Starting phenix.real_space_refine on Wed Mar 20 07:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb4_0402/03_2024/6nb4_0402.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb4_0402/03_2024/6nb4_0402.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/6nb4_0402/03_2024/6nb4_0402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb4_0402/03_2024/6nb4_0402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb4_0402/03_2024/6nb4_0402.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nb4_0402/03_2024/6nb4_0402.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= 0.057 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 133 5.16 5 C 16832 2.51 5 N 4285 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 911": "OD1" <-> "OD2" Residue "B TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 633": "OD1" <-> "OD2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 805": "OD1" <-> "OD2" Residue "C PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 875": "OE1" <-> "OE2" Residue "C PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26681 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "B" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7402 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 45, 'TRANS': 912} Chain breaks: 5 Chain: "C" Number of atoms: 7404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7404 Classifications: {'peptide': 959} Link IDs: {'PTRANS': 45, 'TRANS': 913} Chain breaks: 5 Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 738 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 91 Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 607 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.69, per 1000 atoms: 0.59 Number of scatterers: 26681 At special positions: 0 Unit cell: (152.07, 146.59, 187.69, 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 133 16.00 O 5431 8.00 N 4285 7.00 C 16832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.05 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.10 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.07 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.07 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.08 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.20 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.06 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.11 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.15 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.12 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.09 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.05 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.04 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.07 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.04 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA R 3 " - " MAN R 5 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 5 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " NAG-ASN " NAG A1401 " - " ASN A 66 " " NAG A1418 " - " ASN A 236 " " NAG A1423 " - " ASN A 487 " " NAG A1424 " - " ASN A 592 " " NAG B1433 " - " ASN B 774 " " NAG C1412 " - " ASN C 166 " " NAG C1416 " - " ASN C 236 " " NAG C1419 " - " ASN C 592 " " NAG C1424 " - " ASN C 774 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 155 " " NAG G 1 " - " ASN A 166 " " NAG I 1 " - " ASN A 222 " " NAG J 1 " - " ASN A 244 " " NAG K 1 " - " ASN A 410 " " NAG M 1 " - " ASN A 619 " " NAG N 1 " - " ASN A 719 " " NAG O 1 " - " ASN A 774 " " NAG P 1 " - " ASN A 785 " " NAG Q 1 " - " ASN A 870 " " NAG R 1 " - " ASN A1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 155 " " NAG W 1 " - " ASN B 166 " " NAG X 1 " - " ASN B 222 " " NAG Y 1 " - " ASN B 236 " " NAG Z 1 " - " ASN B 244 " " NAG a 1 " - " ASN B 592 " " NAG b 1 " - " ASN B 619 " " NAG c 1 " - " ASN B 719 " " NAG d 1 " - " ASN B 785 " " NAG e 1 " - " ASN B 870 " " NAG f 1 " - " ASN B1213 " " NAG g 1 " - " ASN C 66 " " NAG h 1 " - " ASN C 104 " " NAG i 1 " - " ASN C 125 " " NAG j 1 " - " ASN C 155 " " NAG k 1 " - " ASN C 222 " " NAG l 1 " - " ASN C 244 " " NAG m 1 " - " ASN C 619 " " NAG n 1 " - " ASN C 719 " " NAG o 1 " - " ASN C 785 " " NAG p 1 " - " ASN C 870 " " NAG q 1 " - " ASN C1213 " Time building additional restraints: 14.12 Conformation dependent library (CDL) restraints added in 6.3 seconds 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 59 sheets defined 23.9% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.937A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.528A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.676A pdb=" N ALA A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.312A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 