Starting phenix.real_space_refine on Mon Feb 19 04:50:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ke7_22833/02_2024/7ke7_22833.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.045 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 99 5.16 5 C 15084 2.51 5 N 3852 2.21 5 O 4653 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 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "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 GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "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 TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" 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 PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" 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 GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "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 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "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 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" 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 748": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" 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 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "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 TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "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 GLU 224": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "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 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 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 GLU 465": "OE1" <-> "OE2" Residue "C PHE 490": "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 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" 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 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" 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 ASP 1127": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23688 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.37, per 1000 atoms: 0.52 Number of scatterers: 23688 At special positions: 0 Unit cell: (135.424, 128.018, 168.222, 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 99 16.00 O 4653 8.00 N 3852 7.00 C 15084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 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 A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 657 " " 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 B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 4.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 49 sheets defined 27.8% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.994A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.551A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.745A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.117A 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 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.543A 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 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.040A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.620A 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: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.674A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (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 1143 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.598A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.585A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.609A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.998A 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 966 removed outlier: 3.615A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.768A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.067A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 4.016A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.795A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.534A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.784A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.627A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.432A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.181A 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 918 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 966 removed outlier: 3.770A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (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 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.143A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.659A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.772A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.148A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.452A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.263A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.632A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.744A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 656 removed outlier: 4.477A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.929A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.204A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.232A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.555A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.348A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.968A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.231A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.177A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.615A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.889A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.276A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.697A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.478A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.380A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.410A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.923A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.923A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.507A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.375A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.667A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 1024 hydrogen bonds defined for protein. 