Starting phenix.real_space_refine on Thu Feb 22 20:00:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/02_2024/7kml_22926.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 156 5.16 5 C 22239 2.51 5 N 5757 2.21 5 O 6984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "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 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "M PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 125": "OE1" <-> "OE2" Residue "N PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35136 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "N" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 18.75, per 1000 atoms: 0.53 Number of scatterers: 35136 At special positions: 0 Unit cell: (147.29, 148.32, 224.54, 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 156 16.00 O 6984 8.00 N 5757 7.00 C 22239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.22 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.22 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 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=2.02 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.22 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.08 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 234 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 234 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 154 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 234 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.04 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 331 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " Time building additional restraints: 15.29 Conformation dependent library (CDL) restraints added in 6.1 seconds 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 78 sheets defined 20.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.774A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (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 885 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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 967 removed outlier: 4.172A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 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 967 removed outlier: 4.172A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (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 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 203 through 207 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'H' and resid 216 through 219 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 143 through 147 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 143 through 147 Processing helix chain 'N' and resid 203 through 207 Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 202 through 206 Processing helix chain 'J' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.241A pdb=" N ILE A 788 " --> pdb=" O ASN B 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: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.411A 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 448 through 454 removed outlier: 7.471A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR B 495 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.241A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.586A 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 removed outlier: 3.652A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR H 37 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR H 57 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AG5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR M 55 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR M 193 " --> pdb=" O ASN M 158 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 173 through 174 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR I 37 " --> pdb=" O TYR I 57 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR I 57 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET I 39 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY I 55 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 166 through 169 Processing sheet with id=AH6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AH7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 55 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR N 193 " --> pdb=" O ASN N 158 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 173 through 174 Processing sheet with id=AI2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'J' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR J 37 " --> pdb=" O TYR J 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR J 57 " --> pdb=" O TYR J 37 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET J 39 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 166 through 169 1481 hydrogen bonds defined for protein. 3897 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: 18.30 Time building geometry restraints manager: 16.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 7113 1.32 - 1.47: 12747 1.47 - 1.61: 15822 1.61 - 1.75: 48 1.75 - 1.89: 186 Bond restraints: 35916 Sorted by residual: bond pdb=" NE ARG B 78 " pdb=" CZ ARG B 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.54e+01 bond pdb=" NE ARG C 78 " pdb=" CZ ARG C 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" CB HIS H 215 " pdb=" CG HIS H 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CB HIS J 215 " pdb=" CG HIS J 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.04e+01 ... (remaining 35911 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.85: 1235 105.85 - 113.55: 18751 113.55 - 121.26: 18813 121.26 - 128.96: 9894 128.96 - 136.66: 174 Bond angle restraints: 48867 Sorted by residual: angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.37e+01 angle pdb=" N LYS C 97 " pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.36e+01 angle pdb=" N LYS B 97 " pdb=" CA LYS B 97 " pdb=" C LYS B 97 " ideal model delta sigma weight residual 114.04 102.06 11.98 1.24e+00 6.50e-01 9.34e+01 angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.82 128.42 -8.60 9.80e-01 1.04e+00 7.71e+01 angle pdb=" C CYS C 336 " pdb=" N PRO C 337 " pdb=" CA PRO C 337 " ideal model delta sigma weight residual 119.82 128.41 -8.59 9.80e-01 1.04e+00 7.69e+01 ... (remaining 48862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 21637 21.26 - 42.52: 527 42.52 - 63.78: 162 63.78 - 85.04: 87 85.04 - 