5.087A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.195A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 954 through 959 removed outlier: 3.985A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 3.940A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.536A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.989A pdb=" N LEU C 820 " --> pdb=" O LYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.845A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.619A pdb=" N GLY C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 removed outlier: 4.059A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.067A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 3.524A pdb=" N ASP C1064 " --> pdb=" O PRO C1060 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.318A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.006A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.653A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.679A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.637A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.807A pdb=" N SER A 215 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.554A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.136A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.999A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 removed outlier: 5.999A pdb=" N CYS A 407 " --> pdb=" O CYS A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.504A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.529A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.695A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 4.616A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 796 removed outlier: 3.601A pdb=" N ASN A 785 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 5.608A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.181A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.061A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.469A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.637A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.605A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.558A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.243A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.393A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.532A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.795A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.914A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AE4, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.128A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.116A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.316A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE8, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.647A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AF1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.745A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.696A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.189A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.541A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.412A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AF8, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.049A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.666A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.516A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2802 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: 13.33 Time building geometry restraints manager: 15.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5115 1.32 - 1.45: 7667 1.45 - 1.58: 14305 1.58 - 1.71: 11 1.71 - 1.84: 175 Bond restraints: 27273 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG A1423 " pdb=" O5 NAG A1423 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 ... (remaining 27268 not shown) Histogram of bond angle deviations from ideal: 90.45 - 100.14: 9 100.14 - 109.83: 5351 109.83 - 119.52: 17162 119.52 - 129.20: 14500 129.20 - 138.89: 99 Bond angle restraints: 37121 Sorted by residual: angle pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta sigma weight residual 111.29 135.81 -24.52 1.64e+00 3.72e-01 2.24e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.89 -28.47 1.99e+00 2.53e-01 2.05e+02 angle pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta sigma weight residual 110.79 129.97 -19.18 1.66e+00 3.63e-01 1.34e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 127.08 -16.80 1.48e+00 4.57e-01 1.29e+02 angle pdb=" N TYR C 905 " pdb=" CA TYR C 905 " pdb=" C TYR C 905 " ideal model delta sigma weight residual 110.80 90.45 20.35 2.13e+00 2.20e-01 9.13e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 16884 21.85 - 43.70: 475 43.70 - 65.55: 