Starting phenix.real_space_refine on Tue Nov 21 21:17:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/11_2023/7kml_22926.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/11_2023/7kml_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_22926/11_2023/7kml_22926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/11_2023/7kml_22926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/11_2023/7kml_22926.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kml_22926/11_2023/7kml_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 18.25, per 1000 atoms: 0.52 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: 15.13 Conformation dependent library (CDL) restraints added in 5.8 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: 4.87 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: 18.66 Time building geometry restraints manager: 16.09 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 - 17.98: 20068 17.98 - 35.96: 497 35.96 - 53.94: 162 53.94 - 71.93: 57 71.93 - 89.91: 42 Dihedral angle restraints: 20826 sinusoidal: 8034 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 20823 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.520 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 96.840 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.670 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.510 ------------------------------------------------------------------------------- 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 : 10.572 89.657 12447 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 *********************** 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 : 3.879 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 outliers start: 15 outliers final: 10 residues processed: 682 average time/residue: 0.5537 time to fit residues: 579.4480 Evaluate side-chains 330 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 320 time to evaluate : 3.980 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3177 time to fit residues: 11.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 113 optimal weight: 0.8980 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: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 440 ASN A 501 ASN A 955 ASN A1011 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 501 ASN B 655 HIS B 762 GLN B 965 GLN C 49 HIS C 239 GLN C 440 ASN C 501 ASN C 762 GLN C 907 ASN C1010 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN N 43 GLN J 186 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35916 Z= 0.266 Angle : 0.783 9.385 48867 Z= 0.422 Chirality : 0.048 0.255 5766 Planarity : 0.005 0.045 6204 Dihedral : 5.529 22.439 4728 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.04 % Allowed : 7.10 % Favored : 90.86 % 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: 0.47 (0.12), residues: 4353 helix: 1.10 (0.19), residues: 681 sheet: 0.53 (0.14), residues: 1302 loop : 0.05 (0.13), residues: 2370 *********************** 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 435 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 357 time to evaluate : 3.744 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 outliers start: 78 outliers final: 48 residues processed: 420 average time/residue: 0.5590 time to fit residues: 363.6282 Evaluate side-chains 319 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 271 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3645 time to fit residues: 36.4191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 331 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 398 optimal weight: 7.9990 chunk 430 optimal weight: 50.0000 chunk 354 optimal weight: 5.9990 chunk 395 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 913 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 913 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 440 ASN C 450 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 804 GLN C 913 GLN C 935 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 HIS L 186 GLN H 214 ASN M 3 GLN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 HIS M 186 GLN M 219 GLN I 214 ASN N 3 GLN N 43 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 HIS N 186 GLN N 219 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 35916 Z= 0.511 Angle : 0.922 12.258 48867 Z= 0.483 Chirality : 0.050 0.364 5766 Planarity : 0.006 0.094 6204 Dihedral : 5.935 26.678 4728 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.83 % Allowed : 8.98 % Favored : 89.19 % 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: -0.16 (0.12), residues: 4353 helix: 0.13 (0.18), residues: 720 sheet: 0.16 (0.13), residues: 1254 loop : -0.22 (0.13), residues: 2379 *********************** 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 322 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 252 time to evaluate : 3.885 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 outliers start: 70 outliers final: 43 residues processed: 312 average time/residue: 0.5397 time to fit residues: 270.7179 Evaluate side-chains 243 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 3.715 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3727 time to fit residues: 32.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 206 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 399 optimal weight: 9.9990 chunk 423 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 379 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 173 GLN A 440 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 440 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 965 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 ASN H 214 ASN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN I 214 ASN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 35916 Z= 0.313 Angle : 0.703 10.213 48867 Z= 0.369 Chirality : 0.046 0.205 5766 Planarity : 0.005 0.054 6204 Dihedral : 5.473 23.437 4728 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 1.86 % Allowed : 10.11 % Favored : 88.03 % 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: -0.13 (0.12), residues: 4353 helix: 0.63 (0.19), residues: 702 sheet: 0.09 (0.13), residues: 1326 loop : -0.32 (0.13), residues: 2325 *********************** 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 305 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 234 time to evaluate : 4.154 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 outliers start: 71 outliers final: 21 residues processed: 292 average time/residue: 0.5247 time to fit residues: 246.5774 Evaluate side-chains 217 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 4.367 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4018 time to fit residues: 20.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 6 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 380 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 440 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 44 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN L 219 GLN H 44 GLN H 186 GLN M 3 GLN M 44 GLN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 167 GLN I 44 GLN I 186 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.184 35916 Z= 0.633 Angle : 0.979 13.119 48867 Z= 0.509 Chirality : 0.050 0.305 5766 Planarity : 0.006 0.069 6204 Dihedral : 6.268 32.944 4728 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 36.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 1.99 % Allowed : 11.99 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4353 helix: -0.36 (0.18), residues: 726 sheet: -0.37 (0.13), residues: 1287 loop : -0.75 (0.13), residues: 2340 *********************** 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 252 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 176 time to evaluate : 3.993 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 outliers start: 76 outliers final: 44 residues processed: 237 average time/residue: 0.5059 time to fit residues: 195.0395 Evaluate side-chains 194 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 4.222 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3412 time to fit residues: 33.3124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 10.0000 chunk 381 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 248 optimal weight: 0.0770 chunk 104 optimal weight: 4.9990 chunk 423 optimal weight: 9.9990 chunk 351 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C1058 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 35916 Z= 0.293 Angle : 0.707 10.465 48867 Z= 0.369 Chirality : 0.046 0.243 5766 Planarity : 0.005 0.044 6204 Dihedral : 5.715 30.135 4728 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 1.34 % Allowed : 12.80 % Favored : 85.86 % 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: -0.62 (0.12), residues: 4353 helix: 0.34 (0.19), residues: 711 sheet: -0.28 (0.13), residues: 1338 loop : -0.66 (0.13), residues: 2304 *********************** 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 246 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 4.040 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 outliers start: 51 outliers final: 27 residues processed: 238 average time/residue: 0.5044 time to fit residues: 192.8925 Evaluate side-chains 189 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 4.155 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.3593 time to fit residues: 21.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 50.0000 chunk 47 optimal weight: 0.0370 chunk 241 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 422 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: