Starting phenix.real_space_refine on Mon Mar 18 23:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdl_22826/03_2024/7kdl_22826.pdb" } resolution = 2.96 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= -0.001 sd= 0.059 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 96 5.16 5 C 14244 2.51 5 N 3683 2.21 5 O 4342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 12, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 11.92, per 1000 atoms: 0.53 Number of scatterers: 22365 At special positions: 0 Unit cell: (137.54, 129.076, 177.744, 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 96 16.00 O 4342 8.00 N 3683 7.00 C 14244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 4.1 seconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 43 sheets defined 28.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.927A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.558A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.712A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.767A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.695A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.354A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.650A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.678A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.579A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.611A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.123A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.349A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.709A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.526A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.529A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.668A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.354A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.052A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.476A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.221A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.928A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.772A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 5.968A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.610A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.504A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.645A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.659A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.899A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.706A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.882A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.584A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.786A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.288A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.703A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.729A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.873A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.365A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.347A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.541A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.541A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.908A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.019A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.620A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.487A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.158A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.605A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.480A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.815A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.006A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.503A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.657A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.909A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.322A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.688A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2754 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: 10.00 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5239 1.33 - 1.45: 4655 1.45 - 1.57: 12799 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22813 Sorted by residual: bond pdb=" CA GLN B 607 " pdb=" CB GLN B 607 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.48e-02 4.57e+03 1.65e+01 bond pdb=" C5 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C5 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 22808 not shown) Histogram of bond angle deviations from ideal: 96.48 - 104.24: 304 104.24 - 112.00: 9974 112.00 - 119.76: 9447 119.76 - 127.51: 11231 127.51 - 135.27: 136 Bond angle restraints: 31092 Sorted by residual: angle pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA PHE A 106 " pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.11 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 117.88 -5.28 1.00e+00 1.00e+00 2.78e+01 ... (remaining 31087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13411 17.67 - 35.34: 705 35.34 - 53.00: 112 53.00 - 70.67: 44 70.67 - 88.34: 22 Dihedral angle restraints: 14294 sinusoidal: 5953 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 177.48 -84.48 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 14291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 3820 0.382 - 0.763: 1 0.763 - 1.145: 0 1.145 - 1.526: 0 1.526 - 1.908: 1 Chirality restraints: 3822 