2787 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: 10.73 Time building geometry restraints manager: 11.06 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: 6042 1.33 - 1.45: 4770 1.45 - 1.58: 13251 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 24186 Sorted by residual: bond pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 1.518 1.556 -0.038 9.60e-03 1.09e+04 1.60e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24181 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.95: 278 103.95 - 111.77: 10097 111.77 - 119.59: 9999 119.59 - 127.41: 12354 127.41 - 135.23: 158 Bond angle restraints: 32886 Sorted by residual: angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 112.24 122.06 -9.82 1.28e+00 6.10e-01 5.89e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 119.98 -11.02 1.49e+00 4.50e-01 5.47e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 118.32 -9.36 1.49e+00 4.50e-01 3.94e+01 angle pdb=" OD1 ASN C 331 " pdb=" CG ASN C 331 " pdb=" ND2 ASN C 331 " ideal model delta sigma weight residual 122.60 116.64 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" CA PHE A 186 " pdb=" CB PHE A 186 " pdb=" CG PHE A 186 " ideal model delta sigma weight residual 113.80 119.59 -5.79 1.00e+00 1.00e+00 3.35e+01 ... (remaining 32881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14138 17.93 - 35.85: 876 35.85 - 53.78: 123 53.78 - 71.71: 46 71.71 - 89.64: 30 Dihedral angle restraints: 15213 sinusoidal: 6729 harmonic: 8484 Sorted by residual: dihedral pdb=" C ASN A 99 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual -122.60 -150.66 28.06 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CA ASN A 99 " pdb=" CB ASN A 99 " ideal model delta harmonic sigma weight residual 122.80 147.77 -24.97 0 2.50e+00 1.60e-01 9.97e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.81 -88.19 1 1.00e+01 1.00e-02 9.30e+01 ... (remaining 15210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 3865 0.226 - 0.452: 80 0.452 - 0.679: 2 0.679 - 0.905: 0 0.905 - 1.131: 1 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.16e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.43e+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 -2.58 0.18 2.00e-02 2.50e+03 7.89e+01 ... (remaining 3945 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.228 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" CG ASN B 331 " -0.147 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.429 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " 0.214 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" CG ASN C 603 " -0.135 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " -0.410 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.304 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.209 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" CG ASN C 165 " -0.132 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.358 2.00e-02 2.50e+03 pdb=" C1 NAG C1309 " 0.279 2.00e-02 2.50e+03 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11764 2.98 - 3.46: 23722 3.46 - 3.94: 39565 3.94 - 4.42: 44948 4.42 - 4.90: 74448 Nonbonded interactions: 194447 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.502 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.514 2.440 nonbonded pdb=" OE2 GLU C 132 " pdb=" OG1 THR C 167 " model vdw 2.518 2.440 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.530 2.440 nonbonded pdb=" OE2 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.548 2.440 ... (remaining 194442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.400 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 67.300 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 0.078 24186 Z= 0.898 Angle : 1.741 11.018 32886 Z= 1.156 Chirality : 0.100 1.131 3948 Planarity : 0.015 0.276 4155 Dihedral : 12.566 89.635 9627 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.49 % Favored : 92.23 % Rotamer: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Cbeta Deviations : 0.18 % 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: -1.34 (0.14), residues: 2844 helix: -0.68 (0.17), residues: 653 sheet: -0.37 (0.24), residues: 408 loop : -1.11 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.152 0.026 TRP C 886 HIS 0.016 0.004 HIS B 519 PHE 0.073 0.013 PHE B 802 TYR 0.141 0.023 TYR C 741 ARG 0.011 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3717 time to fit residues: 158.2608 Evaluate side-chains 136 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 762 GLN A 914 ASN A 957 GLN B 394 ASN B 914 ASN B1088 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 762 GLN C 856 ASN C 955 ASN C1058 HIS C1088 HIS C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24186 Z= 0.222 Angle : 0.706 11.739 32886 Z= 0.377 Chirality : 0.048 0.451 3948 Planarity : 0.004 0.045 4155 Dihedral : 6.850 58.666 4424 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.29 % Allowed : 5.44 % Favored : 93.26 % 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: -0.64 (0.15), residues: 2844 helix: 0.65 (0.19), residues: 660 sheet: -0.56 (0.20), residues: 577 loop : -0.80 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 436 HIS 0.013 0.001 HIS C 519 PHE 0.021 0.002 PHE C 392 TYR 0.020 0.002 TYR B 505 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5072 (OUTLIER) cc_final: 0.4194 (m-80) REVERT: C 645 THR cc_start: 0.6567 (p) cc_final: 0.6154 (p) outliers start: 33 outliers final: 15 residues processed: 185 average time/residue: 0.3557 time to fit residues: 105.7543 Evaluate side-chains 126 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 901 GLN B 935 GLN B1011 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24186 Z= 0.297 Angle : 0.656 16.005 32886 Z= 0.346 Chirality : 0.046 0.363 3948 Planarity : 0.004 0.049 4155 Dihedral : 6.405 59.428 4424 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.12 % Allowed : 6.66 % Favored : 91.23 % 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: -0.60 (0.15), residues: 2844 helix: 0.78 (0.19), residues: 661 sheet: -0.70 (0.19), residues: 597 loop : -0.73 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 436 HIS 0.009 0.001 HIS C 519 PHE 0.023 0.002 PHE C1089 TYR 0.022 0.002 TYR B1067 ARG 0.005 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.5565 (tpp) cc_final: 0.5352 (mmt) REVERT: B 855 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4556 (m-80) REVERT: C 645 THR cc_start: 0.6500 (p) cc_final: 0.6108 (p) outliers start: 54 outliers final: 35 residues processed: 169 average time/residue: 0.3318 time to fit residues: 91.6723 Evaluate side-chains 147 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 251 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24186 Z= 0.188 Angle : 0.590 12.175 32886 Z= 0.311 Chirality : 0.044 0.320 3948 Planarity : 0.004 0.053 4155 Dihedral : 6.040 57.834 4424 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.12 % Allowed : 7.76 % Favored : 90.13 % 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: -0.47 (0.15), residues: 2844 helix: 1.02 (0.20), residues: 660 sheet: -0.73 (0.19), residues: 631 loop : -0.66 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.008 0.001 HIS C 519 PHE 0.032 0.001 PHE A 392 TYR 0.018 0.001 TYR B 505 ARG 0.008 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.4632 (m-80) outliers start: 54 outliers final: 31 residues processed: 179 average time/residue: 0.3159 time to fit residues: 93.6422 Evaluate side-chains 138 