N or name CA or name C or name O or \ name CB )) or resid 387 or (resid 388 through 390 and (name N or name CA or nam \ e C or name O or name CB )) or resid 391 through 392 or (resid 393 and (name N o \ r name CA or name C or name O or name CB )) or resid 394 through 404 or (resid 4 \ 05 through 406 and (name N or name CA or name C or name O or name CB )) or resid \ 407 through 413 or (resid 414 through 415 and (name N or name CA or name C or n \ ame O or name CB )) or resid 416 through 419 or (resid 420 and (name N or name C \ A or name C or name O or name CB )) or resid 421 through 432 or (resid 433 and ( \ name N or name CA or name C or name O or name CB )) or resid 434 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 438 \ through 440 or (resid 441 through 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 447 or (resid 448 and (name N or name CA or \ name C or name O or name CB )) or resid 449 through 451 or (resid 452 and (name \ N or name CA or name C or name O or name CB )) or resid 453 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB )) or resid 456 or \ (resid 457 through 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 467 or (resid 468 through 469 and (name N or name CA or nam \ e C or name O or name CB )) or resid 470 or (resid 471 and (name N or name CA or \ name C or name O or name CB )) or resid 472 through 476 or (resid 477 through 4 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 479 through \ 480 or (resid 481 and (name N or name CA or name C or name O or name CB )) or r \ esid 482 through 492 or (resid 493 and (name N or name CA or name C or name O or \ name CB )) or resid 494 through 500 or (resid 501 and (name N or name CA or nam \ e C or name O or name CB )) or resid 502 through 505 or (resid 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 509 or (resid 5 \ 10 through 512 and (name N or name CA or name C or name O or name CB )) or resid \ 513 or (resid 514 and (name N or name CA or name C or name O or name CB )) or r \ esid 515 through 516 or (resid 517 through 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 523 or (resid 524 and (name N or na \ me CA or name C or name O or name CB )) or resid 525 through 528 or (resid 529 a \ nd (name N or name CA or name C or name O or name CB )) or resid 530 through 531 \ or (resid 532 through 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 539 or (resid 540 and (name N or name CA or name C or n \ ame O or name CB )) or resid 541 or (resid 542 and (name N or name CA or name C \ or name O or name CB )) or resid 543 or (resid 544 and (name N or name CA or nam \ e C or name O or name CB )) or resid 545 or (resid 546 and (name N or name CA or \ name C or name O or name CB )) or resid 547 through 550 or (resid 551 and (name \ N or name CA or name C or name O or name CB )) or resid 552 or (resid 553 throu \ gh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 or (resid 560 and (name N or name CA or name C or name O or name CB \ )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or n \ ame O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 575 or (res \ id 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ through 580 or (resid 581 through 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 or (resid 588 and (name N or name CA or name C or n \ ame O or name CB )) or resid 589 through 590 or (resid 591 through 592 and (name \ N or name CA or name C or name O or name CB )) or resid 593 through 613 or (res \ id 614 and (name N or name CA or name C or name O or name CB )) or resid 615 or \ (resid 616 and (name N or name CA or name C or name O or name CB )) or resid 617 \ through 618 or (resid 619 through 620 and (name N or name CA or name C or name \ O or name CB )) or resid 641 through 650 or (resid 651 and (name N or name CA or \ name C or name O or name CB )) or (resid 652 through 654 and (name N or name CA \ or name C or name O or name CB )) or resid 655 through 663 or (resid 664 and (n \ ame N or name CA or name C or name O or name CB )) or resid 665 through 676 or ( \ resid 690 and (name N or name CA or name C or name O or name CB )) or resid 691 \ through 697 or (resid 698 and (name N or name CA or name C or name O or name CB \ )) or resid 699 through 703 or (resid 704 and (name N or name CA or name C or na \ me O or name CB )) or resid 705 through 709 or (resid 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 718 or (resid 719 and (n \ ame N or name CA or name C or name O or name CB )) or resid 720 through 722 or ( \ resid 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ or (resid 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 729 or (resid 730 and (name N or name CA or name C or name O or name \ CB )) or resid 731 through 736 or (resid 737 and (name N or name CA or name C o \ r name O or name CB )) or resid 738 or (resid 739 through 740 and (name N or nam \ e CA or name C or name O or name CB )) or resid 741 through 744 or (resid 745 an \ d (name N or name CA or name C or name O or name CB )) or resid 746 or (resid 74 \ 7 through 748 and (name N or name CA or name C or name O or name CB )) or resid \ 749 through 750 or (resid 751 and (name N or name CA or name C or name O or name \ CB )) or resid 752 through 754 or (resid 755 and (name N or name CA or name C o \ r name O or name CB )) or resid 756 through 757 or (resid 758 and (name N or nam \ e CA or name C or name O or name CB )) or resid 759 through 760 or (resid 761 an \ d (name N or name CA or name C or name O or name CB )) or resid 762 through 764 \ or (resid 765 through 766 and (name N or name CA or name C or name O or name CB \ )) or resid 767 through 772 or (resid 773 and (name N or name CA or name C or na \ me O or name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA \ or name C or name O or name CB )) or resid 777 through 778 or (resid 779 throug \ h 780 and (name N or name CA or name C or name O or name CB )) or resid 781 thro \ ugh 794 or (resid 795 through 796 and (name N or name CA or name C or name O or \ name CB )) or resid 797 through 809 or (resid 810 through 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 812 or (resid 813 through 814 an \ d (name N or name CA or name C or name O or name CB )) or resid 815 or (resid 81 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 817 through \ 819 or (resid 820 and (name N or name CA or name C or name O or name CB )) or re \ sid 821 through 826 or (resid 827 through 828 and (name N or name CA or name C o \ r name O or name CB )) or (resid 855 and (name N or name CA or name C or name O \ or name CB )) or resid 856 through 857 or (resid 858 and (name N or name CA or n \ ame C or name O or name CB )) or resid 859 or (resid 860 and (name N or name CA \ or name C or name O or name CB )) or resid 861 through 866 or (resid 867 through \ 868 and (name N or name CA or name C or name O or name CB )) or resid 869 throu \ gh 874 or (resid 875 through 876 and (name N or name CA or name C or name O or n \ ame CB )) or resid 877 through 933 or (resid 934 and (name N or name CA or name \ C or name O or name CB )) or resid 935 through 936 or (resid 937 through 944 and \ (name N or name CA or name C or name O or name CB )) or resid 945 through 949 o \ r (resid 950 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 51 through 973 or (resid 974 through 979 and (name N or name CA or name C or nam \ e O or name CB )) or resid 980 through 984 or (resid 985 and (name N or name CA \ or name C or name O or name CB )) or resid 986 through 987 or (resid 988 through \ 991 and (name N or name CA or name C or name O or name CB )) or resid 992 or (r \ esid 993 through 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1018 or (resid 1019 through 1020 and (name N or name CA or na \ me C or name O or name CB )) or resid 1021 through 1030 or (resid 1031 and (name \ N or name CA or name C or name O or name CB )) or resid 1032 through 1039 or (r \ esid 1040 through 1041 and (name N or name CA or name C or name O or name CB )) \ or resid 1042 through 1050 or (resid 1051 and (name N or name CA or name C or na \ me O or name CB )) or resid 1052 through 1054 or (resid 1055 through 1056 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1057 through 1059 or \ (resid 1060 through 1061 and (name N or name CA or name C or name O or name CB \ )) or resid 1062 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O or name CB )) or resid 1067 or (resid 1068 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1069 through 1083 or (resid 1084 and (name \ N or name CA or name C or name O or name CB )) or resid 1085 or (resid 1086 thro \ ugh 1087 and (name N or name CA or name C or name O or name CB )) or resid 1088 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name C \ B )) or resid 1093 through 1096 or (resid 1097 and (name N or name CA or name C \ or name O or name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or \ name CA or name C or name O or name CB )) or resid 1101 through 1110 or (resid \ 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 thro \ ugh 1115 or (resid 1116 through 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1121 or (resid 1122 through 1123 and (name N \ or name CA or name C or name O or name CB )) or resid 1124 or (resid 1125 and ( \ name N or name CA or name C or name O or name CB )) or resid 1126 or (resid 1127 \ through 1128 and (name N or name CA or name C or name O or name CB )) or resid \ 1129 or (resid 1130 and (name N or name CA or name C or name O or name CB )) or \ resid 1131 through 1132 or (resid 1133 and (name N or name CA or name C or name \ O or name CB )) or resid 1134 or (resid 1135 through 1136 and (name N or name CA \ or name C or name O or name CB )) or resid 1137 through 1138 or (resid 1139 and \ (name N or name CA or name C or name O or name CB )) or resid 1140 through 1143 \ or (resid 1144 and (name N or name CA or name C or name O or name CB )) or resi \ d 1301 through 1310)) selection = (chain 'B' and (resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 49 or (resid 50 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 61 or (res \ id 62 through 63 and (name N or name CA or name C or name O or name CB )) or res \ id 64 through 68 or resid 81 through 110 or (resid 115 through 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 141 or resid 166 through 189 or (resid 190 through 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 194 or (resid \ 195 through 198 and (name N or name CA or name C or name O or name CB )) or resi \ d 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) or \ resid 201 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 231 or resid 236 through 272 or (resid 273 thr \ ough 274 and (name N or name CA or name C or name O or name CB )) or resid 275 t \ hrough 283 or (resid 284 and (name N or name CA or name C or name O or name CB ) \ ) or resid 285 through 293 or (resid 294 and (name N or name CA or name C or nam \ e O or name CB )) or resid 295 through 297 or (resid 298 through 299 and (name N \ or name CA or name C or name O or name CB )) or resid 300 through 301 or (resid \ 302 and (name N or name CA or name C or name O or name CB )) or resid 303 throu \ gh 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or \ resid 308 through 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 320 or (resid 321 and (name N or name CA or n \ ame C or name O or name CB )) or resid 322 through 324 or (resid 325 and (name N \ or name CA or name C or name O or name CB )) or resid 326 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or \ resid 369 through 389 or (resid 390 and (name N or name CA or name C or name O \ or name CB )) or resid 391 through 454 or (resid 455 and (name N or name CA or n \ ame C or name O or name CB )) or resid 456 through 459 or (resid 460 and (name N \ or name CA or name C