106.30: 39 Dihedral angle restraints: 22452 sinusoidal: 9660 harmonic: 12792 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.09 -89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.10 -89.90 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.11 -89.89 1 1.00e+01 1.00e-02 9.58e+01 ... (remaining 22449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4375 0.110 - 0.219: 1202 0.219 - 0.329: 171 0.329 - 0.438: 11 0.438 - 0.548: 7 Chirality restraints: 5766 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.76e+01 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.64e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 5763 not shown) Planarity restraints: 6249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR L 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR L 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR L 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR L 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR L 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR M 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR M 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR M 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR M 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR M 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR M 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR N 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR N 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR N 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR N 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR N 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 42 " 0.065 2.00e-02 2.50e+03 ... (remaining 6246 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 14504 2.91 - 3.41: 31878 3.41 - 3.91: 61921 3.91 - 4.40: 70570 4.40 - 4.90: 112736 Nonbonded interactions: 291609 Sorted by model distance: nonbonded pdb=" C4 NAG h 1 " pdb=" O5 NAG h 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG Y 1 " pdb=" O5 NAG Y 2 " model vdw 2.415 2.776 nonbonded pdb=" NZ LYS J 221 " pdb=" OD2 ASP J 223 " model vdw 2.416 2.520 nonbonded pdb=" NZ LYS I 221 " pdb=" OD2 ASP I 223 " model vdw 2.416 2.520 ... (remaining 291604 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 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'U' selection = chain 'V' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.260 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 98.170 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.018 0.127 35916 Z= 1.175 Angle : 1.875 12.002 48867 Z= 1.265 Chirality : 0.099 0.548 5766 Planarity : 0.009 0.042 6204 Dihedral : 12.304 106.302 14073 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.39 % Allowed : 0.76 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.45 (0.12), residues: 4353 helix: -0.37 (0.17), residues: 690 sheet: 0.74 (0.14), residues: 1269 loop : 0.40 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.013 TRP A 353 HIS 0.009 0.002 HIS L 108 PHE 0.039 0.007 PHE B 140 TYR 0.074 0.011 TYR B 204 ARG 0.007 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 667 time to evaluate : 4.408 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 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 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 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 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 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: A 175 PHE cc_start: 0.9546 (m-10) cc_final: 0.8998 (m-80) REVERT: A 369 TYR cc_start: 0.9016 (t80) cc_final: 0.8729 (t80) REVERT: A 727 LEU cc_start: 0.9356 (mp) cc_final: 0.9080 (mt) REVERT: A 759 PHE cc_start: 0.8526 (t80) cc_final: 0.7979 (t80) REVERT: A 763 LEU cc_start: 0.9549 (mt) cc_final: 0.8938 (mp) REVERT: A 781 VAL cc_start: 0.9559 (t) cc_final: 0.9279 (m) REVERT: A 826 VAL cc_start: 0.8347 (t) cc_final: 0.8125 (t) REVERT: A 878 LEU cc_start: 0.9490 (mt) cc_final: 0.9254 (mt) REVERT: A 886 TRP cc_start: 0.6804 (p-90) cc_final: 0.6520 (p-90) REVERT: A 919 ASN cc_start: 0.8948 (m-40) cc_final: 0.8533 (t0) REVERT: A 936 ASP cc_start: 0.9241 (m-30) cc_final: 0.8678 (t0) REVERT: A 1014 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8764 (ttm170) REVERT: A 1021 SER cc_start: 0.9672 (m) cc_final: 0.9098 (t) REVERT: A 1052 PHE cc_start: 0.9070 (m-80) cc_final: 0.8768 (m-10) REVERT: A 1125 ASN cc_start: 0.7713 (t0) cc_final: 0.7490 (t0) REVERT: B 175 PHE cc_start: 0.9515 (m-10) cc_final: 0.8978 (m-80) REVERT: B 318 PHE cc_start: 0.8339 (t80) cc_final: 0.8072 (t80) REVERT: B 369 TYR cc_start: 0.9057 (t80) cc_final: 0.8797 (t80) REVERT: B 610 VAL cc_start: 0.9387 (t) cc_final: 0.9126 (p) REVERT: B 727 LEU cc_start: 0.9388 (mp) cc_final: 0.8892 (mt) REVERT: B 759 PHE cc_start: 0.8612 (t80) cc_final: 0.7846 (t80) REVERT: B 763 LEU cc_start: 0.9598 (mt) cc_final: 0.8985 (mp) REVERT: B 781 VAL cc_start: 0.9512 (t) cc_final: 0.9227 (m) REVERT: B 878 LEU cc_start: 0.9513 (mt) cc_final: 0.9270 (mt) REVERT: B 886 TRP cc_start: 0.6832 (p-90) cc_final: 0.6394 (p-90) REVERT: B 919 ASN cc_start: 0.8906 (m-40) cc_final: 0.8519 (t0) REVERT: B 936 ASP cc_start: 0.9228 (m-30) cc_final: 0.8691 (t0) REVERT: B 973 ILE cc_start: 0.8718 (mt) cc_final: 0.8503 (mm) REVERT: B 1014 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8741 (mtm-85) REVERT: B 1040 VAL cc_start: 0.8769 (t) cc_final: 0.8539 (t) REVERT: B 1052 PHE cc_start: 0.9030 (m-80) cc_final: 0.8248 (m-10) REVERT: B 1125 ASN cc_start: 0.7746 (t0) cc_final: 0.7527 (t0) REVERT: C 175 PHE cc_start: 0.9566 (m-10) cc_final: 0.9175 (m-80) REVERT: C 318 PHE cc_start: 0.8307 (t80) cc_final: 0.8005 (t80) REVERT: C 369 TYR cc_start: 0.9055 (t80) cc_final: 0.8801 (t80) REVERT: C 610 VAL cc_start: 0.9336 (t) cc_final: 0.9026 (p) REVERT: C 759 PHE cc_start: 0.8527 (t80) cc_final: 0.7573 (t80) REVERT: C 763 LEU cc_start: 0.9632 (mt) cc_final: 0.9095 (mp) REVERT: C 781 VAL cc_start: 0.9501 (t) cc_final: 0.9231 (m) REVERT: C 826 VAL cc_start: 0.8091 (t) cc_final: 0.7843 (t) REVERT: C 919 ASN cc_start: 0.8846 (m-40) cc_final: 0.8481 (t0) REVERT: C 922 LEU cc_start: 0.9475 (mp) cc_final: 0.9266 (mm) REVERT: C 936 ASP cc_start: 0.9213 (m-30) cc_final: 0.8689 (t0) REVERT: C 1014 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8868 (ttm170) REVERT: C 1021 SER cc_start: 0.9670 (m) cc_final: 0.9109 (t) REVERT: C 1031 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8003 (mt-10) REVERT: C 1125 ASN cc_start: 0.7675 (t0) cc_final: 0.7454 (t0) REVERT: L 4 MET cc_start: 0.7687 (mmm) cc_final: 0.4264 (tpp) REVERT: H 39 MET cc_start: 0.5272 (mmp) cc_final: 0.4907 (mpp) REVERT: M 4 MET cc_start: 0.7317 (mmm) cc_final: 0.3737 (tpp) REVERT: I 39 MET cc_start: 0.5240 (mmp) cc_final: 0.4888 (mpp) REVERT: N 4 MET cc_start: 0.7524 (mmm) cc_final: 0.4431 (tpp) outliers start: 15 outliers final: 10 residues processed: 682 average time/residue: 0.5393 time to fit residues: 562.9376 Evaluate side-chains 344 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 334 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 6.9990 chunk 331 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 343 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 397 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 440 ASN A 501 ASN A 544 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 440 ASN B 501 ASN B 544 ASN B 762 GLN B 965 GLN C 49 HIS C 439 ASN C 440 ASN C 501 ASN C 544 ASN C 762 GLN C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN I 186 GLN J 186 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 35916 Z= 0.307 Angle : 0.785 9.429 48867 Z= 0.419 Chirality : 0.049 0.336 5766 Planarity : 0.005 0.040 6204 Dihedral : 8.738 64.183 6374 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.25 % Allowed : 6.68 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4353 helix: 1.00 (0.19), residues: 696 sheet: 0.40 (0.14), residues: 1326 loop : 0.03 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 353 HIS 0.008 0.001 HIS C1048 PHE 0.025 0.003 PHE B 377 TYR 0.026 0.002 TYR C1110 ARG 0.008 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 360 time to evaluate : 4.431 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8556 (t80) cc_final: 0.8170 (t80) REVERT: A 513 LEU cc_start: 0.9166 (tp) cc_final: 0.8887 (pp) REVERT: A 740 MET cc_start: 0.8439 (mmt) cc_final: 0.7902 (mmt) REVERT: A 759 PHE cc_start: 0.8381 (t80) cc_final: 0.7863 (t80) REVERT: A 902 MET cc_start: 0.9213 (mmm) cc_final: 0.8847 (tpp) REVERT: A 916 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 936 ASP cc_start: 0.9213 (m-30) cc_final: 0.8801 (t0) REVERT: A 1002 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 1021 SER cc_start: 0.9705 (m) cc_final: 0.9057 (t) REVERT: A 1029 MET cc_start: 0.7238 (tmm) cc_final: 0.6651 (tmm) REVERT: A 1047 TYR cc_start: 0.4063 (OUTLIER) cc_final: 0.2895 (m-80) REVERT: A 1123 SER cc_start: 0.7860 (t) cc_final: 0.7520 (t) REVERT: A 1125 ASN cc_start: 0.7884 (t0) cc_final: 0.7670 (t0) REVERT: B 318 PHE cc_start: 0.8439 (t80) cc_final: 0.8176 (t80) REVERT: B 513 LEU cc_start: 0.9260 (tp) cc_final: 0.8997 (pp) REVERT: B 740 MET cc_start: 0.8516 (mmt) cc_final: 0.8007 (mmt) REVERT: B 759 PHE cc_start: 0.8306 (t80) cc_final: 0.7043 (t80) REVERT: B 780 GLU cc_start: 0.9211 (tp30) cc_final: 0.9010 (mm-30) REVERT: B 796 ASP cc_start: 0.8902 (m-30) cc_final: 0.8642 (p0) REVERT: B 886 TRP cc_start: 0.6927 (p-90) cc_final: 0.6629 (p-90) REVERT: B 902 MET cc_start: 0.8823 (tpp) cc_final: 0.8309 (tpp) REVERT: B 916 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 919 ASN cc_start: 0.8856 (m-40) cc_final: 0.8401 (t0) REVERT: B 936 ASP cc_start: 0.9211 (m-30) cc_final: 0.8782 (t0) REVERT: B 1001 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9398 (pp) REVERT: B 1021 SER cc_start: 0.9576 (m) cc_final: 0.9130 (t) REVERT: B 1052 PHE cc_start: 0.9238 (m-80) cc_final: 0.8775 (m-10) REVERT: B 1125 ASN cc_start: 0.7991 (t0) cc_final: 0.7779 (t0) REVERT: C 318 PHE cc_start: 0.8208 (t80) cc_final: 0.7972 (t80) REVERT: C 513 LEU cc_start: 0.9294 (tp) cc_final: 0.8964 (pp) REVERT: C 709 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8126 (p0) REVERT: C 740 MET cc_start: 0.8486 (mmt) cc_final: 0.8006 (mmt) REVERT: C 780 GLU cc_start: 0.9064 (tp30) cc_final: 0.8751 (tp30) REVERT: C 796 ASP cc_start: 0.8846 (m-30) cc_final: 0.8570 (p0) REVERT: C 902 MET cc_start: 0.9161 (mmm) cc_final: 0.8841 (mmm) REVERT: C 916 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8435 (pp) REVERT: C 919 ASN cc_start: 0.8942 (m-40) cc_final: 0.8500 (t0) REVERT: C 936 ASP cc_start: 0.9209 (m-30) cc_final: 0.8781 (t0) REVERT: C 1021 SER cc_start: 0.9655 (m) cc_final: 0.9333 (p) REVERT: C 1029 MET cc_start: 0.7260 (tmm) cc_final: 0.6908 (tmm) REVERT: C 1123 SER cc_start: 0.7911 (t) cc_final: 0.7624 (t) REVERT: C 1125 ASN cc_start: 0.7795 (t0) cc_final: 0.7552 (t0) REVERT: L 1 ASP cc_start: 0.8230 (m-30) cc_final: 0.7881 (t0) REVERT: L 4 MET cc_start: 0.5913 (mmm) cc_final: 0.4743 (tpp) REVERT: L 11 LEU cc_start: 0.9266 (tp) cc_final: 0.9064 (tt) REVERT: L 162 ARG cc_start: 0.8937 (tpt90) cc_final: 0.8307 (tpp80) REVERT: H 39 MET cc_start: 0.5033 (mmp) cc_final: 0.4816 (mpp) REVERT: H 115 MET cc_start: 0.8265 (tpp) cc_final: 0.7949 (tpp) REVERT: M 1 ASP cc_start: 0.8069 (m-30) cc_final: 0.7843 (t0) REVERT: M 4 MET cc_start: 0.5205 (mmm) cc_final: 0.3786 (tpp) REVERT: M 11 LEU cc_start: 0.9102 (tp) cc_final: 0.8876 (tt) REVERT: M 162 ARG cc_start: 0.8924 (tpt90) cc_final: 0.8271 (tpp80) REVERT: I 81 ASP cc_start: 0.7051 (p0) cc_final: 0.6561 (p0) REVERT: N 4 MET cc_start: 0.5875 (mmm) cc_final: 0.4376 (tpp) REVERT: N 11 LEU cc_start: 0.9237 (tp) cc_final: 0.9022 (tt) REVERT: N 162 ARG cc_start: 0.8947 (tpt90) cc_final: 0.8323 (tpp80) REVERT: J 81 ASP cc_start: 0.7067 (p0) cc_final: 0.6607 (p0) REVERT: J 115 MET cc_start: 0.8129 (mmm) cc_final: 0.7901 (mmt) outliers start: 86 outliers final: 58 residues processed: 426 average time/residue: 0.5690 time to fit residues: 374.7519 Evaluate side-chains 333 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 269 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 398 optimal weight: 7.9990 chunk 430 optimal weight: 20.0000 chunk 354 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 901 GLN A 926 GLN A 935 GLN A 955 ASN A1011 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 935 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 35916 Z= 0.374 Angle : 0.769 9.724 48867 Z= 0.404 Chirality : 0.047 0.292 5766 Planarity : 0.005 0.081 6204 Dihedral : 6.839 59.893 6362 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 7.78 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.14 (0.12), residues: 4353 helix: 