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.10e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.57e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 ... (remaining 3819 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.230 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" CG ASN A 331 " -0.153 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.431 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.138 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C1074 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.129 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" CG ASN A 657 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.209 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.163 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 1 2.16 - 2.85: 6296 2.85 - 3.53: 29937 3.53 - 4.22: 53000 4.22 - 4.90: 91810 Nonbonded interactions: 181044 Sorted by model distance: nonbonded pdb=" OD1 ASN B 343 " pdb=" C1 NAG B1307 " model vdw 1.479 2.776 nonbonded pdb=" OD1 ASN B 343 " pdb=" O5 NAG B1307 " model vdw 2.339 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.493 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.498 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.500 2.440 ... (remaining 181039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 13 \ 10)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and ( \ name N or name CA or name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 131 \ 0)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.830 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.350 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.210 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.014 0.074 22813 Z= 0.892 Angle : 1.758 9.146 31092 Z= 1.175 Chirality : 0.099 1.908 3822 Planarity : 0.012 0.119 3929 Dihedral : 11.913 88.338 8791 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 0.27 % Allowed : 1.11 % Favored : 98.63 % Cbeta Deviations : 0.07 % 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: -0.99 (0.14), residues: 2797 helix: -0.68 (0.16), residues: 679 sheet: 0.12 (0.23), residues: 449 loop : -0.84 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.023 TRP C 886 HIS 0.013 0.003 HIS B1048 PHE 0.110 0.013 PHE A 718 TYR 0.146 0.020 TYR C 265 ARG 0.012 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 321 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7987 (p0) cc_final: 0.7724 (p0) REVERT: A 564 GLN cc_start: 0.6015 (tp40) cc_final: 0.5813 (tp40) REVERT: C 514 SER cc_start: 0.8732 (t) cc_final: 0.8426 (p) outliers start: 6 outliers final: 1 residues processed: 326 average time/residue: 0.9493 time to fit residues: 368.3019 Evaluate side-chains 156 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN A 360 ASN A 394 ASN A 460 ASN A 613 GLN A1010 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 606 ASN B 907 ASN B1010 GLN B1088 HIS C 394 ASN C 965 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22813 Z= 0.215 Angle : 0.651 10.271 31092 Z= 0.341 Chirality : 0.046 0.228 3822 Planarity : 0.004 0.042 3929 Dihedral : 6.192 53.775 4265 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.53 % Allowed : 6.87 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 2797 helix: 0.88 (0.19), residues: 670 sheet: -0.03 (0.19), residues: 629 loop : -0.70 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.012 0.001 HIS A 207 PHE 0.024 0.002 PHE B 238 TYR 0.026 0.002 TYR C 265 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 183 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: A 428 ASP cc_start: 0.8157 (p0) cc_final: 0.7904 (p0) REVERT: A 988 GLU cc_start: 0.6939 (pm20) cc_final: 0.6664 (pm20) REVERT: C 517 LEU cc_start: 0.6656 (mm) cc_final: 0.6377 (mt) outliers start: 57 outliers final: 11 residues processed: 223 average time/residue: 0.9797 time to fit residues: 261.3612 Evaluate side-chains 144 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 258 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 317 ASN A 360 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN B 907 ASN B1048 HIS C 394 ASN C 965 GLN C1048 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22813 Z= 0.257 Angle : 0.587 9.851 31092 Z= 0.307 Chirality : 0.046 0.531 3822 Planarity : 0.004 0.036 3929 Dihedral : 5.696 52.239 4265 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.08 % Allowed : 9.17 % Favored : 88.75 % 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: -0.16 (0.15), residues: 2797 helix: 1.26 (0.20), residues: 659 sheet: -0.14 (0.19), residues: 655 loop : -0.68 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.012 0.001 HIS A 207 PHE 0.024 0.002 PHE B 168 TYR 0.023 0.002 TYR C1067 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8141 (p0) cc_final: 0.7884 (p0) REVERT: A 776 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8264 (ttpt) REVERT: B 740 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7587 (ttt) REVERT: B 776 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8209 (ttpt) REVERT: C 517 LEU cc_start: 0.6757 (mm) cc_final: 0.6449 (mt) REVERT: C 574 ASP cc_start: 0.7490 (t70) cc_final: 0.7258 (t0) REVERT: C 784 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7539 (mt0) outliers start: 47 outliers final: 23 residues processed: 174 average time/residue: 0.9968 time to fit residues: 207.2077 Evaluate side-chains 153 