or name O or name CB )) or resid 461 through 468 or (resid \ 469 and (name N or name CA or name C or name O or name CB )) or resid 470 throu \ gh 477 or (resid 478 and (name N or name CA or name C or name O or name CB )) or \ resid 479 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 505 or (resid 506 and (name N or name CA or n \ ame C or name O or name CB )) or resid 507 through 518 or (resid 519 through 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 5 \ 28 or (resid 529 and (name N or name CA or name C or name O or name CB )) or res \ id 530 through 535 or (resid 536 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 through 539 or (resid 540 and (name N or name \ CA or name C or name O or name CB )) or resid 541 through 545 or (resid 546 and \ (name N or name CA or name C or name O or name CB )) or resid 547 through 559 o \ r (resid 560 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 61 through 618 or (resid 619 through 620 and (name N or name CA or name C or nam \ e O or name CB )) or resid 641 through 738 or (resid 739 through 740 and (name N \ or name CA or name C or name O or name CB )) or resid 741 through 746 or (resid \ 747 through 748 and (name N or name CA or name C or name O or name CB )) or res \ id 749 through 750 or (resid 751 and (name N or name CA or name C or name O or n \ ame CB )) or resid 752 through 757 or (resid 758 and (name N or name CA or name \ C or name O or name CB )) or resid 759 through 760 or (resid 761 and (name N or \ name CA or name C or name O or name CB )) or resid 762 through 772 or (resid 773 \ and (name N or name CA or name C or name O or name CB )) or resid 774 through 7 \ 75 or (resid 776 and (name N or name CA or name C or name O or name CB )) or res \ id 777 through 778 or (resid 779 through 780 and (name N or name CA or name C or \ name O or name CB )) or resid 781 through 794 or (resid 795 through 796 and (na \ me N or name CA or name C or name O or name CB )) or resid 797 through 809 or (r \ esid 810 through 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 through 815 or (resid 816 and (name N or name CA or name C or name O \ or name CB )) or resid 817 through 819 or (resid 820 and (name N or name CA or n \ ame C or name O or name CB )) or resid 821 through 859 or (resid 860 and (name N \ or name CA or name C or name O or name CB )) or resid 861 through 867 or (resid \ 868 and (name N or name CA or name C or name O or name CB )) or resid 869 throu \ gh 874 or (resid 875 through 876 and (name N or name CA or name C or name O or n \ ame CB )) or resid 877 through 933 or (resid 934 and (name N or name CA or name \ C or name O or name CB )) or resid 935 through 936 or (resid 937 through 944 and \ (name N or name CA or name C or name O or name CB )) or resid 945 through 976 o \ r (resid 977 through 979 and (name N or name CA or name C or name O or name CB ) \ ) or resid 980 through 990 or (resid 991 and (name N or name CA or name C or nam \ e O or name CB )) or resid 992 or (resid 993 through 994 and (name N or name CA \ or name C or name O or name CB )) or resid 995 through 1018 or (resid 1019 throu \ gh 1020 and (name N or name CA or name C or name O or name CB )) or resid 1021 t \ hrough 1030 or (resid 1031 and (name N or name CA or name C or name O or name CB \ )) or resid 1032 through 1059 or (resid 1060 through 1061 and (name N or name C \ A or name C or name O or name CB )) or resid 1062 through 1065 or (resid 1066 an \ d (name N or name CA or name C or name O or name CB )) or resid 1067 or (resid 1 \ 068 and (name N or name CA or name C or name O or name CB )) or resid 1069 throu \ gh 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) \ or resid 1074 through 1096 or (resid 1097 and (name N or name CA or name C or na \ me O or name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or name \ CA or name C or name O or name CB )) or resid 1101 through 1115 or (resid 1116 \ through 1118 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 119 through 1121 or (resid 1122 through 1123 and (name N or name CA or name C or \ name O or name CB )) or resid 1124 or (resid 1125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1126 through 1129 or (resid 1130 and (name \ N or name CA or name C or name O or name CB )) or resid 1131 through 1132 or (re \ sid 1133 and (name N or name CA or name C or name O or name CB )) or resid 1134 \ or (resid 1135 through 1136 and (name N or name CA or name C or name O or name C \ B )) or resid 1137 through 1144 or resid 1301 through 1310)) selection = (chain 'C' and (resid 28 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 thr \ ough 44 or (resid 45 through 48 and (name N or name CA or name C or name O or na \ me CB )) or resid 49 or (resid 50 through 54 and (name N or name CA or name C or \ name O or name CB )) or resid 55 through 61 or (resid 62 through 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 65 or (resid 6 \ 6 through 68 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 1 through 82 or (resid 83 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 99 or (resid 100 throu \ gh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 110 or (resid 115 through 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 140 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 172 or (resid 187 through 188 a \ nd (name N or name CA or name C or name O or name CB )) or resid 189 or (resid 1 \ 90 through 191 and (name N or name CA or name C or name O or name CB )) or resid \ 192 through 194 or (resid 195 through 198 and (name N or name CA or name C or n \ ame O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name C \ or name O or name CB )) or resid 201 through 206 or (resid 207 and (name N or na \ me CA or name C or name O or name CB )) or resid 208 through 210 or (resid 215 t \ hrough 216 and (name N or name CA or name C or name O or name CB )) or resid 217 \ through 220 or (resid 221 through 224 and (name N or name CA or name C or name \ O or name CB )) or resid 225 or (resid 226 through 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 or (resid 231 and (name N or name C \ A or name C or name O or name CB )) or resid 236 through 239 or (resid 240 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 272 or (resid 273 through 274 and (name N or name CA or name C or name O or \ name CB )) or resid 275 or (resid 276 through 278 and (name N or name CA or nam \ e C or name O or name CB )) or resid 279 through 288 or (resid 289 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 through 293 \ or (resid 294 and (name N or name CA or name C or name O or name CB )) or resid \ 295 through 297 or (resid 298 through 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB )) or resid 303 through 304 or (resid 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 313 or \ (resid 314 through 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 319 or (resid 320 through 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 324 or (resid 325 and (name N o \ r name CA or name C or name O or name CB )) or resid 326 through 358 or (resid 3 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 363 or (resid 364 and (name N or name CA or name C or name O or name CB )) or r \ esid 365 through 382 or (resid 383 and (name N or name CA or name C or name O or \ name CB )) or resid 384 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 or (resid 388 through 390 and (name N o \ r name CA or name C or name O or name CB )) or resid 391 through 413 or (resid 4 \ 14 through 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or nam \ e CB )) or resid 421 through 432 or (resid 433 and (name N or name CA or name C \ or name O or name CB )) or resid 434 through 436 or (resid 437 and (name N or na \ me CA or name C or name O or name CB )) or resid 438 or (resid 439 through 442 a \ nd (name N or name CA or name C or name O or name CB )) or resid 443 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 456 or (resid 457 through 460 and (name N or name CA or name C or n \ ame O or name CB )) or resid 461 through 467 or (resid 468 through 469 and (name \ N or name CA or name C or name O or name CB )) or resid 470 through 492 or (res \ id 493 and (name N or name CA or name C or name O or name CB )) or resid 494 thr \ ough 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 509 or (resid 510 through 512 and (name N or name CA or nam \ e C or name O or name CB )) or resid 513 or (resid 514 and (name N or name CA or \ name C or name O or name CB )) or resid 515 through 541 or (resid 542 and (name \ N or name CA or name C or name O or name CB )) or resid 543 or (resid 544 and ( \ name N or name CA or name C or name O or name CB )) or resid 545 through 552 or \ (resid 553 through 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 563 or (resid 564 and (name N or name CA or name C or name \ O or name CB )) or resid 565 through 575 or (resid 576 and (name N or name CA or \ name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name C \ A or name C or name O or name CB )) or resid 579 or (resid 580 through 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 590 or \ (resid 591 through 592 and (name N or name CA or name C or name O or name CB )) \ or resid 593 through 615 or (resid 616 and (name N or name CA or name C or name \ O or name CB )) or resid 617 or (resid 618 through 620 and (name N or name CA or \ name C or name O or name CB )) or resid 641 through 650 or (resid 651 and (name \ N or name CA or name C or name O or name CB )) or resid 652 through 663 or (res \ id 664 and (name N or name CA or name C or name O or name CB )) or resid 665 thr \ ough 709 or (resid 710 and (name N or name CA or name C or name O or name CB )) \ or resid 711 through 718 or (resid 719 and (name N or name CA or name C or name \ O or name CB )) or resid 720 through 722 or (resid 723 and (name N or name CA or \ name C or name O or name CB )) or resid 724 through 729 or (resid 730 and (name \ N or name CA or name C or name O or name CB )) or resid 731 through 795 or (res \ id 796 and (name N or name CA or name C or name O or name CB )) or resid 797 thr \ ough 812 or (resid 813 through 814 and (name N or name CA or name C or name O or \ name CB )) or resid 815 through 818 or (resid 819 through 820 and (name N or na \ me CA or name C or name O or name CB )) or resid 821 through 828 or resid 855 th \ rough 977 or (resid 978 through 979 and (name N or name CA or name C or name O o \ r name CB )) or resid 980 through 1144 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'F' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 88 or (resi \ d 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throug \ h 113)) selection = (chain 'H' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 7 and (name N or name CA or name C or \ name O or name CB )) or resid 8 through 44 or (resid 45 through 46 and (name N \ or name CA or name C or name O or name CB )) or resid 47 or (resid 48 and (name \ N or name CA or name C or name O or name CB )) or resid 49 through 60 or (resid \ 61 through 62 and (name N or name CA or name C or name O or name CB )) or resid \ 63 through 72 or (resid 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 113)) selection = (chain 'J' and (resid 1 through 9 or (resid 10 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resid \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name C \ B )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or nam \ e O or name CB )) or resid 44 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N o \ r name CA or name C or name O or name CB )) or resid 52 through 60 or (resid 61 \ through 62 and (name N or name CA or name C or name O or name CB )) or resid 63 \ or (resid 64 and (name N or name CA or name C or name O or name CB )) or (resid \ 65 through 68 and (name N or name CA or