Starting phenix.real_space_refine on Thu Apr 11 12:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tn9_26005/04_2024/7tn9_26005.pdb" } resolution = 3.1 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= 0.030 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 97 5.16 5 C 14320 2.51 5 N 3791 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ASP 55": "OD1" <-> "OD2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "T ARG 85": "NH1" <-> "NH2" Residue "T PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 89": "NH1" <-> "NH2" Residue "T TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 103": "OE1" <-> "OE2" Residue "T TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 134": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 219": "NH1" <-> "NH2" Residue "T PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T ARG 247": "NH1" <-> "NH2" Residue "T PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 292": "OE1" <-> "OE2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S GLU 100": "OE1" <-> "OE2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 134": "NH1" <-> "NH2" Residue "S ARG 136": "NH1" <-> "NH2" Residue "S PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 156": "OE1" <-> "OE2" Residue "S TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ASP 192": "OD1" <-> "OD2" Residue "S PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 219": "NH1" <-> "NH2" Residue "S TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 245": "OE1" <-> "OE2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "S TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 89": "NH1" <-> "NH2" Residue "U ASP 127": "OD1" <-> "OD2" Residue "U ARG 134": "NH1" <-> "NH2" Residue "U ARG 136": "NH1" <-> "NH2" Residue "U TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 150": "OD1" <-> "OD2" Residue "U PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 163": "OD1" <-> "OD2" Residue "U ARG 164": "NH1" <-> "NH2" Residue "U TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "U TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 229": "OE1" <-> "OE2" Residue "U TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 245": "OE1" <-> "OE2" Residue "U ARG 247": "NH1" <-> "NH2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U GLU 280": "OE1" <-> "OE2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "U ARG 302": "NH1" <-> "NH2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 523": "OE1" <-> "OE2" Residue "W PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 540": "OE1" <-> "OE2" Residue "W TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 559": "NH1" <-> "NH2" Residue "W GLU 564": "OE1" <-> "OE2" Residue "W PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 99": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "V TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 523": "OE1" <-> "OE2" Residue "V PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 545": "OE1" <-> "OE2" Residue "V ASP 552": "OD1" <-> "OD2" Residue "V ARG 559": "NH1" <-> "NH2" Residue "V GLU 564": "OE1" <-> "OE2" Residue "V GLU 578": "OE1" <-> "OE2" Residue "V PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 523": "OE1" <-> "OE2" Residue "X TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 540": "OE1" <-> "OE2" Residue "X ARG 559": "NH1" <-> "NH2" Residue "X GLU 564": "OE1" <-> "OE2" Residue "X PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 607": "OD1" <-> "OD2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ASP 54": "OD1" <-> "OD2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 73": "OD1" <-> "OD2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "D ASP 1": "OD1" <-> "OD2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22621 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "T" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2127 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1872 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 3 Chain: "U" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2127 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain breaks: 2 Chain: "R" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 779 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "W" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "Q" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 878 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "M" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "H" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 760 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "O" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "V" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "X" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 839 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 899 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "J" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "D" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.35, per 1000 atoms: 0.50 Number of scatterers: 22621 At special positions: 0 Unit cell: (138.653, 155.459, 143.905, 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 97 16.00 O 4413 8.00 N 3791 7.00 C 14320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS T 108 " - pdb=" SG CYS T 135 " distance=2.02 Simple disulfide: pdb=" SG CYS T 121 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS S 53 " - pdb=" SG CYS V 609 " distance=2.03 Simple disulfide: pdb=" SG CYS S 108 " - pdb=" SG CYS S 135 " distance=2.03 Simple disulfide: pdb=" SG CYS S 121 " - pdb=" SG CYS S 147 " distance=2.02 Simple disulfide: pdb=" SG CYS U 53 " - pdb=" SG CYS X 609 " distance=2.02 Simple disulfide: pdb=" SG CYS U 108 " - pdb=" SG CYS U 135 " distance=2.02 Simple disulfide: pdb=" SG CYS U 121 " - pdb=" SG CYS U 147 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS W 511 " - pdb=" SG CYS W 556 " distance=2.03 Simple disulfide: pdb=" SG CYS W 601 " - pdb=" SG CYS W 608 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 511 " - pdb=" SG CYS V 556 " distance=2.03 Simple disulfide: pdb=" SG CYS V 601 " - pdb=" SG CYS V 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 511 " - pdb=" SG CYS X 556 " distance=2.03 Simple disulfide: pdb=" SG CYS X 601 " - pdb=" SG CYS X 608 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " " BMA Y 3 " - " MAN Y 6 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG K 1 " - " ASN W 563 " " NAG L 1 " - " ASN V 563 " " NAG S 401 " - " ASN S 228 " " NAG S 402 " - " ASN S 238 " " NAG T 601 " - " ASN T 228 " " NAG T 602 " - " ASN T 238 " " NAG T 603 " - " ASN T 257 " " NAG U 601 " - " ASN U 228 " " NAG U 602 " - " ASN U 238 " " NAG U 603 " - " ASN U 257 " " NAG Y 1 " - " ASN X 563 " Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 4.1 seconds 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 11.1% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'T' and resid 71 through 74 removed outlier: 3.503A pdb=" N GLY T 74 " --> pdb=" O GLU T 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 71 through 74' Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.737A pdb=" N LYS T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG T 85 " --> pdb=" O SER T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 264 Processing helix chain 'T' and resid 291 through 296 Processing helix chain 'S' and resid 59 through 61 No H-bonds generated for 'chain 'S' and resid 59 through 61' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'S' and resid 78 through 85 removed outlier: 3.836A pdb=" N LYS S 84 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG S 85 " --> pdb=" O SER S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 196 removed outlier: 3.645A pdb=" N SER S 195 " --> pdb=" O LYS S 191 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER S 196 " --> pdb=" O ASP S 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 191 through 196' Processing helix chain 'S' and resid 249 through 261 removed outlier: 3.750A pdb=" N ASN S 257 " --> pdb=" O LEU S 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR S 261 " --> pdb=" O ASN S 257 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 78 through 85 removed outlier: 3.625A pdb=" N LYS U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG U 85 " --> pdb=" O SER U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 249 through 264 Processing helix chain 'U' and resid 289 through 296 removed outlier: 3.582A pdb=" N LYS U 295 " --> pdb=" O TRP U 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 84 removed outlier: 4.168A pdb=" N ALA N 84 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 541 Processing helix chain 'W' and resid 551 through 576 removed outlier: 3.956A pdb=" N ILE W 555 " --> pdb=" O GLN W 551 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN W 567 " --> pdb=" O ASN W 563 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA W 568 " --> pdb=" O GLU W 564 " (cutoff:3.500A) Processing helix chain 'W' and resid 583 through 597 Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.588A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.691A pdb=" N ALA P 84 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'V' and resid 528 through 532 removed outlier: 3.605A pdb=" N TRP V 531 " --> pdb=" O GLY V 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE V 532 " --> pdb=" O LEU V 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 528 through 532' Processing helix chain 'V' and resid 538 through 542 removed outlier: 3.675A pdb=" N ILE V 542 " --> pdb=" O ALA V 539 " (cutoff:3.500A) Processing helix chain 'V' and resid 551 through 576 removed outlier: 3.784A pdb=" N ILE V 555 " --> pdb=" O GLN V 551 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN V 560 " --> pdb=" O CYS V 556 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN V 567 " --> pdb=" O ASN V 563 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA V 568 " --> pdb=" O GLU V 564 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU V 571 " --> pdb=" O GLN V 567 " (cutoff:3.500A) Processing helix chain 'V' and resid 583 through 597 Processing helix chain 'X' and resid 539 through 541 No H-bonds generated for 'chain 'X' and resid 539 through 541' Processing helix chain 'X' and resid 551 through 576 removed outlier: 3.587A pdb=" N ILE X 555 " --> pdb=" O GLN X 551 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN X 567 " --> pdb=" O ASN X 563 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA X 568 " --> pdb=" O GLU X 564 " (cutoff:3.500A) Processing helix chain 'X' and resid 583 through 597 Processing helix chain 'I' and resid 62 through 65 removed outlier: 4.018A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.975A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'D' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.600A pdb=" N SER A 77 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.020A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.020A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 107 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.974A pdb=" N GLY T 36 " --> pdb=" O ILE T 185 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASN T 69 " --> pdb=" O GLU T 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.974A pdb=" N GLY T 36 " --> pdb=" O ILE T 185 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL T 96 " --> pdb=" O THR W 581 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'T' and resid 105 through 111 removed outlier: 6.272A pdb=" N GLU T 106 " --> pdb=" O TYR T 137 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS T 139 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS T 108 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL T 141 " --> pdb=" O CYS T 108 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN T 110 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY T 143 " --> pdb=" O ASN T 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG T 136 " --> pdb=" O THR T 216 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE T 218 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL T 138 " --> pdb=" O ILE T 218 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR T 220 " --> pdb=" O VAL T 138 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS T 140 " --> pdb=" O TYR T 220 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA T 222 " --> pdb=" O LYS T 140 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER T 142 " --> pdb=" O ALA T 222 " (cutoff:3.500A) removed outlier: 13.768A pdb=" N THR T 217 " --> pdb=" O ASP T 237 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASP T 237 " --> pdb=" O THR T 217 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG T 219 " --> pdb=" O GLU T 235 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR T 240 " --> pdb=" O VAL T 236 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL T 277 " --> pdb=" O GLN T 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 42 through 45 removed outlier: 6.844A pdb=" N GLY S 36 " --> pdb=" O ILE S 185 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA S 101 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER S 65 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLU S 103 " --> pdb=" O SER S 65 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLY S 67 " --> pdb=" O GLU S 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 42 through 45 removed outlier: 6.844A pdb=" N GLY S 36 " --> pdb=" O ILE S 185 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 96 " --> pdb=" O THR V 581 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'S' and resid 105 through 114 removed outlier: 6.279A pdb=" N GLU S 106 " --> pdb=" O TYR S 137 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS S 139 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS S 108 " --> pdb=" O HIS S 139 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL S 141 " --> pdb=" O CYS S 108 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN S 110 " --> pdb=" O VAL S 141 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY S 143 " --> pdb=" O ASN S 110 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU S 112 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG S 219 " --> pdb=" O GLU S 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 42 through 45 removed outlier: 6.822A pdb=" N GLY U 36 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ALA U 101 " --> pdb=" O LEU U 63 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER U 65 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU U 103 " --> pdb=" O SER U 65 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY U 67 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU X 515 " --> pdb=" O MET X 548 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 42 through 45 removed outlier: 6.822A pdb=" N GLY U 36 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL U 96 " --> pdb=" O THR X 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'U' and