0.54 (0.19), residues: 723 sheet: 0.26 (0.14), residues: 1284 loop : -0.03 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 152 HIS 0.009 0.002 HIS B1048 PHE 0.029 0.002 PHE B 782 TYR 0.040 0.002 TYR A1067 ARG 0.010 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 268 time to evaluate : 3.953 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 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 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: A 318 PHE cc_start: 0.8753 (t80) cc_final: 0.8387 (t80) REVERT: A 513 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 740 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8452 (mmt) REVERT: A 922 LEU cc_start: 0.9559 (mm) cc_final: 0.9336 (mp) REVERT: A 936 ASP cc_start: 0.9273 (m-30) cc_final: 0.8877 (t0) REVERT: A 945 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8943 (pp) REVERT: A 1002 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 1040 VAL cc_start: 0.9325 (t) cc_final: 0.9087 (p) REVERT: A 1047 TYR cc_start: 0.4187 (OUTLIER) cc_final: 0.3286 (m-80) REVERT: A 1067 TYR cc_start: 0.6037 (m-80) cc_final: 0.5715 (m-80) REVERT: A 1123 SER cc_start: 0.8065 (t) cc_final: 0.7707 (t) REVERT: B 177 MET cc_start: 0.8334 (ppp) cc_final: 0.8129 (ppp) REVERT: B 318 PHE cc_start: 0.8611 (t80) cc_final: 0.8275 (t80) REVERT: B 513 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9027 (pp) REVERT: B 740 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8431 (mmt) REVERT: B 781 VAL cc_start: 0.9430 (t) cc_final: 0.9214 (p) REVERT: B 796 ASP cc_start: 0.8950 (m-30) cc_final: 0.8659 (p0) REVERT: B 902 MET cc_start: 0.8773 (tpp) cc_final: 0.8499 (tpp) REVERT: B 936 ASP cc_start: 0.9270 (m-30) cc_final: 0.8885 (t0) REVERT: B 1001 LEU cc_start: 0.9698 (tt) cc_final: 0.9449 (pp) REVERT: B 1123 SER cc_start: 0.8164 (t) cc_final: 0.7799 (t) REVERT: C 226 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8784 (mt) REVERT: C 318 PHE cc_start: 0.8431 (t80) cc_final: 0.8157 (t80) REVERT: C 513 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9035 (pp) REVERT: C 740 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8464 (mmt) REVERT: C 936 ASP cc_start: 0.9221 (m-30) cc_final: 0.8831 (t0) REVERT: C 1001 LEU cc_start: 0.9815 (tp) cc_final: 0.9419 (pp) REVERT: C 1031 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8430 (mm-30) REVERT: C 1038 LYS cc_start: 0.9423 (mttp) cc_final: 0.9189 (mmmt) REVERT: C 1050 MET cc_start: 0.8630 (mtp) cc_final: 0.8311 (mtp) REVERT: C 1123 SER cc_start: 0.8112 (t) cc_final: 0.7776 (t) REVERT: C 1125 ASN cc_start: 0.8062 (t0) cc_final: 0.7850 (t0) REVERT: L 4 MET cc_start: 0.6626 (mmm) cc_final: 0.6422 (tpp) REVERT: L 11 LEU cc_start: 0.9305 (tp) cc_final: 0.9083 (tt) REVERT: H 81 ASP cc_start: 0.7448 (p0) cc_final: 0.6768 (p0) REVERT: H 84 LYS cc_start: 0.8954 (tptp) cc_final: 0.8342 (tttt) REVERT: H 91 MET cc_start: 0.7065 (mpp) cc_final: 0.6500 (mpp) REVERT: H 115 MET cc_start: 0.8205 (tpp) cc_final: 0.8000 (mmm) REVERT: M 4 MET cc_start: 0.6052 (mmm) cc_final: 0.5456 (tpp) REVERT: M 11 LEU cc_start: 0.9267 (tp) cc_final: 0.9044 (tt) REVERT: I 159 ASP cc_start: 0.9335 (m-30) cc_final: 0.8799 (p0) REVERT: N 4 MET cc_start: 0.6174 (mmm) cc_final: 0.5508 (tpp) REVERT: J 91 MET cc_start: 0.7072 (mpp) cc_final: 0.6671 (mpp) REVERT: J 115 MET cc_start: 0.8308 (mmm) cc_final: 0.8088 (mmt) outliers start: 114 outliers final: 69 residues processed: 358 average time/residue: 0.5219 time to fit residues: 297.0969 Evaluate side-chains 298 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 220 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 229 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 chunk 423 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 379 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 913 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 907 ASN C 913 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 HIS L 167 GLN H 44 GLN ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 HIS M 167 GLN I 44 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 HIS N 167 GLN J 44 GLN J 186 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 35916 Z= 0.503 Angle : 0.858 9.975 48867 Z= 0.450 Chirality : 0.048 0.304 5766 Planarity : 0.006 0.089 6204 Dihedral : 6.883 57.092 6360 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 30.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 3.85 % Allowed : 8.90 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4353 helix: 0.25 (0.18), residues: 726 sheet: 0.02 (0.13), residues: 1257 loop : -0.46 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.012 0.002 HIS B1048 PHE 0.030 0.003 PHE A 718 TYR 0.031 0.003 TYR A 265 ARG 0.012 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 220 time to evaluate : 4.453 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 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: A 32 PHE cc_start: 0.8536 (t80) cc_final: 0.7821 (t80) REVERT: A 56 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8995 (tt) REVERT: A 269 TYR cc_start: 0.8467 (m-80) cc_final: 0.8241 (m-10) REVERT: A 318 PHE cc_start: 0.8733 (t80) cc_final: 0.8479 (t80) REVERT: A 513 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9027 (pp) REVERT: A 556 ASN cc_start: 0.9485 (OUTLIER) cc_final: 0.9159 (p0) REVERT: A 725 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 740 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8886 (mmt) REVERT: A 936 ASP cc_start: 0.9366 (m-30) cc_final: 0.9047 (t0) REVERT: A 1001 LEU cc_start: 0.9781 (tt) cc_final: 0.9537 (pp) REVERT: A 1002 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8543 (tm-30) REVERT: A 1040 VAL cc_start: 0.9394 (t) cc_final: 0.9106 (p) REVERT: A 1067 TYR cc_start: 0.6339 (m-80) cc_final: 0.6080 (m-80) REVERT: A 1123 SER cc_start: 0.8612 (t) cc_final: 0.8286 (t) REVERT: B 104 TRP cc_start: 0.8761 (m-90) cc_final: 0.8448 (m-90) REVERT: B 318 PHE cc_start: 0.8771 (t80) cc_final: 0.8517 (t80) REVERT: B 556 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9216 (p0) REVERT: B 740 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8965 (mmt) REVERT: B 796 ASP cc_start: 0.9029 (m-30) cc_final: 0.8681 (p0) REVERT: B 867 ASP cc_start: 0.9517 (OUTLIER) cc_final: 0.9266 (m-30) REVERT: B 936 ASP cc_start: 0.9329 (m-30) cc_final: 0.8983 (t0) REVERT: B 1001 LEU cc_start: 0.9785 (tt) cc_final: 