name C or name O or name CB )) or resid \ 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) or resi \ d 71 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 113)) } ncs_group { reference = (chain 'G' and (resid 1 through 25 or (resid 26 through 27B and (name N or name \ CA or name C or name O or name CB )) or resid 27C through 74 or (resid 75 throug \ h 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throug \ h 106A)) selection = (chain 'K' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 17 or (resid 18 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 25 or (resi \ d 26 through 27B and (name N or name CA or name C or name O or name CB )) or res \ id 27C through 58 or (resid 59 through 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 or (resid 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 71 or (resid 72 through 76 and (name N \ or name CA or name C or name O or name CB )) or resid 77 through 106A)) selection = (chain 'L' and (resid 1 through 16 or (resid 17 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 26 or (resid 27 through \ 27B and (name N or name CA or name C or name O or name CB )) or resid 27C throug \ h 58 or (resid 59 through 61 and (name N or name CA or name C or name O or name \ CB )) or resid 62 through 64 or (resid 65 through 67 and (name N or name CA or n \ ame C or name O or name CB )) or resid 68 through 71 or (resid 72 through 76 and \ (name N or name CA or name C or name O or name CB )) or resid 77 through 106A)) \ } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'P' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.880 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 75.640 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.010 0.128 27211 Z= 0.664 Angle : 1.127 28.390 37317 Z= 0.623 Chirality : 0.073 1.657 4481 Planarity : 0.008 0.118 4810 Dihedral : 14.414 116.387 9613 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3610 helix: -0.87 (0.18), residues: 641 sheet: -0.57 (0.18), residues: 796 loop : -1.64 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP H 50 HIS 0.017 0.003 HIS J 35 PHE 0.052 0.004 PHE H 63 TYR 0.057 0.008 TYR F 100I ARG 0.116 0.010 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 3.058 Fit side-chains revert: symmetry clash REVERT: A 763 LEU cc_start: 0.8956 (mm) cc_final: 0.8739 (mm) REVERT: B 484 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 780 GLU cc_start: 0.8230 (tp30) cc_final: 0.7613 (tp30) REVERT: B 980 ILE cc_start: 0.9323 (tp) cc_final: 0.8958 (tp) REVERT: B 984 LEU cc_start: 0.8613 (mt) cc_final: 0.8373 (mp) REVERT: F 50 TRP cc_start: 0.7688 (p-90) cc_final: 0.7413 (p-90) REVERT: F 100 ASN cc_start: 0.8513 (t0) cc_final: 0.8045 (t0) REVERT: H 80 MET cc_start: 0.8338 (tmm) cc_final: 0.8012 (tmm) REVERT: J 32 TYR cc_start: 0.8894 (m-80) cc_final: 0.8548 (m-10) REVERT: J 77 THR cc_start: 0.9331 (p) cc_final: 0.9088 (p) REVERT: J 79 TYR cc_start: 0.8623 (m-10) cc_final: 0.8408 (m-10) REVERT: J 91 TYR cc_start: 0.8884 (m-80) cc_final: 0.8410 (m-80) REVERT: J 100 TYR cc_start: 0.7743 (m-10) cc_final: 0.7288 (m-10) REVERT: K 96 TRP cc_start: 0.8849 (m-90) cc_final: 0.8480 (m-90) REVERT: L 36 TYR cc_start: 0.8746 (m-10) cc_final: 0.8267 (m-10) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.3570 time to fit residues: 149.3113 Evaluate side-chains 201 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 286 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 212 optimal weight: 0.9980 chunk 331 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 901 GLN A1101 HIS B 613 GLN C 710 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27211 Z= 0.196 Angle : 0.688 15.677 37317 Z= 0.353 Chirality : 0.050 0.625 4481 Planarity : 0.005 0.073 4810 Dihedral : 10.755 102.124 5288 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 0.55 % Allowed : 7.19 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3610 helix: 0.01 (0.20), residues: 649 sheet: -0.44 (0.18), residues: 792 loop : -1.25 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.005 0.001 HIS B 519 PHE 0.025 0.002 PHE A 497 TYR 0.026 0.002 TYR G 49 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 3.143 Fit side-chains REVERT: B 353 TRP cc_start: 0.8337 (p-90) cc_final: 0.7205 (p-90) REVERT: B 484 GLU cc_start: 0.7804 (mt-10) cc_final: 0.6718 (mt-10) REVERT: B 980 ILE cc_start: 0.9345 (tp) cc_final: 0.8953 (tp) REVERT: B 1050 MET cc_start: 0.8240 (ptp) cc_final: 0.7867 (ptp) REVERT: C 775 ASP cc_start: 0.8293 (m-30) cc_final: 0.8040 (t0) REVERT: C 878 LEU cc_start: 0.9213 (tp) cc_final: 0.8709 (tt) REVERT: C 882 ILE cc_start: 0.9207 (mt) cc_final: 0.8944 (mt) REVERT: F 80 MET cc_start: 0.8630 (tmm) cc_final: 0.8143 (tmm) REVERT: F 91 TYR cc_start: 0.8875 (m-80) cc_final: 0.8670 (m-80) REVERT: F 100 ASN cc_start: 0.8445 (t0) cc_final: 0.7887 (t0) REVERT: G 37 GLN cc_start: 0.8102 (pt0) cc_final: 0.7771 (tt0) REVERT: H 80 MET cc_start: 0.8440 (tmm) cc_final: 0.7991 (tmm) REVERT: J 32 TYR cc_start: 0.8695 (m-80) cc_final: 0.8181 (m-10) REVERT: J 39 GLN cc_start: 0.8155 (tt0) cc_final: 0.7881 (tt0) REVERT: J 52 ASN cc_start: 0.8321 (t0) cc_final: 0.7390 (t0) REVERT: J 80 MET cc_start: 0.8522 (tmm) cc_final: 0.8213 (tmm) REVERT: J 91 TYR cc_start: 0.8739 (m-80) cc_final: 0.8311 (m-80) REVERT: J 100 TYR cc_start: 0.7300 (m-10) cc_final: 0.6881 (m-10) REVERT: L 36 TYR cc_start: 0.8676 (m-80) cc_final: 0.8361 (m-10) outliers start: 12 outliers final: 6 residues processed: 246 average time/residue: 0.3571 time to fit residues: 145.7143 Evaluate side-chains 214 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain J residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 358 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 329 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 266 optimal weight: 0.8980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A1135 ASN B 955 ASN C 613 GLN C 901 