resid 105 through 109 removed outlier: 6.244A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY U 143 " --> pdb=" O GLU U 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 105 through 109 removed outlier: 6.244A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG U 219 " --> pdb=" O GLU U 235 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL U 277 " --> pdb=" O GLN U 243 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE U 274 " --> pdb=" O VAL U 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.707A pdb=" N LEU R 11 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.707A pdb=" N LEU R 11 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR R 96 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.663A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.682A pdb=" N GLU F 76 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.667A pdb=" N GLU F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.608A pdb=" N TYR F 31 " --> pdb=" O LYS F 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS F 36 " --> pdb=" O TYR F 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.272A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.044A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.639A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.739A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 6 removed outlier: 5.925A pdb=" N THR H 69 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N SER H 67 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ILE H 29 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N SER H 65 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.903A pdb=" N LEU H 11 " --> pdb=" O LYS H 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.414A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.690A pdb=" N THR P 72 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 53 through 54 removed outlier: 5.530A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR P 85 " --> pdb=" O GLN P 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR P 96 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.858A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET O 34 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.764A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.575A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.867A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.852A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.786A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.786A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.769A pdb=" N SER E 77 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.427A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.427A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.697A pdb=" N GLU B 76 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.790A pdb=" N ALA B 90 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 52 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.747A pdb=" N TYR B 31 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 36 " --> pdb=" O TYR B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.604A pdb=" N GLU D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.749A pdb=" N LEU D 39 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR D 55 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.852A pdb=" N THR D 103 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.806A pdb=" N LYS D 36 " --> pdb=" O TYR D 31 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2007 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: 9.05 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7183 1.34 - 1.46: 6027 1.46 - 1.58: 9815 1.58 - 1.70: 1 1.70 - 1.82: 132 Bond restraints: 23158 Sorted by residual: bond pdb=" CG1 ILE V 527 " pdb=" CD1 ILE V 527 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.16e+00 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.583 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C5 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" CB CYS U 53 " pdb=" SG CYS U 53 " ideal model delta sigma weight residual 1.808 1.728 0.080 3.30e-02 9.18e+02 5.82e+00 bond pdb=" C ALA W 507 " pdb=" N GLN W 508 " ideal model delta sigma weight residual 1.329 1.291 0.038 1.60e-02 3.91e+03 5.66e+00 ... (remaining 23153 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.92: 515 105.92 - 112.97: 12328 112.97 - 120.02: 7654 120.02 - 127.07: 10631 127.07 - 134.11: 309 Bond angle restraints: 31437 Sorted by residual: angle pdb=" CB LYS I 76 " pdb=" CG LYS I 76 " pdb=" CD LYS I 76 " ideal model delta sigma weight residual 111.30 125.59 -14.29 2.30e+00 1.89e-01 3.86e+01 angle pdb=" C ALA W 507 " pdb=" N GLN W 508 " pdb=" CA GLN W 508 " ideal model delta sigma weight residual 120.49 127.60 -7.11 1.42e+00 4.96e-01 2.51e+01 angle pdb=" CA LEU T 51 " pdb=" CB LEU T 51 " pdb=" CG LEU T 51 " ideal model delta sigma weight residual 116.30 133.19 -16.89 3.50e+00 8.16e-02 2.33e+01 angle pdb=" CA CYS U 53 " pdb=" CB CYS U 53 " pdb=" SG CYS U 53 " ideal model delta sigma weight residual 114.40 125.23 -10.83 2.30e+00 1.89e-01 2.22e+01 angle pdb=" CA PRO V 606 " pdb=" N PRO V 606 " pdb=" CD PRO V 606 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.20e+01 ... (remaining 31432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 13147 23.80 - 47.60: 632 47.60 - 71.40: 66 71.40 - 95.21: 39 95.21 - 119.01: 16 Dihedral angle restraints: 13900 sinusoidal: 5715 harmonic: 8185 Sorted by residual: dihedral pdb=" CB CYS W 511 " pdb=" SG CYS W 511 " pdb=" SG CYS W 556 " pdb=" CB CYS W 556 " ideal model delta sinusoidal sigma weight residual 93.00 166.04 -73.04 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual 93.00 158.56 -65.56 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS W 601 " pdb=" SG CYS W 601 " pdb=" SG CYS W 608 " pdb=" CB CYS W 608 " ideal model delta sinusoidal sigma weight residual -86.00 -25.48 -60.52 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 13897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3476 0.164 - 0.329: 21 0.329 - 0.493: 2 0.493 - 0.658: 0 0.658 - 0.822: 1 Chirality restraints: 3500 Sorted by residual: chirality pdb=" C5 MAN K 4 " pdb=" C4 MAN K 4 " pdb=" C6 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False -2.51 -1.69 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.67 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA CYS U 53 " pdb=" N CYS U 53 " pdb=" C CYS U 53 " pdb=" CB CYS U 53 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 3497 not shown) Planarity restraints: 3997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY V 605 " -0.117 5.00e-02 4.00e+02 1.76e-01 4.93e+01 pdb=" N PRO V 606 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO V 606 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO V 606 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 101 " 0.087 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO M 102 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO M 102 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO M 102 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 68 " 0.022 2.00e-02 2.50e+03 2.31e-02 9.37e+00 pdb=" CG PHE G 68 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE G 68 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE G 68 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE G 68 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE G 68 