0.9494 (pp) REVERT: B 1040 VAL cc_start: 0.9394 (t) cc_final: 0.9094 (p) REVERT: B 1049 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8169 (mm) REVERT: B 1123 SER cc_start: 0.8657 (t) cc_final: 0.8376 (t) REVERT: C 104 TRP cc_start: 0.8830 (m-90) cc_final: 0.8565 (m-90) REVERT: C 226 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9168 (mt) REVERT: C 318 PHE cc_start: 0.8519 (t80) cc_final: 0.8275 (t80) REVERT: C 556 ASN cc_start: 0.9406 (OUTLIER) cc_final: 0.9132 (p0) REVERT: C 725 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 773 GLU cc_start: 0.9025 (tt0) cc_final: 0.8330 (tm-30) REVERT: C 936 ASP cc_start: 0.9310 (m-30) cc_final: 0.8958 (t0) REVERT: C 1031 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8468 (mm-30) REVERT: C 1049 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8967 (mm) REVERT: C 1123 SER cc_start: 0.8574 (t) cc_final: 0.8272 (t) REVERT: L 4 MET cc_start: 0.7013 (mmm) cc_final: 0.6200 (tpt) REVERT: H 39 MET cc_start: 0.5347 (mpp) cc_final: 0.4474 (mmm) REVERT: H 225 LYS cc_start: 0.9133 (tppt) cc_final: 0.8890 (tppt) REVERT: M 4 MET cc_start: 0.7004 (mmm) cc_final: 0.5865 (tpt) REVERT: I 91 MET cc_start: 0.7174 (mpp) cc_final: 0.6885 (mpp) REVERT: I 115 MET cc_start: 0.7771 (mmm) cc_final: 0.7465 (tpp) REVERT: N 4 MET cc_start: 0.6701 (mmm) cc_final: 0.5757 (tpp) REVERT: J 225 LYS cc_start: 0.8991 (tptt) cc_final: 0.8765 (tptt) outliers start: 147 outliers final: 75 residues processed: 345 average time/residue: 0.4957 time to fit residues: 279.1536 Evaluate side-chains 279 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 193 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 315 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 361 optimal weight: 6.9990 chunk 292 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 95 GLN H 44 GLN H 186 GLN H 212 ASN M 44 GLN M 95 GLN I 44 GLN I 186 GLN N 44 GLN N 95 GLN J 44 GLN J 212 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35916 Z= 0.210 Angle : 0.658 9.561 48867 Z= 0.340 Chirality : 0.047 0.371 5766 Planarity : 0.005 0.101 6204 Dihedral : 6.288 55.611 6360 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 11.70 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 4353 helix: 0.94 (0.19), residues: 687 sheet: 0.12 (0.14), residues: 1173 loop : -0.33 (0.13), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 152 HIS 0.009 0.001 HIS A1048 PHE 0.029 0.002 PHE C 32 TYR 0.030 0.002 TYR A1067 ARG 0.006 0.001 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 234 time to evaluate : 4.255 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 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 revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8652 (t80) cc_final: 0.8326 (t80) REVERT: A 269 TYR cc_start: 0.8305 (m-80) cc_final: 0.8031 (m-10) REVERT: A 318 PHE cc_start: 0.8684 (t80) cc_final: 0.8411 (t80) REVERT: A 513 LEU cc_start: 0.9340 (tp) cc_final: 0.9013 (pp) REVERT: A 936 ASP cc_start: 0.9295 (m-30) cc_final: 0.8914 (t0) REVERT: A 1050 MET cc_start: 0.8834 (mtp) cc_final: 0.8560 (mtp) REVERT: A 1123 SER cc_start: 0.8441 (t) cc_final: 0.8119 (t) REVERT: B 104 TRP cc_start: 0.8598 (m-90) cc_final: 0.8360 (m-90) REVERT: B 318 PHE cc_start: 0.8706 (t80) cc_final: 0.8460 (t80) REVERT: B 556 ASN cc_start: 0.9414 (OUTLIER) cc_final: 0.9130 (p0) REVERT: B 740 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8653 (mmt) REVERT: B 796 ASP cc_start: 0.8932 (m-30) cc_final: 0.8583 (p0) REVERT: B 916 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8743 (pp) REVERT: B 936 ASP cc_start: 0.9256 (m-30) cc_final: 0.8931 (t0) REVERT: B 1001 LEU cc_start: 0.9730 (tt) cc_final: 0.9457 (pp) REVERT: B 1123 SER cc_start: 0.8407 (t) cc_final: 0.8080 (t) REVERT: C 104 TRP cc_start: 0.8627 (m-90) cc_final: 0.8421 (m-90) REVERT: C 226 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9280 (mt) REVERT: C 318 PHE cc_start: 0.8457 (t80) cc_final: 0.8225 (t80) REVERT: C 556 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.8988 (p0) REVERT: C 773 GLU cc_start: 0.9014 (tt0) cc_final: 0.8612 (tp30) REVERT: C 796 ASP cc_start: 0.8843 (m-30) cc_final: 0.8602 (p0) REVERT: C 904 TYR cc_start: 0.8826 (m-10) cc_final: 0.8227 (m-10) REVERT: C 936 ASP cc_start: 0.9244 (m-30) cc_final: 0.8860 (t0) REVERT: C 1031 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8542 (mm-30) REVERT: C 1038 LYS cc_start: 0.9448 (mttt) cc_final: 0.9145 (mttp) REVERT: C 1050 MET cc_start: 0.8866 (mtp) cc_final: 0.8565 (mtp) REVERT: C 1123 SER cc_start: 0.8238 (t) cc_final: 0.7950 (t) REVERT: L 4 MET cc_start: 0.7130 (mmm) cc_final: 0.6374 (tpp) REVERT: H 39 MET cc_start: 0.5429 (mpp) cc_final: 0.4626 (mmm) REVERT: H 115 MET cc_start: 0.8054 (mmt) cc_final: 0.7561 (mmt) REVERT: H 159 ASP cc_start: 0.9296 (m-30) cc_final: 0.8751 (p0) REVERT: M 4 MET cc_start: 0.6763 (mmm) cc_final: 0.5922 (tpp) REVERT: I 39 MET cc_start: 0.5928 (mpp) cc_final: 0.4755 (mmm) REVERT: I 81 ASP cc_start: 0.6981 (p0) cc_final: 0.6721 (p0) REVERT: I 115 MET cc_start: 0.7430 (mmm) cc_final: 0.7153 (tmm) REVERT: I 159 ASP cc_start: 0.9252 (m-30) cc_final: 0.8735 (p0) REVERT: I 225 LYS cc_start: 0.9117 (tptt) cc_final: 0.8891 (tptt) REVERT: N 4 MET cc_start: 0.6581 (mmm) cc_final: 0.5749 (tpp) REVERT: J 115 MET cc_start: 0.8400 (mmp) cc_final: 0.8008 (mmm) REVERT: J 159 ASP cc_start: 0.9193 (m-30) cc_final: 0.8559 (p0) REVERT: J 225 LYS cc_start: 0.9013 (tptt) cc_final: 0.8789 (tptt) outliers start: 70 outliers final: 49 residues processed: 288 average time/residue: 0.5642 time to fit residues: 259.8896 Evaluate side-chains 251 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 248 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 423 optimal weight: 7.9990 chunk 351 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 overall best weight: 5.