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27211 Z= 0.198 Angle : 0.623 16.950 37317 Z= 0.318 Chirality : 0.048 0.622 4481 Planarity : 0.004 0.061 4810 Dihedral : 9.829 102.548 5288 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.95 % Allowed : 9.91 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3610 helix: 0.12 (0.20), residues: 662 sheet: -0.66 (0.17), residues: 864 loop : -1.12 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 50 HIS 0.005 0.001 HIS B 519 PHE 0.021 0.001 PHE A 497 TYR 0.027 0.002 TYR H 33 ARG 0.006 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 3.202 Fit side-chains REVERT: B 353 TRP cc_start: 0.8312 (p-90) cc_final: 0.7232 (p-90) REVERT: B 484 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 507 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8304 (Cg_endo) REVERT: C 775 ASP cc_start: 0.8372 (m-30) cc_final: 0.8169 (t0) REVERT: C 878 LEU cc_start: 0.9192 (tp) cc_final: 0.8773 (tp) REVERT: C 882 ILE cc_start: 0.9207 (mt) cc_final: 0.8987 (mp) REVERT: F 80 MET cc_start: 0.8610 (tmm) cc_final: 0.8171 (tmm) REVERT: F 100 ASN cc_start: 0.8447 (t0) cc_final: 0.8172 (t0) REVERT: H 63 PHE cc_start: 0.7061 (m-10) cc_final: 0.6776 (m-80) REVERT: H 80 MET cc_start: 0.8549 (tmm) cc_final: 0.8058 (tmm) REVERT: J 32 TYR cc_start: 0.8640 (m-80) cc_final: 0.8133 (m-80) REVERT: J 39 GLN cc_start: 0.8120 (tt0) cc_final: 0.7851 (tt0) REVERT: J 52 ASN cc_start: 0.8242 (t0) cc_final: 0.7731 (t0) REVERT: J 80 MET cc_start: 0.8542 (tmm) cc_final: 0.8250 (tmm) REVERT: J 91 TYR cc_start: 0.8690 (m-80) cc_final: 0.8307 (m-80) REVERT: J 94 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7164 (ttp80) REVERT: J 100 TYR cc_start: 0.7359 (m-10) cc_final: 0.6930 (m-10) REVERT: L 36 TYR cc_start: 0.8662 (m-80) cc_final: 0.8407 (m-10) outliers start: 21 outliers final: 15 residues processed: 224 average time/residue: 0.3511 time to fit residues: 132.1146 Evaluate side-chains 207 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 352 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1088 HIS C 926 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27211 Z= 0.418 Angle : 0.719 11.442 37317 Z= 0.370 Chirality : 0.052 0.803 4481 Planarity : 0.005 0.078 4810 Dihedral : 9.743 90.262 5288 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.64 % Allowed : 11.14 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3610 helix: -0.00 (0.20), residues: 651 sheet: -0.68 (0.17), residues: 845 loop : -1.27 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 50 HIS 0.005 0.001 HIS C1064 PHE 0.024 0.003 PHE H 63 TYR 0.026 0.002 TYR C 265 ARG 0.004 0.001 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 3.143 Fit side-chains REVERT: B 351 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7854 (t80) REVERT: B 353 TRP cc_start: 0.8414 (p-90) cc_final: 0.8194 (p-90) REVERT: B 484 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7390 (mt-10) REVERT: B 1029 MET cc_start: 0.9091 (tpp) cc_final: 0.8580 (ttm) REVERT: C 565 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6098 (t80) REVERT: F 30 THR cc_start: 0.9216 (p) cc_final: 0.8907 (p) REVERT: F 54 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8761 (m) REVERT: F 80 MET cc_start: 0.8549 (tmm) cc_final: 0.8080 (tmm) REVERT: F 91 TYR cc_start: 0.8892 (m-80) cc_final: 0.8659 (m-80) REVERT: F 100 ASN cc_start: 0.8382 (t0) cc_final: 0.8110 (t0) REVERT: H 33 TYR cc_start: 0.8591 (m-10) cc_final: 0.8272 (m-10) REVERT: J 10 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6585 (tm-30) REVERT: J 52 ASN cc_start: 0.8430 (t0) cc_final: 0.7653 (t0) REVERT: J 80 MET cc_start: 0.8595 (tmm) cc_final: 0.8158 (tmm) REVERT: J 91 TYR cc_start: 0.8763 (m-80) cc_final: 0.8306 (m-80) REVERT: J 94 ARG cc_start: 0.8565 (ttp80) cc_final: 0.7252 (ttp80) REVERT: J 100 TYR cc_start: 0.7702 (m-10) cc_final: 0.7176 (m-10) outliers start: 58 outliers final: 32 residues processed: 232 average time/residue: 0.3812 time to fit residues: 150.0926 Evaluate side-chains 215 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 703 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS J 39 GLN K 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27211 Z= 0.206 Angle : 0.603 12.626 37317 Z= 0.307 Chirality : 0.048 0.603 4481 Planarity : 0.004 0.057 4810 Dihedral : 9.229 87.177 5288 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.41 % Allowed : 12.73 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3610 helix: 0.29 (0.21), residues: 646 sheet: -0.68 (0.17), residues: 854 loop : -1.14 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 50 HIS 0.006 0.001 HIS B 519 PHE 0.015 0.001 PHE A 565 TYR 0.028 0.001 TYR H 100J ARG 0.005 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.857 Fit side-chains revert: symmetry clash REVERT: B 351 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 353 TRP cc_start: 0.8374 (p-90) cc_final: 0.8039 (p-90) REVERT: B 484 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 507 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8345 (Cg_endo) REVERT: F 30 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8836 (p) REVERT: F 54 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8650 (m) REVERT: F 80 MET cc_start: 0.8562 (tmm) cc_final: 0.8125 (tmm) REVERT: F 100 ASN cc_start: 0.8238 (t0) cc_final: 0.7978 (t0) REVERT: H 30 THR cc_start: 0.8598 (p) cc_final: 0.7760 (t) REVERT: H 33 TYR cc_start: 0.8553 (m-10) cc_final: 0.8324 (m-10) REVERT: H 53 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7752 (m-40) REVERT: H 96 LEU cc_start: 0.8899 (tp) cc_final: 0.8554 (tp) REVERT: J 36 TRP cc_start: 0.9109 (m100) cc_final: 0.8670 (m100) REVERT: J 52 ASN cc_start: 0.8382 (t0) cc_final: 0.7661 (t0) REVERT: J 80 MET cc_start: 0.8567 (tmm) cc_final: 0.8209 (tmm) REVERT: J 100 TYR cc_start: 0.7560 (m-10) cc_final: 0.7102 (m-10) REVERT: L 36 TYR cc_start: 0.8566 (m-10) cc_final: 0.8150 (m-10) outliers start: 53 outliers final: 31 