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 68 " 0.001 2.00e-02 2.50e+03 ... (remaining 3994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 306 2.60 - 3.17: 20546 3.17 - 3.75: 35950 3.75 - 4.32: 52450 4.32 - 4.90: 86037 Nonbonded interactions: 195289 Sorted by model distance: nonbonded pdb=" OG SER N 63 " pdb=" OG1 THR N 74 " model vdw 2.024 2.440 nonbonded pdb=" NE1 TRP S 104 " pdb=" OE2 GLU V 545 " model vdw 2.059 2.520 nonbonded pdb=" NZ LYS B 24 " pdb=" OE1 GLU B 76 " model vdw 2.076 2.520 nonbonded pdb=" O SER H 63 " pdb=" OG1 THR H 74 " model vdw 2.104 2.440 nonbonded pdb=" NE2 GLN N 6 " pdb=" O GLN N 99 " model vdw 2.114 2.520 ... (remaining 195284 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1 through 113) selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 99 through 1 \ 03)) selection = (chain 'J' and (resid 2 through 30 or resid 33 or resid 35 through 52 or resid 5 \ 4 through 91 or resid 93 through 94 or resid 99 through 103)) selection = (chain 'N' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) selection = (chain 'P' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) selection = (chain 'R' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'Y' } ncs_group { reference = chain 'M' selection = chain 'O' selection = (chain 'Q' and resid 2 through 116) } ncs_group { reference = chain 'S' selection = (chain 'T' and (resid 32 through 261 or resid 271 through 279 or resid 283 throu \ gh 292 or resid 602 through 603)) selection = (chain 'U' and (resid 32 through 261 or resid 271 through 279 or resid 283 throu \ gh 292 or resid 602 through 603)) } ncs_group { reference = (chain 'V' and resid 507 through 613) selection = (chain 'W' and resid 507 through 613) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 29.720 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 60.800 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.006 0.111 23158 Z= 0.427 Angle : 0.857 16.893 31437 Z= 0.456 Chirality : 0.054 0.822 3500 Planarity : 0.006 0.176 3986 Dihedral : 14.198 119.008 8620 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2817 helix: 1.41 (0.37), residues: 196 sheet: 0.85 (0.16), residues: 1008 loop : -0.15 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP U 86 HIS 0.011 0.002 HIS O 103 PHE 0.052 0.003 PHE G 68 TYR 0.033 0.002 TYR O 32 ARG 0.009 0.001 ARG I 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 79 TYR cc_start: 0.8381 (m-80) cc_final: 0.8124 (m-80) REVERT: S 251 GLN cc_start: 0.8113 (mp10) cc_final: 0.7673 (mp10) REVERT: R 42 LYS cc_start: 0.8521 (mppt) cc_final: 0.7984 (mppt) REVERT: R 79 GLN cc_start: 0.7668 (mp10) cc_final: 0.7195 (mp10) REVERT: R 87 TYR cc_start: 0.9317 (m-80) cc_final: 0.9041 (m-80) REVERT: R 105 ILE cc_start: 0.7980 (tp) cc_final: 0.7615 (tp) REVERT: N 75 ILE cc_start: 0.9131 (mp) cc_final: 0.8846 (mm) REVERT: N 89 GLN cc_start: 0.8636 (tt0) cc_final: 0.8046 (tt0) REVERT: N 90 GLN cc_start: 0.8467 (pp30) cc_final: 0.8004 (pp30) REVERT: F 4 MET cc_start: 0.8943 (mmm) cc_final: 0.8269 (mmm) REVERT: F 24 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8767 (ttmm) REVERT: W 552 ASP cc_start: 0.8203 (t70) cc_final: 0.7884 (t0) REVERT: Q 3 GLN cc_start: 0.7958 (mm110) cc_final: 0.7754 (mm110) REVERT: Q 4 LEU cc_start: 0.9081 (mt) cc_final: 0.8709 (mt) REVERT: M 13 GLN cc_start: 0.8900 (mm110) cc_final: 0.8403 (mm-40) REVERT: M 18 LEU cc_start: 0.7362 (tp) cc_final: 0.7157 (tp) REVERT: M 27 PHE cc_start: 0.6221 (m-80) cc_final: 0.5989 (m-10) REVERT: M 60 TYR cc_start: 0.8064 (m-80) cc_final: 0.7351 (m-80) REVERT: M 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7274 (t70) REVERT: M 76 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8620 (mmtm) REVERT: M 106 ASP cc_start: 0.7550 (p0) cc_final: 0.7263 (p0) REVERT: H 2 ILE cc_start: 0.7651 (mt) cc_final: 0.7432 (tp) REVERT: P 3 GLN cc_start: 0.7990 (mp10) cc_final: 0.7497 (mp10) REVERT: P 27 GLN cc_start: 0.7142 (mp10) cc_final: 0.6500 (mp10) REVERT: P 38 GLN cc_start: 0.8362 (tt0) cc_final: 0.7300 (tt0) REVERT: P 61 ARG cc_start: 0.8889 (ptp90) cc_final: 0.8542 (ptp90) REVERT: P 90 GLN cc_start: 0.8005 (pp30) cc_final: 0.7780 (pp30) REVERT: P 92 TYR cc_start: 0.9158 (t80) cc_final: 0.8709 (t80) REVERT: O 20 LEU cc_start: 0.8329 (mp) cc_final: 0.8036 (mt) REVERT: O 34 MET cc_start: 0.8775 (mmt) cc_final: 0.8274 (mmt) REVERT: O 39 GLN cc_start: 0.8424 (tt0) cc_final: 0.8017 (tt0) REVERT: O 50 THR cc_start: 0.8574 (m) cc_final: 0.8231 (m) REVERT: O 87 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7412 (mtm180) REVERT: V 522 ASP cc_start: 0.7919 (m-30) cc_final: 0.7675 (t0) REVERT: V 578 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7353 (mm-30) REVERT: I 32 TYR cc_start: 0.7173 (m-80) cc_final: 0.6803 (m-10) REVERT: I 38 ARG cc_start: 0.6208 (ttp-110) cc_final: 0.5754 (ttm110) REVERT: I 53 HIS cc_start: 0.8803 (p-80) cc_final: 0.8593 (p-80) REVERT: I 57 ASP cc_start: 0.8507 (t0) cc_final: 0.8287 (t0) REVERT: I 81 LEU cc_start: 0.8630 (tp) cc_final: 0.8288 (tp) REVERT: I 99 ASN cc_start: 0.8737 (t0) cc_final: 0.8089 (t0) REVERT: J 45 LYS cc_start: 0.8460 (mptt) cc_final: 0.8209 (mmtt) REVERT: J 55 GLN cc_start: 0.8556 (tt0) cc_final: 0.8284 (tt0) REVERT: E 2 VAL cc_start: 0.9216 (t) cc_final: 0.8950 (t) REVERT: B 35 ASN cc_start: 0.9169 (t0) cc_final: 0.8944 (t0) REVERT: B 55 TYR cc_start: 0.9078 (p90) cc_final: 0.8643 (p90) REVERT: D 35 ASN cc_start: 0.9180 (t0) cc_final: 0.8905 (t0) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.3607 time to fit residues: 261.6726 Evaluate side-chains 385 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 0.8980 chunk 209 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.0470 chunk 112 optimal weight: 0.0870 chunk 217 optimal weight: 0.0870 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 221 GLN N 6 GLN F 27 GLN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN O 39 GLN V 521 GLN X 551 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23158 Z= 0.206 Angle : 0.650 12.985 31437 Z= 0.339 Chirality : 0.046 0.389 3500 Planarity : 0.005 0.095 3986 Dihedral : 10.014 89.870 3646 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.91 % Allowed : 8.23 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2817 helix: 1.14 (0.40), residues: 196 sheet: 0.73 (0.16), residues: 1001 loop : -0.19 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 86 HIS 0.008 0.001 HIS C 35 PHE 0.024 0.002 PHE M 27 TYR 0.028 0.002 TYR T 162 ARG 0.008 0.001 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 446 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 34 MET cc_start: 0.8290 (mmm) cc_final: 0.7889 (mmt) REVERT: S 251 GLN cc_start: 0.8284 (mp10) cc_final: 0.7892 (mp10) REVERT: U 221 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8259 (mm-40) REVERT: R 4 MET cc_start: 0.8638 (mmp) cc_final: 0.8067 (mmp) REVERT: R 27 GLN cc_start: 0.8870 (pp30) cc_final: 0.8556 (pp30) REVERT: R 79 GLN cc_start: 0.7761 (mp10) cc_final: 0.7297 (mp10) REVERT: R 87 TYR cc_start: 0.9124 (m-80) cc_final: 0.8681 (m-80) REVERT: R 105 ILE cc_start: 0.8035 (tp) cc_final: 0.7771 (tp) REVERT: N 3 GLN cc_start: 0.7860 (mp10) cc_final: 0.7553 (mp10) REVERT: N 45 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8648 (ptmm) REVERT: N 61 ARG cc_start: 0.7944 (mtm110) cc_final: 0.6913 (ptp90) REVERT: N 75 ILE cc_start: 0.9216 (mp) cc_final: 0.8988 (mm) REVERT: N 79 GLN cc_start: 0.7297 (mp10) cc_final: 0.6720 (mp10) REVERT: N 89 GLN