102 65.55 - 87.40: 93 87.40 - 109.24: 47 Dihedral angle restraints: 17601 sinusoidal: 7994 harmonic: 9607 Sorted by residual: dihedral pdb=" C LEU A 450 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual -122.60 -159.37 36.77 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C VAL B 711 " pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual -122.00 -158.60 36.60 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " ideal model delta harmonic sigma weight residual 122.80 154.44 -31.64 0 2.50e+00 1.60e-01 1.60e+02 ... (remaining 17598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4432 0.305 - 0.610: 22 0.610 - 0.915: 1 0.915 - 1.220: 0 1.220 - 1.525: 2 Chirality restraints: 4457 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" CA LEU A 450 " pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CB LEU A 450 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.12e+01 ... (remaining 4454 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 2 " -0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG q 2 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG q 2 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG q 2 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG q 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.033 2.00e-02 2.50e+03 3.48e-02 1.52e+01 pdb=" CG ASN B 166 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.035 2.00e-02 2.50e+03 2.84e-02 1.01e+01 pdb=" C7 NAG R 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.045 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 110 2.57 - 3.15: 21986 3.15 - 3.73: 39357 3.73 - 4.32: 57613 4.32 - 4.90: 91153 Nonbonded interactions: 210219 Sorted by model distance: nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 1.986 3.440 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.249 2.440 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.284 2.520 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.295 2.440 nonbonded pdb=" OG SER A 328 " pdb=" OD1 ASP A 330 " model vdw 2.374 2.440 ... (remaining 210214 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 'B' and (resid 18 through 378 or resid 591 through 1222 or resid 1433)) selection = (chain 'C' and (resid 18 through 378 or resid 591 through 1222 or resid 1412)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'R' selection = chain 'W' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'X' selection = chain 'f' } ncs_group { reference = chain 'Y' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 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: 0.000 Extract box with map and model: 16.750 Check model and map are aligned: 0.400 Set scattering table: 0.320 Process input model: 80.460 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.600 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.016 0.141 27273 Z= 1.038 Angle : 1.336 28.470 37121 Z= 0.855 Chirality : 0.089 1.525 4457 Planarity : 0.006 0.057 4677 Dihedral : 13.877 109.244 11344 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.13 % Rotamer: Outliers : 0.45 % Allowed : 1.35 % Favored : 98.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3277 helix: 0.40 (0.19), residues: 677 sheet: 0.49 (0.18), residues: 711 loop : -0.23 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP C1184 HIS 0.007 0.001 HIS C1138 PHE 0.024 0.004 PHE C 313 TYR 0.042 0.006 TYR A 77 ARG 0.006 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 624 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7564 (ttp) cc_final: 0.7303 (ttp) REVERT: A 148 MET cc_start: 0.7854 (ttm) cc_final: 0.7484 (mtp) REVERT: A 225 LEU cc_start: 0.6792 (tp) cc_final: 0.6460 (tt) REVERT: A 231 TYR cc_start: 0.6438 (m-80) cc_final: 0.6211 (m-80) REVERT: A 290 ILE cc_start: 0.8228 (mt) cc_final: 0.7910 (mm) REVERT: A 469 TYR cc_start: 0.7951 (t80) cc_final: 0.7706 (t80) REVERT: A 473 PHE cc_start: 0.7428 (p90) cc_final: 0.7151 (p90) REVERT: A 491 ILE cc_start: 0.7187 (tt) cc_final: 0.6962 (pt) REVERT: B 199 ASN cc_start: 0.5801 (m-40) cc_final: 0.5426 (p0) REVERT: B 674 PHE cc_start: 0.7919 (m-80) cc_final: 0.7642 (m-80) REVERT: B 686 MET cc_start: 0.7533 (mmm) cc_final: 0.6933 (tpp) REVERT: B 724 VAL cc_start: 0.7658 (p) cc_final: 0.6990 (p) REVERT: B 798 THR cc_start: 0.8171 (p) cc_final: 0.7075 (p) REVERT: B 938 LEU cc_start: 0.8173 (tt) cc_final: 0.7609 (tt) REVERT: B 1043 THR cc_start: 0.8321 (m) cc_final: 0.7994 (p) REVERT: B 1054 ILE cc_start: 0.8377 (pt) cc_final: 0.8083 (mt) REVERT: C 677 VAL cc_start: 0.8909 (t) cc_final: 0.8683 (m) REVERT: C 807 LYS cc_start: 0.8577 (tttt) cc_final: 0.8002 (tppt) REVERT: C 913 MET cc_start: 0.6064 (mtm) cc_final: 0.5830 (mtp) REVERT: C 961 THR cc_start: 0.5897 (p) cc_final: 