residues processed: 240 average time/residue: 0.3537 time to fit residues: 142.1844 Evaluate side-chains 224 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 207 optimal weight: 0.0020 chunk 87 optimal weight: 0.0570 chunk 353 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.9108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN C 969 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27211 Z= 0.191 Angle : 0.586 11.584 37317 Z= 0.296 Chirality : 0.047 0.563 4481 Planarity : 0.004 0.053 4810 Dihedral : 8.670 81.058 5288 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.00 % Allowed : 12.37 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3610 helix: 0.38 (0.21), residues: 646 sheet: -0.62 (0.17), residues: 875 loop : -1.11 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 50 HIS 0.005 0.001 HIS B 519 PHE 0.015 0.001 PHE C 238 TYR 0.019 0.001 TYR H 32 ARG 0.008 0.000 ARG J 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 202 time to evaluate : 3.335 Fit side-chains revert: symmetry clash REVERT: B 351 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7706 (t80) REVERT: B 353 TRP cc_start: 0.8384 (p-90) cc_final: 0.7392 (p-90) REVERT: B 484 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 507 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.8407 (Cg_endo) REVERT: C 351 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7673 (t80) REVERT: F 30 THR cc_start: 0.9120 (p) cc_final: 0.8756 (p) REVERT: F 80 MET cc_start: 0.8532 (tmm) cc_final: 0.8115 (tmm) REVERT: F 100 ASN cc_start: 0.8140 (t0) cc_final: 0.7898 (t0) REVERT: H 30 THR cc_start: 0.8565 (p) cc_final: 0.7900 (t) REVERT: H 33 TYR cc_start: 0.8580 (m-10) cc_final: 0.8072 (m-10) REVERT: J 10 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6613 (tm-30) REVERT: J 36 TRP cc_start: 0.9138 (m100) cc_final: 0.8732 (m100) REVERT: J 52 ASN cc_start: 0.8437 (t0) cc_final: 0.7629 (t0) REVERT: J 80 MET cc_start: 0.8549 (tmm) cc_final: 0.8240 (tmm) REVERT: J 100 TYR cc_start: 0.7391 (m-10) cc_final: 0.6975 (m-10) REVERT: L 36 TYR cc_start: 0.8613 (m-10) cc_final: 0.8109 (m-10) REVERT: L 61 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7194 (mtm110) outliers start: 66 outliers final: 37 residues processed: 249 average time/residue: 0.3808 time to fit residues: 159.3647 Evaluate side-chains 232 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 201 optimal weight: 7.9990 chunk 257 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27211 Z= 0.296 Angle : 0.626 13.571 37317 Z= 0.317 Chirality : 0.049 0.644 4481 Planarity : 0.004 0.053 4810 Dihedral : 8.618 79.221 5288 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.18 % Allowed : 12.69 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3610 helix: 0.35 (0.21), residues: 640 sheet: -0.72 (0.17), residues: 893 loop : -1.18 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 50 HIS 0.004 0.001 HIS B 519 PHE 0.015 0.002 PHE A 392 TYR 0.022 0.002 TYR H 100J ARG 0.007 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 210 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 351 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (t80) REVERT: B 353 TRP cc_start: 0.8456 (p-90) cc_final: 0.7418 (p-90) REVERT: B 484 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 351 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 565 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6287 (t80) REVERT: F 30 THR cc_start: 0.9139 (p) cc_final: 0.8780 (p) REVERT: F 33 TYR cc_start: 0.8478 (m-10) cc_final: 0.8276 (m-10) REVERT: F 54 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8708 (m) REVERT: F 80 MET cc_start: 0.8537 (tmm) cc_final: 0.8065 (tmm) REVERT: F 91 TYR cc_start: 0.8839 (m-80) cc_final: 0.8541 (m-80) REVERT: F 100 ASN cc_start: 0.8198 (t0) cc_final: 0.7985 (t0) REVERT: F 100 TYR cc_start: 0.7909 (m-10) cc_final: 0.7706 (m-10) REVERT: H 33 TYR cc_start: 0.8619 (m-10) cc_final: 0.7881 (m-10) REVERT: J 36 TRP cc_start: 0.9164 (m100) cc_final: 0.8840 (m100) REVERT: J 52 ASN cc_start: 0.8391 (t0) cc_final: 0.7566 (t0) REVERT: J 80 MET cc_start: 0.8580 (tmm) cc_final: 0.8251 (tmm) REVERT: J 100 TYR cc_start: 0.7627 (m-10) cc_final: 0.7241 (m-10) outliers start: 70 outliers final: 51 residues processed: 261 average time/residue: 0.3455 time to fit residues: 150.8711 Evaluate side-chains 255 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.0770 chunk 140 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27211 Z= 0.166 Angle : 0.576 13.211 37317 Z= 0.290 Chirality : 0.047 0.519 4481 Planarity : 0.004 0.051 4810 Dihedral : 8.153 74.962 5288 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.77 % Allowed : 13.51 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3610 helix: 0.47 (0.21), residues: 642 sheet: -0.61 (0.17), residues: 880 loop : -1.10 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 50 HIS 0.004 0.001 HIS B 519 PHE 0.015 0.001 PHE A 565 TYR 0.025 0.001 TYR L 32 ARG 0.007 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 218 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 351 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 353 TRP cc_start: 0.8398 (p-90) cc_final: 0.7409 (p-90) REVERT: B 484 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 886 TRP cc_start: 0.8819 (p90) cc_final: 0.8617 (p90) REVERT: C 351 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7658 (t80) REVERT: C 565 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6335 (t80) REVERT: F 30 THR cc_start: 0.9081 (p) cc_final: 0.8718 (p) REVERT: F 54 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8634 (m) REVERT: F 74 SER cc_start: 0.8978 (t) cc_final: 0.8772 (p) REVERT: F 80 MET cc_start: 0.8517 (tmm) cc_final: 0.8112 (tmm) REVERT: F 91 TYR cc_start: 0.8800 (m-80) cc_final: 0.8536 (m-80) REVERT: F 100 ASN cc_start: 0.8113 (t0) cc_final: 0.7883 (t0) REVERT: H 33 TYR cc_start: 0.8436 (m-80) cc_final: 0.7723 (m-10) REVERT: J 10 