cc_start: 0.8499 (tt0) cc_final: 0.8072 (tt0) REVERT: N 90 GLN cc_start: 0.8539 (pp30) cc_final: 0.8285 (pp30) REVERT: F 11 LEU cc_start: 0.8738 (tp) cc_final: 0.8431 (tt) REVERT: F 17 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7687 (mt-10) REVERT: F 24 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8835 (ttmm) REVERT: W 552 ASP cc_start: 0.8055 (t70) cc_final: 0.7771 (t0) REVERT: Q 4 LEU cc_start: 0.9046 (mt) cc_final: 0.8784 (mt) REVERT: Q 32 TYR cc_start: 0.7735 (m-80) cc_final: 0.7285 (m-80) REVERT: M 3 GLN cc_start: 0.7759 (mm110) cc_final: 0.7518 (mm110) REVERT: M 13 GLN cc_start: 0.8920 (mm110) cc_final: 0.8474 (mm-40) REVERT: M 27 PHE cc_start: 0.6314 (m-80) cc_final: 0.6072 (m-10) REVERT: M 34 MET cc_start: 0.8330 (mmt) cc_final: 0.8071 (mmt) REVERT: M 60 TYR cc_start: 0.8177 (m-80) cc_final: 0.7549 (m-80) REVERT: M 73 ASP cc_start: 0.7844 (t0) cc_final: 0.7014 (t0) REVERT: M 76 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8821 (mmtm) REVERT: M 106 ASP cc_start: 0.7566 (p0) cc_final: 0.7296 (p0) REVERT: H 4 MET cc_start: 0.8060 (tpp) cc_final: 0.7226 (mmm) REVERT: H 23 CYS cc_start: 0.3206 (t) cc_final: 0.1361 (t) REVERT: P 3 GLN cc_start: 0.7923 (mp10) cc_final: 0.7529 (mp10) REVERT: P 4 MET cc_start: 0.6890 (mmm) cc_final: 0.5906 (tpp) REVERT: P 27 GLN cc_start: 0.7155 (mp10) cc_final: 0.6532 (mp10) REVERT: P 38 GLN cc_start: 0.8420 (tt0) cc_final: 0.7762 (tt0) REVERT: P 61 ARG cc_start: 0.8980 (ptp90) cc_final: 0.8614 (ptp90) REVERT: P 92 TYR cc_start: 0.9151 (t80) cc_final: 0.8814 (t80) REVERT: O 34 MET cc_start: 0.8707 (mmt) cc_final: 0.8183 (mmt) REVERT: O 39 GLN cc_start: 0.8194 (tt0) cc_final: 0.7883 (tt0) REVERT: O 50 THR cc_start: 0.8633 (m) cc_final: 0.8302 (m) REVERT: O 84 ASN cc_start: 0.6904 (t0) cc_final: 0.6519 (t0) REVERT: O 87 ARG cc_start: 0.7596 (mtm180) cc_final: 0.7253 (mtm180) REVERT: I 30 ASN cc_start: 0.8896 (m-40) cc_final: 0.8688 (m-40) REVERT: I 32 TYR cc_start: 0.7200 (m-80) cc_final: 0.6810 (m-10) REVERT: I 53 HIS cc_start: 0.8817 (p-80) cc_final: 0.8589 (p-80) REVERT: I 57 ASP cc_start: 0.8495 (t0) cc_final: 0.8230 (t0) REVERT: I 81 LEU cc_start: 0.7966 (tp) cc_final: 0.7724 (tt) REVERT: I 82 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8539 (mm-40) REVERT: I 83 MET cc_start: 0.8370 (mpp) cc_final: 0.8098 (mtm) REVERT: I 99 ASN cc_start: 0.8751 (t0) cc_final: 0.8211 (t0) REVERT: J 45 LYS cc_start: 0.8580 (mptt) cc_final: 0.8306 (mmtt) REVERT: J 87 TYR cc_start: 0.6928 (m-80) cc_final: 0.6425 (m-80) REVERT: E 58 TYR cc_start: 0.8236 (m-80) cc_final: 0.7997 (m-80) REVERT: B 35 ASN cc_start: 0.9083 (t0) cc_final: 0.8771 (t0) REVERT: D 4 MET cc_start: 0.8780 (mmm) cc_final: 0.7414 (mmm) REVERT: D 35 ASN cc_start: 0.9221 (t0) cc_final: 0.9010 (t0) outliers start: 22 outliers final: 13 residues processed: 455 average time/residue: 0.3551 time to fit residues: 251.0943 Evaluate side-chains 395 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 382 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain C residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 139 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 224 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN T 107 ASN T 278 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN F 27 GLN F 35 ASN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23158 Z= 0.273 Angle : 0.624 11.311 31437 Z= 0.321 Chirality : 0.045 0.355 3500 Planarity : 0.004 0.069 3986 Dihedral : 9.143 83.228 3646 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.66 % Allowed : 11.01 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2817 helix: 1.00 (0.39), residues: 198 sheet: 0.41 (0.16), residues: 1011 loop : -0.30 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 35 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.001 PHE S 234 TYR 0.027 0.002 TYR T 162 ARG 0.006 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 400 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8072 (tm-30) REVERT: S 221 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: S 251 GLN cc_start: 0.8390 (mp10) cc_final: 0.8068 (mp10) REVERT: U 221 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8131 (mm-40) REVERT: R 3 GLN cc_start: 0.8414 (mm110) cc_final: 0.8204 (mm-40) REVERT: R 4 MET cc_start: 0.8729 (mmp) cc_final: 0.8218 (mmp) REVERT: R 79 GLN cc_start: 0.7829 (mp10) cc_final: 0.7410 (mp10) REVERT: R 105 ILE cc_start: 0.7582 (tp) cc_final: 0.7294 (tp) REVERT: N 3 GLN cc_start: 0.8112 (mp10) cc_final: 0.7800 (mp10) REVERT: N 37 GLN cc_start: 0.8400 (tt0) cc_final: 0.7758 (tt0) REVERT: N 45 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8713 (ptmm) REVERT: N 61 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7167 (ptp90) REVERT: N 75 ILE cc_start: 0.9228 (mp) cc_final: 0.8955 (mm) REVERT: N 79 GLN cc_start: 0.7187 (mp10) cc_final: 0.6622 (mp10) REVERT: N 89 GLN cc_start: 0.8533 (tt0) cc_final: 0.7716 (tt0) REVERT: N 90 GLN cc_start: 0.8460 (pp30) cc_final: 0.8046 (pp30) REVERT: F 11 LEU cc_start: 0.8677 (tp) cc_final: 0.8466 (tt) REVERT: F 24 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8798 (ttmm) REVERT: W 552 ASP cc_start: 0.8103 (t70) cc_final: 0.7863 (t0) REVERT: Q 4 LEU cc_start: 0.9129 (mt) cc_final: 0.8811 (mt) REVERT: M 3 GLN cc_start: 0.7747 (mm110) cc_final: 0.7480 (mm110) REVERT: M 13 GLN cc_start: 0.8920 (mm110) cc_final: 0.8459 (mm-40) REVERT: M 34 MET cc_start: 0.8394 (mmt) cc_final: 0.7991 (mmt) REVERT: M 50 THR cc_start: 0.8424 (t) cc_final: 0.8125 (t) REVERT: M 60 TYR cc_start: 0.8245 (m-80) cc_final: 0.7637 (m-80) REVERT: M 73 ASP cc_start: 0.7731 (t0) cc_final: 0.6588 (t0) REVERT: M 76 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8815 (mptt) REVERT: M 106 ASP cc_start: 0.7545 (p0) cc_final: 0.7309 (p0) REVERT: M 114 VAL cc_start: 0.8910 (t) cc_final: 0.8613 (t) REVERT: G 65 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8612 (mmmm) REVERT: H 4 MET cc_start: 0.8104 (tpp) cc_final: 0.7673 (mmm) REVERT: H 23 CYS cc_start: 0.3243 (t) cc_final: 0.1211 (t) REVERT: P 3 GLN cc_start: 0.7887 (mp10) cc_final: 0.7370 (mp10) REVERT: P 27 GLN cc_start: 0.7163 (mp10) cc_final: 0.6472 (mp10) REVERT: P 38 GLN cc_start: 0.8414 (tt0) cc_final: 0.7719 (tt0) REVERT: P 61 ARG cc_start: 0.8968 (ptp90) cc_final: 0.8600 (ptp90) REVERT: O 34 MET cc_start: 0.8672 (mmt) cc_final: 0.8441 (mmp) REVERT: O 39 GLN cc_start: 0.8181 (tt0) cc_final: 0.7947 (tt0) REVERT: O 50 THR cc_start: 0.8666 (m) cc_final: 0.8341 (m) REVERT: O 84 ASN cc_start: 0.6859 (t0) cc_final: 0.6577 (t0) REVERT: I 20 LEU cc_start: 0.8556 (pt) cc_final: 0.8353 (pt) REVERT: I 30 ASN cc_start: 0.8859 (m-40) cc_final: 0.8636 (m-40) REVERT: I 32 TYR cc_start: 0.7317 (m-80) cc_final: 0.6926 (m-80) REVERT: I 57 ASP cc_start: 0.8486 (t0) cc_final: 0.8155 (t0) REVERT: I 80 TYR cc_start: 0.8133 (m-10) cc_final: 0.7865 (m-10) REVERT: I 83 MET cc_start: 0.8503 (mpp) cc_final: 0.7921 (mpp) REVERT: I 99 ASN cc_start: 0.8749 (t0) cc_final: 0.8167 (t0) REVERT: I 105 TYR cc_start: 0.7620 (m-10) cc_final: 0.7412 (m-10) REVERT: J 45 LYS cc_start: 0.8588 (mptt) cc_final: 0.8290 (mmtt) REVERT: J 87 TYR cc_start: 0.6897 (m-80) cc_final: 0.6412 (m-80) REVERT: E 33 ASP cc_start: 0.8283 (p0) cc_final: 0.8080 (p0) REVERT: B 35 ASN cc_start: 0.9151 (t0) cc_final: 0.8820 (t0) REVERT: D 4 MET cc_start: 0.8839 (mmm) cc_final: 0.7427 (mmm) outliers start: 40 outliers final: 30 residues processed: 421 average time/residue: 