0.5572 (p) outliers start: 12 outliers final: 0 residues processed: 633 average time/residue: 0.3811 time to fit residues: 375.2217 Evaluate side-chains 251 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 257 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 297 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 258 GLN A1009 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 ASN B1056 GLN B1066 GLN B1129 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN C 927 GLN C1042 ASN C1085 GLN C1129 ASN C1169 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27273 Z= 0.251 Angle : 0.668 7.935 37121 Z= 0.349 Chirality : 0.046 0.278 4457 Planarity : 0.005 0.059 4677 Dihedral : 10.414 83.714 5901 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 8.18 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3277 helix: 1.67 (0.20), residues: 675 sheet: 0.48 (0.18), residues: 734 loop : -0.39 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 310 HIS 0.011 0.001 HIS B 208 PHE 0.024 0.002 PHE B 254 TYR 0.020 0.002 TYR A 77 ARG 0.010 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 288 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.8010 (ttm) cc_final: 0.7761 (ttm) REVERT: A 473 PHE cc_start: 0.7422 (p90) cc_final: 0.7161 (p90) REVERT: A 812 ASN cc_start: 0.7550 (t0) cc_final: 0.6961 (t0) REVERT: B 686 MET cc_start: 0.7452 (mmm) cc_final: 0.7071 (tpp) REVERT: B 1008 MET cc_start: 0.6951 (mtp) cc_final: 0.6664 (mtp) REVERT: C 84 MET cc_start: 0.6928 (pmm) cc_final: 0.6657 (pmm) REVERT: C 147 PHE cc_start: 0.8005 (m-80) cc_final: 0.7545 (m-10) REVERT: C 317 LYS cc_start: 0.8638 (mmmt) cc_final: 0.7990 (mttt) outliers start: 66 outliers final: 45 residues processed: 342 average time/residue: 0.3453 time to fit residues: 192.8169 Evaluate side-chains 252 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain L residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 chunk 322 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 295 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 927 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 769 GLN C 812 ASN C1042 ASN C1138 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 27273 Z= 0.272 Angle : 0.632 12.362 37121 Z= 0.326 Chirality : 0.045 0.270 4457 Planarity : 0.005 0.062 4677 Dihedral : 9.060 77.657 5901 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.95 % Allowed : 9.45 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.14), residues: 3277 helix: 1.67 (0.20), residues: 677 sheet: 0.53 (0.17), residues: 762 loop : -0.54 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.009 0.001 HIS C1138 PHE 0.020 0.002 PHE A 850 TYR 0.018 0.002 TYR H 112 ARG 0.009 0.001 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 234 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.8024 (ttm) cc_final: 0.7783 (ttm) REVERT: A 291 LYS cc_start: 0.7363 (mttt) cc_final: 0.7137 (tmtt) REVERT: A 729 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (pp) REVERT: A 812 ASN cc_start: 0.7511 (t0) cc_final: 0.6962 (t0) REVERT: A 820 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8381 (mp) REVERT: B 261 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 686 MET cc_start: 0.7583 (mmm) cc_final: 0.7270 (tpp) REVERT: B 765 ASN cc_start: 0.6833 (p0) cc_final: 0.6544 (p0) REVERT: C 147 PHE cc_start: 0.7945 (m-80) cc_final: 0.7328 (m-10) REVERT: C 317 LYS cc_start: 0.8658 (mmmt) cc_final: 0.7969 (mttt) REVERT: C 352 GLU cc_start: 0.7480 (pt0) cc_final: 0.7175 (mt-10) REVERT: C 805 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.6686 (p0) outliers start: 79 outliers final: 49 residues processed: 303 average time/residue: 0.3371 time to fit residues: 170.5250 Evaluate side-chains 243 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 191 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1121 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain L residue 33 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 142 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 283 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 346 GLN A 348 HIS A 421 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS A1122 HIS A1145 ASN B 258 GLN B 277 ASN B 348 HIS B 812 ASN B 836 HIS ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS C 618 GLN C 636 GLN C 915 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27273 Z= 0.262 Angle : 0.633 17.480 37121 Z= 0.321 Chirality : 0.045 0.252 4457 Planarity : 0.005 0.060 4677 Dihedral : 7.731 67.942 5901 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 3.14 % Allowed : 10.69 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3277 helix: 1.59 (0.20), residues: 678 sheet: 0.48 (0.18), residues: 726 loop : -0.73 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 117 HIS 0.011 0.001 HIS A1138 PHE 0.022 0.002 PHE C 40 TYR 0.017 0.002 TYR B 184 ARG 0.012 0.001 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 226 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6527 (m-10) cc_final: 0.6202 (m-10) REVERT: A 474 SER cc_start: 0.8207 (p) cc_final: 0.7738 (t) REVERT: A 729 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 812 ASN cc_start: 0.7364 (t0) cc_final: 0.6821 (t0) REVERT: A 820 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 875 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7340 (mp0) REVERT: A 1153 TYR cc_start: 0.7754 (m-80) cc_final: 0.7378 (m-80) REVERT: C 31 ILE cc_start: 0.8033 (mm) cc_final: 0.7751 (tp) REVERT: C 317 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8035 (mttt) REVERT: C 674 PHE cc_start: 0.8385 (m-80) cc_final: 0.8038 (m-80) REVERT: C 805 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7000 (p0) outliers start: 84 outliers final: 59 residues processed: 296 average time/residue: 0.3314 time to fit residues: 164.9030 Evaluate side-chains 253 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 191 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1151 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain B residue 1210 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 0.2980 chunk 179 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 284 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 167 HIS B 258 GLN B 636 GLN B 812 ASN C 708 GLN C1122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27273 Z= 0.352 Angle : 0.678 20.950 37121 Z= 0.344 Chirality : 0.046 0.280 4457 Planarity : 0.005 0.055 4677 Dihedral : 7.540 61.545 5901 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 3.25 % Allowed : 12.11 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3277 helix: 1.37 (0.20), residues: 673 sheet: 0.35 (0.18), residues: 759 loop : -0.92 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 117 HIS 0.013 0.002 HIS A1138 PHE 0.034 0.002 PHE B 239 TYR 0.023 0.002 TYR B 184 ARG 0.007 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 204 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6418 (m-10) cc_final: 0.6093 (m-10) REVERT: A 474 SER cc_start: 0.8245 (p) cc_final: 0.7774 (t) REVERT: A 729 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 812 ASN cc_start: 0.7550 (t0) cc_final: 0.7029 (t0) REVERT: A 820 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 875 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7294 (mp0) REVERT: A 1112 LYS cc_start: 0.8348 (tttm) cc_final: 0.8087 (ttmm) REVERT: B 726 ASP cc_start: 0.7770 (m-30) cc_final: 0.6902 (p0) REVERT: B 807 LYS cc_start: 0.7445 (mttt) cc_final: 0.7139 (mtmm) REVERT: C 31 ILE cc_start: 0.8147 (mm) cc_final: 0.7889 (tp) REVERT: C 805 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.6938 (p0) REVERT: C 938 LEU cc_start: 0.8865 (tp) cc_final: 0.8620 (tp) REVERT: C 964 LEU cc_start: 0.7922 (mm) cc_final: 0.7686 (mp) outliers start: 87 outliers final: 67 residues processed: 280 average time/residue: 0.3393 time to fit residues: 156.9323 Evaluate side-chains 252 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 182 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1024 ASP Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain H residue 62 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 186 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 263 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 812 ASN B1020 GLN B1056 GLN C 91 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27273 Z= 0.224 Angle : 0.606 21.981 37121 Z= 0.305 Chirality : 0.044 0.264 4457 Planarity : 0.004 0.060 4677 Dihedral : 7.021 58.376 5901 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 2.54 % Allowed : 12.71 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3277 helix: 1.61 (0.20), residues: 670 sheet: 0.45 (0.18), residues: 757 loop : -0.92 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 117 HIS 0.008 0.001 HIS B 208 PHE 0.022 0.002 PHE C 40 TYR 0.016 0.001 TYR A1141 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 208 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 729 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 812 ASN cc_start: 0.7549 (t0) cc_final: 0.7035 (t0) REVERT: A 820 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 875 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7250 (mp0) REVERT: B 726 ASP cc_start: 0.7796 (m-30) cc_final: 0.6926 (p0) REVERT: C 147 PHE cc_start: 0.7837 (m-80) cc_final: 0.7506 (m-10) REVERT: C 148 MET cc_start: 0.7963 (ttm) cc_final: 0.7734 (ttm) REVERT: C 240 MET cc_start: 0.8152 (tpp) cc_final: 0.7422 (mmm) REVERT: C 317 LYS cc_start: 0.8682 (mmmt) cc_final: 0.7964 (mttt) REVERT: C 805 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.6963 (p0) REVERT: C 964 LEU cc_start: 0.7774 (mm) cc_final: 0.7470 (mp) REVERT: H 33 TRP cc_start: 0.5676 (m-10) cc_final: 0.4565 (m-10) outliers start: 68 outliers final: 57 residues processed: 264 average time/residue: 0.3428 time to fit residues: 150.3744 Evaluate side-chains 250 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 180 optimal weight: 0.0030 chunk 231 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 316 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 636 GLN B 812 ASN B1085 GLN C 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27273 Z= 0.192 Angle : 0.587 20.907 37121 Z= 0.296 Chirality : 0.043 0.260 4457 Planarity : 0.004 0.059 4677 Dihedral : 6.592 55.560 5901 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.88 % Allowed : 12.89 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.14), residues: 3277 helix: 1.74 (0.21), residues: 672 sheet: 0.46 (0.18), residues: 760 loop : -0.88 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 117 HIS 0.008 0.001 HIS B 208 PHE 0.019 0.001 PHE B 239 TYR 0.016 0.001 TYR A1141 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 203 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 ILE cc_start: 0.8479 (mm) cc_final: 0.8260 (mt) REVERT: A 729 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 812 ASN cc_start: 0.7552 (t0) cc_final: 0.7052 (t0) REVERT: A 820 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 875 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7345 (mp0) REVERT: B 49 ASP cc_start: 0.8221 (t0) cc_final: 0.7237 (p0) REVERT: B 726 ASP cc_start: 0.7798 (m-30) cc_final: 0.6901 (p0) REVERT: B 871 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7958 (pp) REVERT: C 240 MET cc_start: 0.8216 (tpp) cc_final: 0.7522 (mmm) REVERT: C 272 ASP cc_start: 0.6734 (t70) cc_final: 0.6275 (t0) REVERT: C 805 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.6974 (p0) REVERT: C 868 ASP cc_start: 0.6990 (t70) cc_final: 0.6766 (t70) REVERT: H 33 TRP cc_start: 0.5610 (m-10) cc_final: 0.4496 (m-10) outliers start: 77 outliers final: 60 residues processed: 268 average time/residue: 0.3273 time to fit residues: 147.5642 Evaluate side-chains 248 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 184 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27273 Z= 0.220 Angle : 0.595 20.498 37121 Z= 0.300 Chirality : 0.044 0.257 4457 Planarity : 0.004 0.059 4677 Dihedral : 6.396 53.235 5901 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 2.99 % Allowed : 12.74 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3277 helix: 1.77 (0.21), residues: 672 sheet: 0.45 (0.18), residues: 744 loop : -0.90 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 PHE 0.016 0.001 PHE C 147 TYR 0.016 0.001 TYR A1141 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 190 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6745 (m-10) cc_final: 0.6532 (m-10) REVERT: A 729 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8353 (pp) REVERT: A 812 ASN cc_start: 0.7490 (t0) cc_final: 0.7058 (t0) REVERT: A 820 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 875 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7265 (mp0) REVERT: B 726 ASP cc_start: 0.7812 (m-30) cc_final: 0.6916 (p0) REVERT: B 807 LYS cc_start: 0.7500 (mttt) cc_final: 0.7182 (mtmm) REVERT: C 240 MET cc_start: 0.8229 (tpp) cc_final: 0.7634 (mmm) REVERT: C 272 ASP cc_start: 0.6709 (t70) cc_final: 0.6262 (t0) REVERT: C 805 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7035 (p0) REVERT: C 868 ASP cc_start: 0.6627 (t70) cc_final: 0.6418 (t70) REVERT: C 964 LEU cc_start: 0.7740 (mm) cc_final: 0.7539 (mp) REVERT: H 33 TRP cc_start: 0.5482 (m-10) cc_final: 0.4454 (m-10) outliers start: 80 outliers final: 69 residues processed: 256 average time/residue: 0.3381 time to fit residues: 145.7369 Evaluate side-chains 256 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 184 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 266 optimal weight: 0.5980 chunk 278 optimal weight: 0.1980 chunk 293 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN B 636 GLN B 812 ASN C 792 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27273 Z= 0.211 Angle : 0.594 20.364 37121 Z= 0.298 Chirality : 0.043 0.254 4457 Planarity : 0.004 0.058 4677 Dihedral : 6.243 51.268 5901 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.91 % Allowed : 13.19 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3277 helix: 1.70 (0.21), residues: 686 sheet: 0.46 (0.18), residues: 739 loop : -0.88 