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 252 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 334 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 675 GLN B1058 HIS C 901 GLN C 949 GLN C1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 24186 Z= 0.443 Angle : 0.697 12.126 32886 Z= 0.366 Chirality : 0.047 0.297 3948 Planarity : 0.004 0.050 4155 Dihedral : 6.211 57.801 4424 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.06 % Allowed : 8.85 % Favored : 88.09 % 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: -0.74 (0.15), residues: 2844 helix: 0.67 (0.19), residues: 661 sheet: -0.77 (0.19), residues: 642 loop : -0.83 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 64 HIS 0.007 0.001 HIS C 519 PHE 0.041 0.002 PHE A 392 TYR 0.028 0.002 TYR B1067 ARG 0.005 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 116 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4605 (m-80) outliers start: 78 outliers final: 52 residues processed: 174 average time/residue: 0.3114 time to fit residues: 91.6077 Evaluate side-chains 156 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 103 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 281 optimal weight: 0.6980 chunk 233 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24186 Z= 0.249 Angle : 0.594 12.112 32886 Z= 0.314 Chirality : 0.044 0.271 3948 Planarity : 0.004 0.056 4155 Dihedral : 5.953 59.571 4424 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.35 % Allowed : 10.03 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.15), residues: 2844 helix: 0.84 (0.20), residues: 667 sheet: -0.64 (0.20), residues: 622 loop : -0.83 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.006 0.001 HIS C 519 PHE 0.028 0.001 PHE C 186 TYR 0.025 0.001 TYR A 495 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 121 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.5940 (mt) cc_final: 0.5715 (mp) REVERT: B 855 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4608 (m-80) outliers start: 60 outliers final: 43 residues processed: 165 average time/residue: 0.3179 time to fit residues: 88.9462 Evaluate side-chains 149 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 105 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24186 Z= 0.201 Angle : 0.566 13.400 32886 Z= 0.297 Chirality : 0.044 0.272 3948 Planarity : 0.004 0.054 4155 Dihedral : 5.635 59.943 4424 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.59 % Allowed : 10.11 % Favored : 87.31 % 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: -0.42 (0.15), residues: 2844 helix: 1.07 (0.20), residues: 660 sheet: -0.55 (0.20), residues: 632 loop : -0.71 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS C 519 PHE 0.039 0.001 PHE C 186 TYR 0.025 0.001 TYR A 495 ARG 0.004 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 123 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4662 (m-80) REVERT: C 740 MET cc_start: 0.4989 (tpt) cc_final: 0.4649 (mmt) outliers start: 66 outliers final: 45 residues processed: 174 average time/residue: 0.3245 time to fit residues: 94.1116 Evaluate side-chains 153 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 107 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 24186 Z= 0.431 Angle : 0.673 13.518 32886 Z= 0.353 Chirality : 0.046 0.293 3948 Planarity : 0.004 0.052 4155 Dihedral : 5.857 59.344 4424 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.90 % Allowed : 10.18 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.69 (0.15), residues: 2844 helix: 0.77 (0.19), residues: 667 sheet: -0.68 (0.19), residues: 677 loop : -0.86 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS C 519 PHE 0.031 0.002 PHE A 392 TYR 0.026 0.002 TYR B1067 ARG 0.004 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 107 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: C 740 MET cc_start: 0.5137 (tpt) cc_final: 0.4787 (mmt) outliers start: 74 outliers final: 62 residues processed: 165 average time/residue: 0.3166 time to fit residues: 88.7098 Evaluate side-chains 159 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 96 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24186 Z= 0.191 Angle : 0.574 13.273 32886 Z= 0.302 Chirality : 0.044 0.266 3948 Planarity : 0.004 0.053 4155 Dihedral : 5.542 59.664 4424 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.15 % Allowed : 11.16 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.51 (0.15), residues: 2844 helix: 0.96 (0.20), residues: 672 sheet: -0.53 (0.20), residues: 623 loop : -0.81 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.005 0.001 HIS C 519 PHE 0.028 0.001 PHE A 392 TYR 0.024 0.001 TYR A 495 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5217 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: C 740 MET cc_start: 0.5038 (tpt) cc_final: 0.4721 (mmt) outliers start: 55 outliers final: 45 residues processed: 151 average time/residue: 0.3263 time to fit residues: 80.9239 Evaluate side-chains 150 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24186 Z= 0.252 Angle : 0.582 13.411 32886 Z= 0.305 Chirality : 0.044 0.268 3948 Planarity : 0.004 0.051 4155 Dihedral : 5.477 58.942 4424 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.04 % Allowed : 11.44 % Favored : 86.53 % 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: -0.50 (0.15), residues: 2844 helix: 0.98 (0.20), residues: 666 sheet: -0.59 (0.19), residues: 641 loop : -0.77 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.005 0.001 HIS C 519 PHE 0.026 0.001 PHE A 392 TYR 0.036 0.001 TYR A 495 ARG 0.007 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 855 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: C 740 MET cc_start: 0.5101 (tpt) cc_final: 0.4777 (mmt) outliers start: 52 outliers final: 48 residues processed: 146 average time/residue: 0.3197 time to fit residues: 78.7713 Evaluate side-chains 153 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN B 965 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.091490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062005 restraints weight = 64315.861| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.01 r_work: 0.3010 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24186 Z= 0.398 Angle : 0.659 13.601 32886 Z= 0.344 Chirality : 0.046 0.273 3948 Planarity : 0.004 0.051 4155 Dihedral : 5.722 59.925 4424 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.23 % Allowed : 11.44 % Favored : 86.33 % 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: -0.74 (0.15), residues: 2844 helix: 0.74 (0.19), residues: 664 sheet: -0.81 (0.19), residues: 700 loop : -0.85 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.005 0.001 HIS C 519 PHE 0.026 0.002 PHE B1121 TYR 0.032 0.002 TYR A 495 ARG 0.007 0.001 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.49 seconds wall clock time: 83 minutes 19.89 seconds (4999.89 seconds total)