0.3661 time to fit residues: 243.0896 Evaluate side-chains 410 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 379 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 248 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 35 ASN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 560 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23158 Z= 0.274 Angle : 0.609 11.042 31437 Z= 0.311 Chirality : 0.044 0.360 3500 Planarity : 0.004 0.059 3986 Dihedral : 8.520 77.938 3646 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.04 % Allowed : 12.80 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2817 helix: 0.98 (0.39), residues: 198 sheet: 0.28 (0.16), residues: 1016 loop : -0.34 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 288 HIS 0.007 0.001 HIS E 35 PHE 0.014 0.001 PHE S 234 TYR 0.027 0.001 TYR T 162 ARG 0.006 0.000 ARG R 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 403 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8028 (tm-30) REVERT: S 221 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: S 251 GLN cc_start: 0.8395 (mp10) cc_final: 0.8098 (mp10) REVERT: U 221 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8054 (mm-40) REVERT: R 3 GLN cc_start: 0.8438 (mm110) cc_final: 0.8180 (mm-40) REVERT: R 4 MET cc_start: 0.8741 (mmp) cc_final: 0.8292 (mmp) REVERT: R 79 GLN cc_start: 0.7826 (mp10) cc_final: 0.7375 (mp10) REVERT: R 105 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7016 (tp) REVERT: N 37 GLN cc_start: 0.8385 (tt0) cc_final: 0.8009 (tt0) REVERT: N 45 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8755 (ptmm) REVERT: N 61 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7312 (ptp90) REVERT: N 75 ILE cc_start: 0.9135 (mp) cc_final: 0.8870 (mm) REVERT: N 79 GLN cc_start: 0.7252 (mp10) cc_final: 0.6886 (mp10) REVERT: N 89 GLN cc_start: 0.8518 (tt0) cc_final: 0.7660 (tt0) REVERT: N 90 GLN cc_start: 0.8477 (pp30) cc_final: 0.8034 (pp30) REVERT: F 11 LEU cc_start: 0.8650 (tp) cc_final: 0.8431 (tt) REVERT: F 17 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7682 (mt-10) REVERT: F 24 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8821 (ttmm) REVERT: W 552 ASP cc_start: 0.8155 (t70) cc_final: 0.7928 (t0) REVERT: Q 4 LEU cc_start: 0.9115 (mt) cc_final: 0.8836 (mt) REVERT: M 3 GLN cc_start: 0.7814 (mm110) cc_final: 0.7597 (mm110) REVERT: M 13 GLN cc_start: 0.8904 (mm110) cc_final: 0.8426 (mm-40) REVERT: M 50 THR cc_start: 0.8567 (t) cc_final: 0.8305 (t) REVERT: M 73 ASP cc_start: 0.7661 (t0) cc_final: 0.6534 (t0) REVERT: M 76 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8796 (mptt) REVERT: M 87 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7851 (mtm-85) REVERT: M 106 ASP cc_start: 0.7586 (p0) cc_final: 0.7360 (p0) REVERT: G 65 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8563 (mmmm) REVERT: G 68 PHE cc_start: 0.8114 (m-10) cc_final: 0.6800 (m-10) REVERT: G 83 MET cc_start: 0.8569 (mpp) cc_final: 0.7989 (mmp) REVERT: H 4 MET cc_start: 0.8161 (tpp) cc_final: 0.7800 (mmm) REVERT: H 23 CYS cc_start: 0.3175 (t) cc_final: 0.2353 (t) REVERT: P 3 GLN cc_start: 0.7907 (mp10) cc_final: 0.7426 (mp10) REVERT: P 38 GLN cc_start: 0.8439 (tt0) cc_final: 0.7687 (tt0) REVERT: P 61 ARG cc_start: 0.8913 (ptp90) cc_final: 0.8566 (ptp90) REVERT: O 34 MET cc_start: 0.8643 (mmt) cc_final: 0.8382 (mmp) REVERT: O 50 THR cc_start: 0.8675 (m) cc_final: 0.8376 (m) REVERT: O 84 ASN cc_start: 0.7054 (t0) cc_final: 0.6783 (t0) REVERT: I 32 TYR cc_start: 0.7261 (m-80) cc_final: 0.6826 (m-80) REVERT: I 57 ASP cc_start: 0.8514 (t0) cc_final: 0.8199 (t0) REVERT: I 80 TYR cc_start: 0.8069 (m-10) cc_final: 0.7737 (m-10) REVERT: I 83 MET cc_start: 0.8319 (mpp) cc_final: 0.7768 (mpp) REVERT: I 99 ASN cc_start: 0.8761 (t0) cc_final: 0.8193 (t0) REVERT: J 45 LYS cc_start: 0.8625 (mptt) cc_final: 0.8351 (mmtt) REVERT: J 87 TYR cc_start: 0.7138 (m-80) cc_final: 0.6605 (m-80) REVERT: B 35 ASN cc_start: 0.9164 (t0) cc_final: 0.8814 (t0) REVERT: D 4 MET cc_start: 0.8829 (mmm) cc_final: 0.7345 (mmm) outliers start: 49 outliers final: 35 residues processed: 426 average time/residue: 0.3396 time to fit residues: 228.4224 Evaluate side-chains 414 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 377 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 222 optimal weight: 0.0170 chunk 151 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN F 27 GLN F 35 ASN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23158 Z= 0.266 Angle : 0.604 12.181 31437 Z= 0.308 Chirality : 0.044 0.362 3500 Planarity : 0.004 0.057 3986 Dihedral : 8.161 74.045 3646 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 13.92 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2817 helix: 1.03 (0.39), residues: 198 sheet: 0.19 (0.16), residues: 1009 loop : -0.37 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 288 HIS 0.010 0.001 HIS I 53 PHE 0.021 0.001 PHE S 234 TYR 0.027 0.001 TYR T 162 ARG 0.008 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 397 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7999 (tm-30) REVERT: S 221 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: S 251 GLN cc_start: 0.8408 (mp10) cc_final: 0.8185 (mp10) REVERT: U 221 GLN cc_start: 0.8666 (mm-40) cc_final: 0.7957 (mm-40) REVERT: R 3 GLN cc_start: 0.8400 (mm110) cc_final: 0.8182 (mm-40) REVERT: R 4 MET cc_start: 0.8759 (mmp) cc_final: 0.8339 (mmp) REVERT: R 24 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8301 (mtp-110) REVERT: R 79 GLN cc_start: 0.7826 (mp10) cc_final: 0.7327 (mp10) REVERT: R 104 GLU cc_start: 0.6121 (tt0) cc_final: 0.5791 (tt0) REVERT: R 105 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7102 (tp) REVERT: N 3 GLN cc_start: 0.8442 (mp-120) cc_final: 0.8082 (mp10) REVERT: N 37 GLN cc_start: 0.8349 (tt0) cc_final: 0.7621 (tt0) REVERT: N 61 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7446 (ptp90) REVERT: N 75 ILE cc_start: 0.9086 (mp) cc_final: 0.8841 (mm) REVERT: N 79 GLN cc_start: 0.7236 (mp10) cc_final: 0.6952 (mp10) REVERT: N 89 GLN cc_start: 0.8497 (tt0) cc_final: 0.7645 (tt0) REVERT: N 90 GLN cc_start: 0.8473 (pp30) cc_final: 0.8096 (pp30) REVERT: F 11 LEU cc_start: 0.8639 (tp) cc_final: 0.8258 (tt) REVERT: F 17 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7748 (mt-10) REVERT: F 24 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8805 (ttmm) REVERT: W 548 MET cc_start: 0.8412 (mtp) cc_final: 0.8149 (mtt) REVERT: W 552 ASP cc_start: 0.8217 (t70) cc_final: 0.7999 (t0) REVERT: Q 4 LEU cc_start: 0.9085 (mt) cc_final: 0.8796 (mt) REVERT: M 13 GLN cc_start: 0.8933 (mm110) cc_final: 0.8434 (mm-40) REVERT: M 34 MET cc_start: 0.8448 (mmt) cc_final: 0.8046 (mmt) REVERT: M 50 THR cc_start: 0.8631 (t) cc_final: 0.8376 (t) REVERT: M 106 ASP cc_start: 0.7616 (p0) cc_final: 0.7398 (p0) REVERT: G 65 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8535 (mmmm) REVERT: G 68 PHE cc_start: 0.8130 (m-10) cc_final: 0.6340 (m-10) REVERT: G 83 MET cc_start: 0.8547 (mpp) cc_final: 0.7880 (mmp) REVERT: H 4 MET cc_start: 0.8072 (tpp) cc_final: 0.7820 (mmm) REVERT: H 23 CYS cc_start: 0.3278 (t) cc_final: 0.1328 (t) REVERT: H 32 TYR cc_start: 0.8447 (m-10) cc_final: 0.8149 (m-10) REVERT: P 3 GLN cc_start: 0.7908 (mp10) cc_final: 0.7441 (mp10) REVERT: P 4 MET cc_start: 0.7053 (mmm) cc_final: 0.6791 (tpp) REVERT: P 38 GLN cc_start: 0.8279 (tt0) cc_final: 0.7698 (tt0) REVERT: P 61 ARG cc_start: 0.8924 (ptp90) cc_final: 0.8508 (ptp90) REVERT: O 34 