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 chunk 174 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 907 ASN A 913 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 804 GLN B 935 GLN C 394 ASN C 690 GLN C 804 GLN C 935 GLN C 955 ASN C 965 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22813 Z= 0.379 Angle : 0.620 8.435 31092 Z= 0.321 Chirality : 0.047 0.309 3822 Planarity : 0.004 0.039 3929 Dihedral : 5.598 51.505 4265 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.70 % Allowed : 11.39 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2797 helix: 1.10 (0.20), residues: 662 sheet: -0.28 (0.19), residues: 671 loop : -0.70 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 64 HIS 0.012 0.001 HIS A 207 PHE 0.025 0.002 PHE B 168 TYR 0.025 0.002 TYR C1067 ARG 0.010 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8153 (p0) cc_final: 0.7888 (p0) REVERT: A 776 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: B 319 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7197 (mtp180) REVERT: B 740 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: B 776 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8214 (ttpt) REVERT: C 424 LYS cc_start: 0.7717 (tttp) cc_final: 0.7460 (ttpp) REVERT: C 428 ASP cc_start: 0.7999 (p0) cc_final: 0.7691 (p0) REVERT: C 574 ASP cc_start: 0.7545 (t70) cc_final: 0.7253 (t0) REVERT: C 784 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7495 (mt0) outliers start: 61 outliers final: 32 residues processed: 186 average time/residue: 0.9187 time to fit residues: 207.0174 Evaluate side-chains 165 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.0970 chunk 156 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 235 optimal weight: 0.0270 chunk 191 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1088 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN C 317 ASN C 394 ASN C 965 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22813 Z= 0.150 Angle : 0.525 8.800 31092 Z= 0.272 Chirality : 0.043 0.222 3822 Planarity : 0.003 0.041 3929 Dihedral : 5.162 49.589 4265 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.68 % Allowed : 12.94 % Favored : 85.38 % 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 (0.16), residues: 2797 helix: 1.51 (0.20), residues: 663 sheet: -0.22 (0.19), residues: 646 loop : -0.56 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.011 0.001 HIS A 207 PHE 0.030 0.001 PHE B 168 TYR 0.024 0.001 TYR A 508 ARG 0.010 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 428 ASP cc_start: 0.8146 (p0) cc_final: 0.7897 (p0) REVERT: B 319 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7144 (mtp180) REVERT: B 560 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 740 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7567 (ttt) REVERT: C 424 LYS cc_start: 0.7691 (tttp) cc_final: 0.7434 (ttmp) REVERT: C 428 ASP cc_start: 0.7886 (p0) cc_final: 0.7580 (p0) REVERT: C 574 ASP cc_start: 0.7372 (t70) cc_final: 0.7106 (t0) outliers start: 38 outliers final: 18 residues processed: 173 average time/residue: 0.9641 time to fit residues: 200.5080 Evaluate side-chains 147 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 907 ASN B1002 GLN C 394 ASN C 965 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22813 Z= 0.170 Angle : 0.514 8.089 31092 Z= 0.266 Chirality : 0.043 0.230 3822 Planarity : 0.003 0.043 3929 Dihedral : 4.928 48.740 4265 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 13.34 % Favored : 84.94 % 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: 0.09 (0.16), residues: 2797 helix: 1.61 (0.20), residues: 667 sheet: -0.21 (0.19), residues: 664 loop : -0.48 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.011 0.001 HIS A 207 PHE 0.028 0.001 PHE C 168 TYR 0.021 0.001 TYR A 380 ARG 0.012 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 428 ASP cc_start: 0.8101 (p0) cc_final: 0.7870 (p0) REVERT: B 54 LEU cc_start: 0.8323 (mt) cc_final: 0.8025 (mp) REVERT: B 560 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7967 (mm) REVERT: C 424 LYS cc_start: 0.7653 (tttp) cc_final: 0.7446 (ttmp) REVERT: C 428 ASP cc_start: 0.7890 (p0) cc_final: 0.7595 (p0) REVERT: C 574 ASP cc_start: 0.7352 (t70) cc_final: 0.7060 (t0) outliers start: 39 outliers final: 18 residues processed: 161 average time/residue: 0.8886 time to fit residues: 175.1308 Evaluate side-chains 139 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 275 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN B1002 GLN C 188 ASN C 394 ASN C 965 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22813 Z= 0.217 Angle : 0.528 9.883 31092 Z= 0.271 Chirality : 0.043 0.231 3822 Planarity : 0.003 0.043 3929 Dihedral : 4.824 47.714 4265 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.64 % Allowed : 13.78 % Favored : 84.58 % 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 (0.16), residues: 2797 helix: 1.61 (0.20), residues: 666 sheet: -0.19 (0.19), residues: 666 loop : -0.50 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.011 0.001 HIS A 207 PHE 0.026 0.001 PHE B 168 TYR 0.021 0.001 TYR B 170 ARG 0.010 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 428 ASP cc_start: 0.8077 (p0) cc_final: 0.7845 (p0) REVERT: A 988 GLU cc_start: 0.6554 (pm20) cc_final: 0.6280 (pt0) REVERT: B 54 LEU cc_start: 0.8395 (mt) cc_final: 0.8081 (mp) REVERT: B 560 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8001 (mm) REVERT: C 424 LYS cc_start: 0.7661 (tttp) cc_final: 0.7452 (ttmp) REVERT: C 428 ASP cc_start: 0.7921 (p0) cc_final: 0.7677 (p0) REVERT: C 574 ASP cc_start: 0.7354 (t70) cc_final: 0.7048 (t0) REVERT: C 900 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7350 (mtp) outliers start: 37 outliers final: 19 residues processed: 154 average time/residue: 0.9063 time to fit residues: 170.2792 Evaluate side-chains 151 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 394 ASN C 965 GLN C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22813 Z= 0.174 Angle : 0.512 10.308 31092 Z= 0.263 Chirality : 0.043 0.237 3822 Planarity : 0.003 0.043 3929 Dihedral : 4.693 47.920 4264 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.60 % Allowed : 14.09 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2797 helix: 1.75 (0.20), residues: 659 sheet: -0.15 (0.19), residues: 666 loop : -0.46 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.011 0.001 HIS A 207 PHE 0.022 0.001 PHE B 192 TYR 0.024 0.001 TYR A 380 ARG 0.009 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8052 (p0) cc_final: 0.7850 (p0) REVERT: A 988 GLU cc_start: 0.6544 (pm20) cc_final: 0.6272 (pt0) REVERT: B 54 LEU cc_start: 0.8308 (mt) cc_final: 0.8019 (mp) REVERT: B 560 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7957 (mm) REVERT: C 424 LYS cc_start: 0.7591 (tttp) cc_final: 0.7376 (ttmp) REVERT: C 428 ASP cc_start: 0.7912 (p0) cc_final: 0.7668 (p0) REVERT: C 574 ASP cc_start: 0.7322 (t70) cc_final: 0.7014 (t0) outliers start: 36 outliers final: 18 residues processed: 159 average time/residue: 0.8647 time to fit residues: 169.4189 Evaluate side-chains 142 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.5980 chunk 264 optimal weight: 0.4980 chunk 240 optimal weight: 0.7980 chunk 256 optimal weight: 0.7980 chunk 154 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN B1002 GLN C 394 ASN C 613 GLN C 965 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 22813 Z= 0.160 Angle : 0.524 14.855 31092 Z= 0.269 Chirality : 0.043 0.319 3822 Planarity : 0.003 0.044 3929 Dihedral : 4.686 50.615 4264 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.42 % Allowed : 14.62 % Favored : 83.96 % 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: 0.25 (0.16), residues: 2797 helix: 1.80 (0.20), residues: 662 sheet: -0.13 (0.20), residues: 635 loop : -0.39 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.011 0.001 HIS A 207 PHE 0.028 0.001 PHE B 168 TYR 0.022 0.001 TYR B 170 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8007 (p0) cc_final: 0.7676 (p0) REVERT: B 54 LEU cc_start: 0.8333 (mt) cc_final: 0.8034 (mp) REVERT: B 560 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 424 LYS cc_start: 0.7582 (tttp) cc_final: 0.7372 (ttmp) REVERT: C 428 ASP cc_start: 0.7899 (p0) cc_final: 0.7665 (p0) REVERT: C 574 ASP cc_start: 0.7270 (t70) cc_final: 0.6950 (t0) outliers start: 32 outliers final: 19 residues processed: 158 average time/residue: 0.8966 time to fit residues: 173.2370 Evaluate side-chains 142 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 188 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 262 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 690 GLN B 907 ASN B1002 GLN C 394 ASN C 613 GLN C 804 GLN C 935 GLN C 965 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22813 Z= 0.165 Angle : 0.518 12.365 31092 Z= 0.266 Chirality : 0.043 0.274 3822 Planarity : 0.003 0.043 3929 Dihedral : 4.644 59.727 4264 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.11 % Allowed : 15.20 % Favored : 83.70 % 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: 0.30 (0.16), residues: 2797 helix: 1.86 (0.21), residues: 659 sheet: -0.10 (0.20), residues: 637 loop : -0.38 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.011 0.001 HIS A 207 PHE 0.027 0.001 PHE C 238 TYR 0.023 0.001 TYR A 380 ARG 0.011 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8381 (mt) cc_final: 0.8137 (mp) REVERT: B 560 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7924 (mm) REVERT: C 424 LYS cc_start: 0.7594 (tttp) cc_final: 0.7299 (ttpp) REVERT: C 428 ASP cc_start: 0.7897 (p0) cc_final: 0.7661 (p0) REVERT: C 574 ASP cc_start: 0.7250 (t70) cc_final: 0.6912 (t0) outliers start: 25 outliers final: 15 residues processed: 156 average time/residue: 0.9009 time to fit residues: 171.8468 Evaluate side-chains 138 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 0.0670 chunk 241 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN C 804 GLN C 935 GLN C 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.148130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.105998 restraints weight = 34750.207| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.96 r_work: 0.3480 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22813 Z= 0.198 Angle : 0.526 12.222 31092 Z= 0.270 Chirality : 0.043 0.299 3822 Planarity : 0.003 0.044 3929 Dihedral : 4.537 47.404 4264 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 15.20 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2797 helix: 1.82 (0.20), residues: 659 sheet: -0.08 (0.20), residues: 634 loop : -0.37 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.011 0.001 HIS A 207 PHE 0.025 0.001 PHE C 238 TYR 0.021 0.001 TYR A 380 ARG 0.010 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.28 seconds wall clock time: 99 minutes 36.83 seconds (5976.83 seconds total)