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6761 (tm-30) REVERT: J 36 TRP cc_start: 0.9107 (m100) cc_final: 0.8781 (m100) REVERT: J 80 MET cc_start: 0.8534 (tmm) cc_final: 0.8199 (tmm) REVERT: J 100 TYR cc_start: 0.7379 (m-10) cc_final: 0.7074 (m-10) outliers start: 61 outliers final: 46 residues processed: 259 average time/residue: 0.3531 time to fit residues: 152.9585 Evaluate side-chains 241 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 7.9990 chunk 337 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 336 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 0.0050 chunk 257 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27211 Z= 0.237 Angle : 0.596 13.562 37317 Z= 0.300 Chirality : 0.047 0.570 4481 Planarity : 0.004 0.051 4810 Dihedral : 8.014 71.866 5288 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 14.14 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3610 helix: 0.46 (0.21), residues: 647 sheet: -0.64 (0.17), residues: 889 loop : -1.08 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 50 HIS 0.004 0.001 HIS B 519 PHE 0.015 0.001 PHE C 238 TYR 0.030 0.001 TYR L 32 ARG 0.006 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 204 time to evaluate : 3.071 Fit side-chains REVERT: B 351 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 353 TRP cc_start: 0.8432 (p-90) cc_final: 0.7378 (p-90) REVERT: B 484 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7324 (mt-10) REVERT: C 351 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 565 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6304 (t80) REVERT: F 30 THR cc_start: 0.9050 (p) cc_final: 0.8661 (p) REVERT: F 32 TYR cc_start: 0.8541 (m-80) cc_final: 0.7390 (m-10) REVERT: F 54 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8661 (m) REVERT: F 74 SER cc_start: 0.9000 (t) cc_final: 0.8796 (p) REVERT: F 80 MET cc_start: 0.8512 (tmm) cc_final: 0.8070 (tmm) REVERT: F 94 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8120 (ttt180) REVERT: F 100 ASN cc_start: 0.8542 (t0) cc_final: 0.8254 (t0) REVERT: J 10 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6653 (tm-30) REVERT: J 36 TRP cc_start: 0.9152 (m100) cc_final: 0.8825 (m100) REVERT: J 52 ASN cc_start: 0.8233 (t0) cc_final: 0.7569 (t0) REVERT: J 80 MET cc_start: 0.8511 (tmm) cc_final: 0.8193 (tmm) REVERT: J 100 TYR cc_start: 0.7501 (m-10) cc_final: 0.7169 (m-10) outliers start: 61 outliers final: 49 residues processed: 249 average time/residue: 0.3929 time to fit residues: 165.1530 Evaluate side-chains 251 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 164 optimal weight: 0.1980 chunk 240 optimal weight: 5.9990 chunk 363 optimal weight: 0.0970 chunk 334 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27211 Z= 0.369 Angle : 0.659 12.281 37317 Z= 0.335 Chirality : 0.050 0.659 4481 Planarity : 0.004 0.051 4810 Dihedral : 8.285 72.272 5288 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.91 % Allowed : 14.05 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3610 helix: 0.34 (0.21), residues: 633 sheet: -0.82 (0.16), residues: 932 loop : -1.17 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 50 HIS 0.004 0.001 HIS A 519 PHE 0.018 0.002 PHE C 92 TYR 0.034 0.002 TYR L 32 ARG 0.006 0.000 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 3.008 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7724 (m-80) cc_final: 0.7474 (t80) REVERT: A 987 PRO cc_start: 0.8773 (Cg_exo) cc_final: 0.8568 (Cg_endo) REVERT: C 351 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.8051 (t80) REVERT: C 565 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6258 (t80) REVERT: F 30 THR cc_start: 0.9027 (p) cc_final: 0.8645 (p) REVERT: F 54 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8740 (m) REVERT: F 74 SER cc_start: 0.9018 (t) cc_final: 0.8809 (p) REVERT: F 80 MET cc_start: 0.8544 (tmm) cc_final: 0.8089 (tmm) REVERT: F 94 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8059 (ttt180) REVERT: F 100 ASN cc_start: 0.8557 (t0) cc_final: 0.8266 (t0) REVERT: H 52 ASN cc_start: 0.8120 (t0) cc_final: 0.7797 (t0) REVERT: J 10 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6688 (tm-30) REVERT: J 36 TRP cc_start: 0.9182 (m100) cc_final: 0.8903 (m100) REVERT: J 52 ASN cc_start: 0.8277 (t0) cc_final: 0.7248 (p0) REVERT: J 74 SER cc_start: 0.9099 (t) cc_final: 0.8831 (p) REVERT: J 80 MET cc_start: 0.8546 (tmm) cc_final: 0.8218 (tmm) REVERT: J 100 TYR cc_start: 0.7726 (m-10) cc_final: 0.7342 (m-10) REVERT: L 36 TYR cc_start: 0.8635 (m-80) cc_final: 0.8414 (m-10) outliers start: 64 outliers final: 51 residues processed: 245 average time/residue: 0.3467 time to fit residues: 141.1739 Evaluate side-chains 241 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain L residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 2.9990 chunk 230 optimal weight: 0.4980 chunk 308 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 266 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 297 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074504 restraints weight = 75447.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075979 restraints weight = 41909.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076972 restraints weight = 28185.131| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27211 Z= 0.182 Angle : 0.585 14.156 37317 Z= 0.295 Chirality : 0.047 0.527 4481 Planarity : 0.004 0.051 4810 Dihedral : 7.853 70.109 5288 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 2.46 % Allowed : 14.60 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3610 helix: 0.43 (0.21), residues: 642 sheet: -0.71 (0.17), residues: 917 loop : -1.13 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 50 HIS 0.003 0.001 HIS A 519 PHE 0.015 0.001 PHE A 565 TYR 0.025 0.001 TYR L 32 ARG 0.006 0.000 ARG F 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4570.55 seconds wall clock time: 84 minutes 47.45 seconds (5087.45 seconds total)