MET cc_start: 0.8611 (mmt) cc_final: 0.8321 (mmp) REVERT: O 50 THR cc_start: 0.8626 (m) cc_final: 0.8322 (m) REVERT: O 84 ASN cc_start: 0.7155 (t0) cc_final: 0.6932 (t0) REVERT: X 591 ASP cc_start: 0.8756 (t0) cc_final: 0.8497 (t0) REVERT: I 25 SER cc_start: 0.8160 (t) cc_final: 0.7732 (p) REVERT: I 32 TYR cc_start: 0.7274 (m-80) cc_final: 0.6832 (m-80) REVERT: I 57 ASP cc_start: 0.8500 (t0) cc_final: 0.8248 (t0) REVERT: I 80 TYR cc_start: 0.7910 (m-10) cc_final: 0.7614 (m-10) REVERT: I 83 MET cc_start: 0.8641 (mpp) cc_final: 0.7983 (mpp) REVERT: I 99 ASN cc_start: 0.8734 (t0) cc_final: 0.8164 (t0) REVERT: J 45 LYS cc_start: 0.8563 (mptt) cc_final: 0.8317 (mmtt) REVERT: J 87 TYR cc_start: 0.7249 (m-80) cc_final: 0.6661 (m-80) REVERT: B 35 ASN cc_start: 0.9166 (t0) cc_final: 0.8818 (t0) REVERT: D 4 MET cc_start: 0.8864 (mmm) cc_final: 0.7359 (mmm) outliers start: 63 outliers final: 45 residues processed: 436 average time/residue: 0.3749 time to fit residues: 260.8632 Evaluate side-chains 425 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 378 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 38 GLN O 39 GLN O 110 GLN ** V 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23158 Z= 0.427 Angle : 0.648 9.642 31437 Z= 0.333 Chirality : 0.045 0.366 3500 Planarity : 0.004 0.067 3986 Dihedral : 8.154 71.170 3646 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.49 % Allowed : 15.34 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2817 helix: 0.91 (0.40), residues: 194 sheet: 0.07 (0.16), residues: 993 loop : -0.46 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP U 288 HIS 0.008 0.001 HIS E 35 PHE 0.021 0.002 PHE S 234 TYR 0.028 0.002 TYR T 162 ARG 0.008 0.001 ARG R 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 380 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7939 (tm-30) REVERT: S 221 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: S 251 GLN cc_start: 0.8410 (mp10) cc_final: 0.8158 (mp10) REVERT: R 3 GLN cc_start: 0.8448 (mm110) cc_final: 0.8243 (mm-40) REVERT: R 4 MET cc_start: 0.8799 (mmp) cc_final: 0.8424 (mmp) REVERT: R 79 GLN cc_start: 0.7871 (mp10) cc_final: 0.7358 (mp10) REVERT: R 102 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7734 (ptm-80) REVERT: R 105 ILE cc_start: 0.7470 (tp) cc_final: 0.7167 (tp) REVERT: N 3 GLN cc_start: 0.8585 (mp-120) cc_final: 0.8170 (mp10) REVERT: N 37 GLN cc_start: 0.8360 (tt0) cc_final: 0.7951 (tt0) REVERT: N 61 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7600 (mtp-110) REVERT: N 79 GLN cc_start: 0.7251 (mp10) cc_final: 0.6656 (mp10) REVERT: N 89 GLN cc_start: 0.8388 (tt0) cc_final: 0.7448 (tt0) REVERT: N 90 GLN cc_start: 0.8463 (pp30) cc_final: 0.8015 (pp30) REVERT: F 17 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7747 (mt-10) REVERT: F 24 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8793 (ttmm) REVERT: W 548 MET cc_start: 0.8401 (mtp) cc_final: 0.8160 (mtt) REVERT: M 13 GLN cc_start: 0.8934 (mm110) cc_final: 0.8442 (mm-40) REVERT: M 50 THR cc_start: 0.8710 (t) cc_final: 0.8456 (t) REVERT: M 73 ASP cc_start: 0.7470 (t0) cc_final: 0.6817 (t0) REVERT: M 76 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8521 (mmtm) REVERT: G 65 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8574 (mmmm) REVERT: G 68 PHE cc_start: 0.8242 (m-10) cc_final: 0.6728 (m-10) REVERT: G 83 MET cc_start: 0.8499 (mpp) cc_final: 0.7971 (mmp) REVERT: H 4 MET cc_start: 0.8121 (tpp) cc_final: 0.7794 (mmm) REVERT: P 3 GLN cc_start: 0.7901 (mp10) cc_final: 0.7419 (mp10) REVERT: P 61 ARG cc_start: 0.8923 (ptp90) cc_final: 0.8457 (ptp90) REVERT: O 34 MET cc_start: 0.8643 (mmt) cc_final: 0.8337 (mmp) REVERT: O 50 THR cc_start: 0.8537 (m) cc_final: 0.8262 (m) REVERT: O 84 ASN cc_start: 0.7169 (t0) cc_final: 0.6932 (t0) REVERT: I 25 SER cc_start: 0.8064 (t) cc_final: 0.7642 (p) REVERT: I 32 TYR cc_start: 0.7409 (m-80) cc_final: 0.6976 (m-80) REVERT: I 57 ASP cc_start: 0.8541 (t0) cc_final: 0.8223 (t0) REVERT: I 80 TYR cc_start: 0.8013 (m-10) cc_final: 0.7731 (m-10) REVERT: I 83 MET cc_start: 0.8483 (mpp) cc_final: 0.8083 (mpp) REVERT: I 99 ASN cc_start: 0.8727 (t0) cc_final: 0.8172 (t0) REVERT: J 45 LYS cc_start: 0.8537 (mptt) cc_final: 0.8273 (mmtt) REVERT: J 87 TYR cc_start: 0.7339 (m-80) cc_final: 0.6758 (m-80) REVERT: B 35 ASN cc_start: 0.9213 (t0) cc_final: 0.8875 (t0) outliers start: 60 outliers final: 45 residues processed: 420 average time/residue: 0.3615 time to fit residues: 241.0628 Evaluate side-chains 418 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 372 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 152 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 35 ASN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** V 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23158 Z= 0.234 Angle : 0.620 16.884 31437 Z= 0.314 Chirality : 0.044 0.377 3500 Planarity : 0.004 0.062 3986 Dihedral : 7.731 68.035 3646 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.37 % Allowed : 16.25 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2817 helix: 1.04 (0.40), residues: 194 sheet: 0.01 (0.16), residues: 1017 loop : -0.46 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 288 HIS 0.007 0.001 HIS E 35 PHE 0.021 0.001 PHE S 234 TYR 0.026 0.001 TYR T 162 ARG 0.008 0.000 ARG R 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7912 (tm-30) REVERT: S 251 GLN cc_start: 0.8396 (mp10) cc_final: 0.8069 (mp10) REVERT: U 221 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8126 (mm-40) REVERT: R 4 MET cc_start: 0.8782 (mmp) cc_final: 0.8422 (mmp) REVERT: R 24 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8335 (mtp-110) REVERT: R 42 LYS cc_start: 0.8580 (mppt) cc_final: 0.7986 (mppt) REVERT: R 79 GLN cc_start: 0.7824 (mp10) cc_final: 0.7294 (mp10) REVERT: R 104 GLU cc_start: 0.5903 (tt0) cc_final: 0.5639 (tt0) REVERT: R 105 ILE cc_start: 0.7593 (tp) cc_final: 0.7301 (tp) REVERT: N 3 GLN cc_start: 0.8649 (mp-120) cc_final: 0.8310 (mp10) REVERT: N 37 GLN cc_start: 0.8364 (tt0) cc_final: 0.7661 (tt0) REVERT: N 61 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7459 (ptp90) REVERT: N 79 GLN cc_start: 0.7112 (mp10) cc_final: 0.6873 (mp10) REVERT: N 89 GLN cc_start: 0.8374 (tt0) cc_final: 0.7493 (tt0) REVERT: N 90 GLN cc_start: 0.8346 (pp30) cc_final: 0.7886 (pp30) REVERT: F 17 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7748 (mt-10) REVERT: F 24 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8814 (ttmm) REVERT: W 548 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (mtt) REVERT: W 552 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7642 (t0) REVERT: M 13 GLN cc_start: 0.8906 (mm110) cc_final: 0.8419 (mm-40) REVERT: M 50 THR cc_start: 0.8731 (t) cc_final: 0.8485 (t) REVERT: M 73 ASP cc_start: 0.7525 (t0) cc_final: 0.6780 (t0) REVERT: M 76 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8649 (mmtm) REVERT: G 65 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8605 (mmmm) REVERT: G 68 PHE cc_start: 0.8187 (m-10) cc_final: 0.6645 (m-10) REVERT: G 83 MET cc_start: 0.8468 (mpp) cc_final: 0.7944 (mmp) REVERT: H 32 TYR cc_start: 0.8446 (m-10) cc_final: 0.8134 (m-10) REVERT: H 70 ASP cc_start: 0.9020 (t0) cc_final: 0.8789 (m-30) REVERT: P 61 ARG cc_start: 0.8908 (ptp90) cc_final: 0.8481 (ptp90) REVERT: O 34 MET cc_start: 0.8624 (mmt) cc_final: 0.8318 (mmp) REVERT: O 50 THR cc_start: 0.8533 (m) cc_final: 0.8293 (m) REVERT: O 84 ASN cc_start: 0.7144 (t0) cc_final: 