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 926 GLN B 935 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 219 GLN M 44 GLN M 219 GLN I 44 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 44 GLN N 219 GLN J 44 GLN J 186 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 35916 Z= 0.445 Angle : 0.784 9.526 48867 Z= 0.408 Chirality : 0.046 0.307 5766 Planarity : 0.005 0.056 6204 Dihedral : 6.436 57.276 6360 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 3.27 % Allowed : 11.78 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.43 (0.13), residues: 4353 helix: 0.72 (0.19), residues: 690 sheet: -0.20 (0.14), residues: 1224 loop : -0.57 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1102 HIS 0.010 0.002 HIS C1083 PHE 0.034 0.003 PHE B 759 TYR 0.031 0.003 TYR B 904 ARG 0.011 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 183 time to evaluate : 4.116 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 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: A 104 TRP cc_start: 0.8843 (m-90) cc_final: 0.8567 (m-90) REVERT: A 513 LEU cc_start: 0.9301 (tp) cc_final: 0.9042 (pp) REVERT: A 556 ASN cc_start: 0.9519 (OUTLIER) cc_final: 0.9221 (p0) REVERT: A 740 MET cc_start: 0.8968 (mmt) cc_final: 0.8688 (mmt) REVERT: A 936 ASP cc_start: 0.9386 (m-30) cc_final: 0.9062 (t0) REVERT: A 1001 LEU cc_start: 0.9793 (tp) cc_final: 0.9425 (pp) REVERT: A 1031 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8800 (mm-30) REVERT: A 1040 VAL cc_start: 0.9524 (t) cc_final: 0.9243 (p) REVERT: A 1123 SER cc_start: 0.8580 (t) cc_final: 0.8256 (t) REVERT: B 104 TRP cc_start: 0.8766 (m-90) cc_final: 0.8440 (m-90) REVERT: B 318 PHE cc_start: 0.8822 (t80) cc_final: 0.8577 (t80) REVERT: B 556 ASN cc_start: 0.9522 (OUTLIER) cc_final: 0.9301 (p0) REVERT: B 796 ASP cc_start: 0.9020 (m-30) cc_final: 0.8648 (p0) REVERT: B 936 ASP cc_start: 0.9312 (m-30) cc_final: 0.9030 (t0) REVERT: B 979 ASP cc_start: 0.8979 (t70) cc_final: 0.8565 (t0) REVERT: B 1001 LEU cc_start: 0.9785 (tt) cc_final: 0.9502 (pp) REVERT: B 1040 VAL cc_start: 0.9433 (t) cc_final: 0.9175 (p) REVERT: B 1123 SER cc_start: 0.8552 (t) cc_final: 0.8246 (t) REVERT: C 104 TRP cc_start: 0.8783 (m-90) cc_final: 0.8466 (m-90) REVERT: C 226 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9285 (mt) REVERT: C 556 ASN cc_start: 0.9452 (OUTLIER) cc_final: 0.9166 (p0) REVERT: C 725 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 759 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: C 796 ASP cc_start: 0.8947 (m-30) cc_final: 0.8632 (p0) REVERT: C 902 MET cc_start: 0.9101 (tpp) cc_final: 0.8736 (tpp) REVERT: C 936 ASP cc_start: 0.9326 (m-30) cc_final: 0.8969 (t0) REVERT: C 979 ASP cc_start: 0.8823 (t70) cc_final: 0.8410 (t0) REVERT: C 1001 LEU cc_start: 0.9835 (tp) cc_final: 0.9427 (pp) REVERT: C 1031 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 1050 MET cc_start: 0.9040 (mtp) cc_final: 0.8753 (mtp) REVERT: C 1123 SER cc_start: 0.8447 (t) cc_final: 0.8109 (t) REVERT: L 11 LEU cc_start: 0.9482 (tt) cc_final: 0.9186 (pt) REVERT: H 39 MET cc_start: 0.5316 (mpp) cc_final: 0.4714 (mmm) REVERT: H 115 MET cc_start: 0.8204 (mmt) cc_final: 0.7784 (tpp) REVERT: M 4 MET cc_start: 0.7400 (mmm) cc_final: 0.6620 (tpt) REVERT: M 11 LEU cc_start: 0.9534 (tt) cc_final: 0.9219 (pt) REVERT: I 39 MET cc_start: 0.5636 (mpp) cc_final: 0.4664 (mmm) REVERT: I 115 MET cc_start: 0.7754 (mmm) cc_final: 0.7394 (tmm) REVERT: I 159 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8700 (p0) REVERT: J 115 MET cc_start: 0.8694 (mmp) cc_final: 0.8440 (mmm) REVERT: J 159 ASP cc_start: 0.9263 (m-30) cc_final: 0.8674 (p0) REVERT: J 225 LYS cc_start: 0.9043 (tptt) cc_final: 0.8799 (tppt) outliers start: 125 outliers final: 88 residues processed: 285 average time/residue: 0.4932 time to fit residues: 225.5919 Evaluate side-chains 263 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 169 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 239 optimal weight: 0.8980 chunk 356 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 173 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN M 44 GLN I 44 GLN I 186 GLN ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN J 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35916 Z= 0.196 Angle : 0.645 9.777 48867 Z= 0.331 Chirality : 0.046 0.245 5766 Planarity : 0.004 0.051 6204 Dihedral : 6.040 55.594 6360 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 1.96 % Allowed : 13.33 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4353 helix: 0.95 (0.19), residues: 702 sheet: 0.07 (0.14), residues: 1149 loop : -0.49 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 152 HIS 0.007 0.001 HIS A1048 PHE 0.026 0.002 PHE B 823 TYR 0.027 0.002 TYR C1067 ARG 0.009 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 212 time to evaluate : 3.874 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 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: A 32 PHE cc_start: 0.8488 (t80) cc_final: 0.8286 (t80) REVERT: A 104 TRP cc_start: 0.8634 (m-90) cc_final: 0.8395 (m-90) REVERT: A 269 TYR cc_start: 0.8614 (m-80) cc_final: 0.8290 (m-10) REVERT: A 513 LEU cc_start: 0.9332 (tp) cc_final: 0.8965 (pp) REVERT: A 740 MET cc_start: 0.8832 (mmt) cc_final: 0.8621 (mmt) REVERT: A 877 LEU cc_start: 0.9586 (mt) cc_final: 0.9369 (mt) REVERT: A 936 ASP cc_start: 0.9313 (m-30) cc_final: 0.8981 (t0) REVERT: A 1001 LEU cc_start: 0.9728 (tp) cc_final: 0.9367 (pp) REVERT: A 1123 SER cc_start: 0.8304 (t) cc_final: 0.7990 (t) REVERT: B 104 TRP cc_start: 0.8594 (m-90) cc_final: 0.8339 (m-90) REVERT: B 556 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.9170 (p0) REVERT: B 773 GLU cc_start: 0.9191 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 796 ASP cc_start: 0.8883 (m-30) cc_final: 0.8595 (p0) REVERT: B 936 ASP cc_start: 0.9254 (m-30) cc_final: 0.8942 (t0) REVERT: B 954 GLN cc_start: 0.9354 (mt0) cc_final: 0.9107 (pt0) REVERT: B 979 ASP cc_start: 0.9029 (t70) cc_final: 0.8608 (t0) REVERT: B 1001 LEU cc_start: 0.9742 (tt) cc_final: 0.9457 (pp) REVERT: B 1123 SER cc_start: 0.8292 (t) cc_final: 0.7986 (t) REVERT: C 104 TRP cc_start: 0.8637 (m-90) cc_final: 0.8384 (m-90) REVERT: C 226 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9314 (mt) REVERT: C 556 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9073 (p0) REVERT: C 759 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8148 (t80) REVERT: C 773 GLU cc_start: 0.9031 (tt0) cc_final: 0.8266 (tm-30) REVERT: C 796 ASP cc_start: 0.8842 (m-30) cc_final: 0.8616 (p0) REVERT: C 822 LEU cc_start: 0.9707 (mt) cc_final: 0.9433 (pp) REVERT: C 902 MET cc_start: 0.9054 (tpp) cc_final: 0.8727 (tpp) REVERT: C 936 ASP cc_start: 0.9250 (m-30) cc_final: 0.8889 (t0) REVERT: C 979 ASP cc_start: 0.8872 (t70) cc_final: 0.8452 (t0) REVERT: C 1001 LEU cc_start: 0.9818 (tp) cc_final: 0.9399 (pp) REVERT: C 1123 SER cc_start: 0.8072 (t) cc_final: 0.7821 (t) REVERT: L 11 LEU cc_start: 0.9471 (tt) cc_final: 0.9181 (pt) REVERT: H 39 MET cc_start: 0.5419 (mpp) cc_final: 0.4686 (mmm) REVERT: H 115 MET cc_start: 0.8197 (mmt) cc_final: 0.7963 (tpp) REVERT: H 159 ASP cc_start: 0.9289 (m-30) cc_final: 0.8742 (p0) REVERT: M 4 MET cc_start: 0.7102 (mmm) cc_final: 0.6279 (tpt) REVERT: M 11 LEU cc_start: 0.9505 (tt) cc_final: 0.9175 (pt) REVERT: I 39 MET cc_start: 0.5989 (mpp) cc_final: 0.4904 (mmm) REVERT: I 115 MET cc_start: 0.7484 (mmm) cc_final: 0.7210 (tmm) REVERT: I 159 ASP cc_start: 0.9274 (m-30) cc_final: 0.8771 (p0) REVERT: N 4 MET cc_start: 0.6508 (tmm) cc_final: 0.6266 (tmm) REVERT: J 115 MET cc_start: 0.8661 (mmp) cc_final: 0.8355 (mmm) REVERT: J 159 ASP cc_start: 0.9201 (m-30) cc_final: 0.8584 (p0) outliers start: 75 outliers final: 62 residues processed: 274 average time/residue: 0.5136 time to fit residues: 227.2926 Evaluate side-chains 249 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 183 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 252 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 331 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN I 44 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 35916 Z= 0.417 Angle : 0.756 13.157 48867 Z= 0.389 Chirality : 0.046 0.291 5766 Planarity : 0.005 0.044 6204 Dihedral : 6.285 57.517 6360 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 2.54 % Allowed : 13.14 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.13), residues: 4353 helix: 0.71 (0.19), residues: 690 sheet: -0.25 (0.14), residues: 1215 loop : -0.59 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 353 HIS 0.010 0.002 HIS C1083 PHE 0.030 0.002 PHE B 759 TYR 0.025 0.002 TYR C 265 ARG 0.009 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 169 time to evaluate : 4.260 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 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 104 TRP cc_start: 0.8716 (m-90) cc_final: 0.8415 (m-90) REVERT: A 556 ASN cc_start: 0.9526 (OUTLIER) cc_final: 0.9249 (p0) REVERT: A 740 MET cc_start: 0.8986 (mmt) cc_final: 0.8778 (mmt) REVERT: A 936 ASP cc_start: 0.9389 (m-30) cc_final: 0.9126 (t0) REVERT: A 1031 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8755 (mm-30) REVERT: A 1123 SER cc_start: 0.8507 (t) cc_final: 0.8206 (t) REVERT: B 104 TRP cc_start: 0.8720 (m-90) cc_final: 0.8403 (m-90) REVERT: B 556 ASN cc_start: 0.9570 (OUTLIER) cc_final: 0.9321 (p0) REVERT: B 773 GLU cc_start: 0.9208 (tt0) cc_final: 0.8429 (tm-30) REVERT: B 796 ASP cc_start: 0.9021 (m-30) cc_final: 0.8710 (p0) REVERT: B 936 ASP cc_start: 0.9327 (m-30) cc_final: 0.9052 (t0) REVERT: B 979 ASP cc_start: 0.8992 (t70) cc_final: 0.8628 (t0) REVERT: B 1001 LEU cc_start: 0.9780 (tt) cc_final: 0.9507 (pp) REVERT: B 1123 SER cc_start: 0.8558 (t) cc_final: 0.8277 (t) REVERT: C 104 TRP cc_start: 0.8714 (m-90) cc_final: 0.8422 (m-90) REVERT: C 226 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9246 (mt) REVERT: C 556 ASN cc_start: 0.9471 (OUTLIER) cc_final: 0.9214 (p0) REVERT: C 759 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8232 (t80) REVERT: C 773 GLU cc_start: 0.9039 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 796 ASP cc_start: 0.8944 (m-30) cc_final: 0.8657 (p0) REVERT: C 902 MET cc_start: 0.9105 (tpp) cc_final: 0.8790 (tpp) REVERT: C 936 ASP cc_start: 0.9312 (m-30) cc_final: 0.8973 (t0) REVERT: C 979 ASP cc_start: 0.8865 (t70) cc_final: 0.8484 (t0) REVERT: C 1001 LEU cc_start: 0.9832 (tp) cc_final: 0.9462 (pp) REVERT: C 1123 SER cc_start: 0.8336 (t) cc_final: 0.8042 (t) REVERT: L 11 LEU cc_start: 0.9490 (tt) cc_final: 0.9204 (pt) REVERT: H 39 MET cc_start: 0.5384 (mpp) cc_final: 0.4696 (mmm) REVERT: H 159 ASP cc_start: 0.9339 (m-30) cc_final: 0.8842 (p0) REVERT: M 11 LEU cc_start: 0.9541 (tt) cc_final: 0.9244 (pt) REVERT: I 39 MET cc_start: 0.5623 (mpp) cc_final: 0.4728 (mmm) REVERT: I 115 MET cc_start: 0.7696 (mmm) cc_final: 0.7381 (tmm) REVERT: I 159 ASP cc_start: 0.9315 (m-30) cc_final: 0.8837 (p0) REVERT: N 4 MET cc_start: 0.6835 (tmm) cc_final: 0.6612 (tmm) REVERT: N 11 LEU cc_start: 0.9478 (tt) cc_final: 0.9163 (pt) REVERT: J 14 GLN cc_start: 0.9048 (pm20) cc_final: 0.8798 (pm20) REVERT: J 115 MET cc_start: 0.8688 (mmp) cc_final: 0.8401 (mmm) REVERT: J 159 ASP cc_start: 0.9275 (m-30) cc_final: 0.8682 (p0) outliers start: 97 outliers final: 75 residues processed: 246 average time/residue: 0.5356 time to fit residues: 214.5626 Evaluate side-chains 237 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 157 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 chunk 368 optimal weight: 40.0000 chunk 393 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 44 GLN I 44 GLN ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 35916 Z= 0.307 Angle : 0.681 11.163 48867 Z= 0.352 Chirality : 0.045 0.237 5766 Planarity : 0.005 0.044 6204 Dihedral : 6.228 56.162 6360 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 2.46 % Allowed : 13.67 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: -0.46 (0.13), residues: 4353 helix: 0.88 (0.20), residues: 678 sheet: -0.26 (0.14), residues: 1191 loop : -0.61 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 152 HIS 0.008 0.001 HIS A1083 PHE 0.022 0.002 PHE B 759 TYR 0.036 0.002 TYR C 266 ARG 0.009 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 168 time to evaluate : 3.946 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 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 104 TRP cc_start: 0.8643 (m-90) cc_final: 0.8362 (m-90) REVERT: A 556 ASN cc_start: 0.9522 (OUTLIER) cc_final: 0.9267 (p0) REVERT: A 740 MET cc_start: 0.8969 (mmt) cc_final: 0.8689 (mmt) REVERT: A 936 ASP cc_start: 0.9349 (m-30) cc_final: 0.9009 (t0) REVERT: A 1001 LEU cc_start: 0.9734 (tt) cc_final: 0.9480 (pp) REVERT: A 1123 SER cc_start: 0.8496 (t) cc_final: 0.8190 (t) REVERT: B 104 TRP cc_start: 0.8666 (m-90) cc_final: 0.8369 (m-90) REVERT: B 556 ASN cc_start: 0.9562 (OUTLIER) cc_final: 0.9308 (p0) REVERT: B 773 GLU cc_start: 0.9215 (tt0) cc_final: 0.8392 (tm-30) REVERT: B 796 ASP cc_start: 0.8959 (m-30) cc_final: 0.8667 (p0) REVERT: B 936 ASP cc_start: 0.9303 (m-30) cc_final: 0.8995 (t0) REVERT: B 979 ASP cc_start: 0.9002 (t70) cc_final: 0.8623 (t0) REVERT: B 1001 LEU cc_start: 0.9767 (tt) cc_final: 0.9491 (pp) REVERT: B 1034 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 1123 SER cc_start: 0.8498 (t) cc_final: 0.8209 (t) REVERT: C 104 TRP cc_start: 0.8663 (m-90) cc_final: 0.8390 (m-90) REVERT: C 226 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9314 (mt) REVERT: C 556 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.9196 (p0) REVERT: C 796 ASP cc_start: 0.8890 (m-30) cc_final: 0.8616 (p0) REVERT: C 902 MET cc_start: 0.9096 (tpp) cc_final: 0.8792 (tpp) REVERT: C 936 ASP cc_start: 0.9299 (m-30) cc_final: 0.8961 (t0) REVERT: C 979 ASP cc_start: 0.8826 (t70) cc_final: 0.8436 (t0) REVERT: C 1001 LEU cc_start: 0.9833 (tp) cc_final: 0.9462 (pp) REVERT: C 1038 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9185 (ptmt) REVERT: C 1123 SER cc_start: 0.8264 (t) cc_final: 0.8006 (t) REVERT: L 11 LEU cc_start: 0.9470 (tt) cc_final: 0.9186 (pt) REVERT: H 39 MET cc_start: 0.5440 (mpp) cc_final: 0.4778 (mmm) REVERT: H 159 ASP cc_start: 0.9334 (m-30) cc_final: 0.8834 (p0) REVERT: M 11 LEU cc_start: 0.9508 (tt) cc_final: 0.9181 (pt) REVERT: I 39 MET cc_start: 0.5621 (mpp) cc_final: 0.4674 (mmm) REVERT: I 115 MET cc_start: 0.7600 (mmm) cc_final: 0.7353 (tmm) REVERT: I 159 ASP cc_start: 0.9311 (m-30) cc_final: 0.8836 (p0) REVERT: N 11 LEU cc_start: 0.9479 (tt) cc_final: 0.9164 (pt) REVERT: J 115 MET cc_start: 0.8689 (mmp) cc_final: 0.8250 (mmm) REVERT: J 159 ASP cc_start: 0.9252 (m-30) cc_final: 0.8641 (p0) REVERT: J 225 LYS cc_start: 0.8956 (tptt) cc_final: 0.8723 (tppt) outliers start: 94 outliers final: 80 residues processed: 243 average time/residue: 0.5131 time to fit residues: 201.0551 Evaluate side-chains 250 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 164 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 1.9990 chunk 415 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 436 optimal weight: 7.9990 chunk 401 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 35916 Z= 0.233 Angle : 0.651 11.651 48867 Z= 0.333 Chirality : 0.045 0.274 5766 Planarity : 0.004 0.045 6204 Dihedral : 5.955 56.328 6360 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4353 helix: 0.94 (0.20), residues: 690 sheet: -0.17 (0.14), residues: 1227 loop : -0.54 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 118 HIS 0.006 0.001 HIS A1048 PHE 0.020 0.002 PHE B 759 TYR 0.034 0.002 TYR B 266 ARG 0.008 0.001 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 182 time to evaluate : 4.518 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 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 104 TRP cc_start: 0.8592 (m-90) cc_final: 0.8345 (m-90) REVERT: A 740 MET cc_start: 0.8917 (mmt) cc_final: 0.8627 (mmt) REVERT: A 936 ASP cc_start: 0.9308 (m-30) cc_final: 0.9008 (t0) REVERT: A 1001 LEU cc_start: 0.9731 (tt) cc_final: 0.9474 (pp) REVERT: A 1038 LYS cc_start: 0.9370 (mttp) cc_final: 0.9129 (mmmt) REVERT: A 1123 SER cc_start: 0.8442 (t) cc_final: 0.8113 (t) REVERT: B 104 TRP cc_start: 0.8593 (m-90) cc_final: 0.8331 (m-90) REVERT: B 556 ASN cc_start: 0.9549 (OUTLIER) cc_final: 0.9296 (p0) REVERT: B 740 MET cc_start: 0.8684 (mmm) cc_final: 0.8430 (mmt) REVERT: B 773 GLU cc_start: 0.9225 (tt0) cc_final: 0.8377 (tm-30) REVERT: B 796 ASP cc_start: 0.8954 (m-30) cc_final: 0.8670 (p0) REVERT: B 936 ASP cc_start: 0.9280 (m-30) cc_final: 0.8987 (t0) REVERT: B 979 ASP cc_start: 0.9012 (t70) cc_final: 0.8673 (t0) REVERT: B 1001 LEU cc_start: 0.9754 (tt) cc_final: 0.9470 (pp) REVERT: B 1031 GLU cc_start: 0.8887 (tt0) cc_final: 0.8399 (tp30) REVERT: B 1034 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8130 (pp) REVERT: B 1123 SER cc_start: 0.8380 (t) cc_final: 0.8084 (t) REVERT: C 104 TRP cc_start: 0.8613 (m-90) cc_final: 0.8363 (m-90) REVERT: C 135 PHE cc_start: 0.8724 (t80) cc_final: 0.8504 (t80) REVERT: C 226 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9314 (mt) REVERT: C 796 ASP cc_start: 0.8851 (m-30) cc_final: 0.8619 (p0) REVERT: C 822 LEU cc_start: 0.9697 (mt) cc_final: 0.9460 (pp) REVERT: C 902 MET cc_start: 0.9087 (tpp) cc_final: 0.8715 (tpp) REVERT: C 936 ASP cc_start: 0.9276 (m-30) cc_final: 0.8973 (t0) REVERT: C 979 ASP cc_start: 0.8882 (t70) cc_final: 0.8484 (t0) REVERT: C 1001 LEU cc_start: 0.9789 (tp) cc_final: 0.9488 (pp) REVERT: C 1123 SER cc_start: 0.8207 (t) cc_final: 0.7977 (t) REVERT: L 11 LEU cc_start: 0.9455 (tt) cc_final: 0.9173 (pt) REVERT: H 39 MET cc_start: 0.5530 (mpp) cc_final: 0.4877 (mmm) REVERT: H 115 MET cc_start: 0.6404 (tpp) cc_final: 0.5915 (tpp) REVERT: H 159 ASP cc_start: 0.9355 (m-30) cc_final: 0.8839 (p0) REVERT: M 4 MET cc_start: 0.6465 (tmm) cc_final: 0.5741 (tmm) REVERT: M 11 LEU cc_start: 0.9497 (tt) cc_final: 0.9179 (pt) REVERT: I 39 MET cc_start: 0.5853 (mpp) cc_final: 0.4812 (mmm) REVERT: I 115 MET cc_start: 0.7422 (mmm) cc_final: 0.7218 (tmm) REVERT: I 159 ASP cc_start: 0.9319 (m-30) cc_final: 0.8829 (p0) REVERT: N 11 LEU cc_start: 0.9495 (tt) cc_final: 0.9210 (pt) REVERT: J 115 MET cc_start: 0.8619 (mmp) cc_final: 0.8356 (mmm) REVERT: J 225 LYS cc_start: 0.8921 (tptt) cc_final: 0.8712 (tppt) outliers start: 77 outliers final: 70 residues processed: 245 average time/residue: 0.5231 time to fit residues: 207.6616 Evaluate side-chains 244 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 171 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 320 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 357 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.050936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.036127 restraints weight = 304641.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.037269 restraints weight = 171708.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.038011 restraints weight = 115350.506| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35916 Z= 0.205 Angle : 0.639 11.766 48867 Z= 0.325 Chirality : 0.045 0.298 5766 Planarity : 0.004 0.069 6204 Dihedral : 5.752 56.056 6360 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.91 % Allowed : 14.48 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4353 helix: 0.81 (0.20), residues: 705 sheet: -0.08 (0.14), residues: 1260 loop : -0.51 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 886 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.002 PHE C 759 TYR 0.033 0.002 TYR B 266 ARG 0.012 0.001 ARG C 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6712.59 seconds wall clock time: 126 minutes 13.35 seconds (7573.35 seconds total)