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 PHE 0.013 0.001 PHE B 266 TYR 0.015 0.001 TYR A1141 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 194 time to evaluate : 2.810 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8749 (tt) cc_final: 0.8543 (tp) REVERT: A 729 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 820 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 875 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7287 (mp0) REVERT: B 726 ASP cc_start: 0.7799 (m-30) cc_final: 0.6908 (p0) REVERT: B 807 LYS cc_start: 0.7500 (mttt) cc_final: 0.7129 (mtmm) REVERT: B 871 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8006 (pp) REVERT: C 147 PHE cc_start: 0.7733 (m-80) cc_final: 0.7328 (m-10) REVERT: C 240 MET cc_start: 0.8228 (tpp) cc_final: 0.7642 (mmm) REVERT: C 272 ASP cc_start: 0.6741 (t70) cc_final: 0.6312 (t0) REVERT: C 805 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7075 (p0) REVERT: C 868 ASP cc_start: 0.6690 (t70) cc_final: 0.6471 (t70) REVERT: C 964 LEU cc_start: 0.7739 (mm) cc_final: 0.7536 (mp) REVERT: H 33 TRP cc_start: 0.5442 (m-10) cc_final: 0.4392 (m-10) outliers start: 78 outliers final: 68 residues processed: 257 average time/residue: 0.3355 time to fit residues: 145.1067 Evaluate side-chains 257 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 185 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 805 ASP Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 300 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 466 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN B 636 GLN B 812 ASN C 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27273 Z= 0.374 Angle : 0.694 20.532 37121 Z= 0.351 Chirality : 0.046 0.263 4457 Planarity : 0.005 0.062 4677 Dihedral : 6.794 59.165 5901 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 2.77 % Allowed : 13.49 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3277 helix: 1.39 (0.20), residues: 676 sheet: 0.24 (0.18), residues: 758 loop : -1.13 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 117 HIS 0.012 0.001 HIS A1138 PHE 0.021 0.002 PHE C 116 TYR 0.017 0.002 TYR C 85 ARG 0.006 0.001 ARG A 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6554 Ramachandran restraints generated. 3277 Oldfield, 0 Emsley, 3277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 188 time to evaluate : 2.850 Fit side-chains REVERT: A 456 LEU cc_start: 0.6617 (mt) cc_final: 0.6281 (mt) REVERT: A 729 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8390 (pp) REVERT: A 820 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 875 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 943 MET cc_start: 0.7396 (ttt) cc_final: 0.7121 (ttt) REVERT: B 672 THR cc_start: 0.8670 (t) cc_final: 0.8042 (p) REVERT: B 726 ASP cc_start: 0.7622 (m-30) cc_final: 0.6843 (p0) REVERT: B 807 LYS cc_start: 0.7549 (mttt) cc_final: 0.7115 (mtmm) REVERT: C 148 MET cc_start: 0.8063 (ttm) cc_final: 0.7808 (ttm) REVERT: C 868 ASP cc_start: 0.6931 (t70) cc_final: 0.6715 (t70) REVERT: C 938 LEU cc_start: 0.8909 (tp) cc_final: 0.8695 (tp) REVERT: C 964 LEU cc_start: 0.7831 (mm) cc_final: 0.7612 (mp) REVERT: H 33 TRP cc_start: 0.5527 (m-10) cc_final: 0.4429 (m-10) outliers start: 74 outliers final: 66 residues processed: 251 average time/residue: 0.3419 time to fit residues: 142.3238 Evaluate side-chains 246 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 178 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 800 GLN Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 986 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 260 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 267 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 466 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN B 636 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124253 restraints weight = 48447.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123600 restraints weight = 43203.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124201 restraints weight = 38049.666| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27273 Z= 0.184 Angle : 0.597 20.903 37121 Z= 0.298 Chirality : 0.043 0.249 4457 Planarity : 0.004 0.063 4677 Dihedral : 6.249 53.265 5901 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.20 % Allowed : 14.28 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3277 helix: 1.84 (0.21), residues: 663 sheet: 0.42 (0.18), residues: 748 loop : -0.99 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 117 HIS 0.007 0.001 HIS B 208 PHE 0.017 0.001 PHE B 977 TYR 0.016 0.001 TYR A1141 ARG 0.006 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.15 seconds wall clock time: 89 minutes 37.04 seconds (5377.04 seconds total)