0.6876 (t0) REVERT: V 578 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 25 SER cc_start: 0.7983 (t) cc_final: 0.7613 (p) REVERT: I 32 TYR cc_start: 0.7333 (m-80) cc_final: 0.6880 (m-80) REVERT: I 53 HIS cc_start: 0.8836 (p90) cc_final: 0.8595 (p90) REVERT: I 57 ASP cc_start: 0.8509 (t0) cc_final: 0.8261 (t0) REVERT: I 83 MET cc_start: 0.8477 (mpp) cc_final: 0.8071 (mpp) REVERT: I 99 ASN cc_start: 0.8711 (t0) cc_final: 0.8152 (t0) REVERT: J 45 LYS cc_start: 0.8567 (mptt) cc_final: 0.8341 (mmtt) REVERT: J 87 TYR cc_start: 0.7300 (m-80) cc_final: 0.6807 (m-80) REVERT: B 35 ASN cc_start: 0.9157 (t0) cc_final: 0.8814 (t0) REVERT: D 4 MET cc_start: 0.8856 (mmm) cc_final: 0.7442 (mmm) outliers start: 57 outliers final: 46 residues processed: 421 average time/residue: 0.3371 time to fit residues: 223.8344 Evaluate side-chains 424 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 376 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 548 MET Chi-restraints excluded: chain W residue 552 ASP Chi-restraints excluded: chain W residue 556 CYS Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 165 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.7346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN F 27 GLN ** W 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** V 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23158 Z= 0.236 Angle : 0.616 16.126 31437 Z= 0.310 Chirality : 0.044 0.369 3500 Planarity : 0.004 0.068 3986 Dihedral : 7.467 67.239 3646 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.49 % Allowed : 16.46 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2817 helix: 1.07 (0.40), residues: 194 sheet: 0.06 (0.16), residues: 1011 loop : -0.48 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 PHE 0.020 0.001 PHE S 234 TYR 0.026 0.001 TYR T 162 ARG 0.009 0.000 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 387 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7901 (tm-30) REVERT: S 221 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: S 251 GLN cc_start: 0.8347 (mp10) cc_final: 0.7965 (mp10) REVERT: U 221 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8069 (mm-40) REVERT: R 4 MET cc_start: 0.8845 (mmp) cc_final: 0.8528 (mmp) REVERT: R 42 LYS cc_start: 0.8539 (mppt) cc_final: 0.7933 (mppt) REVERT: R 79 GLN cc_start: 0.7826 (mp10) cc_final: 0.7292 (mp10) REVERT: R 104 GLU cc_start: 0.5702 (tt0) cc_final: 0.5427 (tt0) REVERT: R 105 ILE cc_start: 0.7674 (tp) cc_final: 0.7371 (tp) REVERT: N 37 GLN cc_start: 0.8384 (tt0) cc_final: 0.7666 (tt0) REVERT: N 61 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7450 (ptp90) REVERT: N 89 GLN cc_start: 0.8375 (tt0) cc_final: 0.7523 (tt0) REVERT: N 90 GLN cc_start: 0.8439 (pp30) cc_final: 0.8106 (pp30) REVERT: F 17 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7749 (mt-10) REVERT: F 24 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8823 (ttmm) REVERT: W 548 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: M 13 GLN cc_start: 0.8887 (mm110) cc_final: 0.8391 (mm-40) REVERT: M 50 THR cc_start: 0.8743 (t) cc_final: 0.8533 (t) REVERT: M 73 ASP cc_start: 0.7577 (t0) cc_final: 0.6787 (t0) REVERT: M 76 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8672 (mmtm) REVERT: G 65 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8586 (mmmm) REVERT: G 68 PHE cc_start: 0.8173 (m-10) cc_final: 0.5805 (m-10) REVERT: G 83 MET cc_start: 0.8463 (mpp) cc_final: 0.7810 (mmt) REVERT: H 23 CYS cc_start: 0.3273 (t) cc_final: 0.2243 (t) REVERT: H 32 TYR cc_start: 0.8445 (m-10) cc_final: 0.8080 (m-10) REVERT: H 70 ASP cc_start: 0.9044 (t0) cc_final: 0.8786 (m-30) REVERT: P 3 GLN cc_start: 0.7795 (mp10) cc_final: 0.7263 (mp10) REVERT: P 4 MET cc_start: 0.7020 (mmm) cc_final: 0.6781 (mmm) REVERT: P 61 ARG cc_start: 0.8895 (ptp90) cc_final: 0.8479 (ptp90) REVERT: P 81 GLU cc_start: 0.8232 (pm20) cc_final: 0.7963 (pm20) REVERT: O 34 MET cc_start: 0.8602 (mmt) cc_final: 0.7795 (mmp) REVERT: O 50 THR cc_start: 0.8455 (m) cc_final: 0.8229 (m) REVERT: O 84 ASN cc_start: 0.7043 (t0) cc_final: 0.6753 (t0) REVERT: X 596 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7504 (ttm110) REVERT: I 25 SER cc_start: 0.8014 (t) cc_final: 0.7639 (p) REVERT: I 32 TYR cc_start: 0.7307 (m-80) cc_final: 0.6830 (m-80) REVERT: I 53 HIS cc_start: 0.8848 (p90) cc_final: 0.8592 (p90) REVERT: I 57 ASP cc_start: 0.8504 (t0) cc_final: 0.8272 (t0) REVERT: I 82 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8931 (mm110) REVERT: I 83 MET cc_start: 0.8499 (mpp) cc_final: 0.8047 (mpp) REVERT: I 95 TYR cc_start: 0.8581 (m-80) cc_final: 0.8056 (m-80) REVERT: I 99 ASN cc_start: 0.8679 (t0) cc_final: 0.8097 (t0) REVERT: J 45 LYS cc_start: 0.8556 (mptt) cc_final: 0.8317 (mmtt) REVERT: J 87 TYR cc_start: 0.7289 (m-80) cc_final: 0.6786 (m-80) REVERT: B 35 ASN cc_start: 0.9159 (t0) cc_final: 0.8809 (t0) REVERT: D 4 MET cc_start: 0.8814 (mmm) cc_final: 0.7442 (mmm) outliers start: 60 outliers final: 49 residues processed: 422 average time/residue: 0.3533 time to fit residues: 232.2982 Evaluate side-chains 431 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 379 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 548 MET Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 195 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 107 ASN ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN F 27 GLN F 35 ASN ** W 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN V 521 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN B 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23158 Z= 0.219 Angle : 0.628 16.051 31437 Z= 0.315 Chirality : 0.044 0.358 3500 Planarity : 0.004 0.063 3986 Dihedral : 7.246 64.798 3646 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.33 % Allowed : 17.12 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2817 helix: 1.03 (0.40), residues: 194 sheet: 0.04 (0.16), residues: 1012 loop : -0.47 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 PHE 0.021 0.001 PHE S 234 TYR 0.024 0.001 TYR T 162 ARG 0.008 0.000 ARG R 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 390 time to evaluate : 2.617 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: A 3 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7908 (tm-30) REVERT: S 221 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: S 251 GLN cc_start: 0.8304 (mp10) cc_final: 0.8020 (mp10) REVERT: U 221 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8050 (mm-40) REVERT: R 4 MET cc_start: 0.8847 (mmp) cc_final: 0.8557 (mmp) REVERT: R 42 LYS cc_start: 0.8517 (mppt) cc_final: 0.7925 (mppt) REVERT: R 79 GLN cc_start: 0.7844 (mp10) cc_final: 0.7284 (mp10) REVERT: R 105 ILE cc_start: 0.7668 (tp) cc_final: 0.7390 (tp) REVERT: N 3 GLN cc_start: 0.8624 (mp-120) cc_final: 0.8263 (mp10) REVERT: N 37 GLN cc_start: 0.8389 (tt0) cc_final: 0.7693 (tt0) REVERT: N 61 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7360 (ptp90) REVERT: N 89 GLN cc_start: 0.8418 (tt0) cc_final: 0.7576 (tt0) REVERT: N 90 GLN cc_start: 0.8365 (pp30) cc_final: 0.8003 (pp30) REVERT: F 17 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7793 (mt-10) REVERT: F 24 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8852 (ttmm) REVERT: W 548 MET cc_start: 0.8403 (mtp) cc_final: 0.8097 (mtt) REVERT: M 13 GLN cc_start: 0.8882 (mm110) cc_final: 0.8364 (mm-40) REVERT: M 50 THR cc_start: 0.8808 (t) cc_final: 0.8559 (t) REVERT: M 73 ASP cc_start: 0.7617 (t0) cc_final: 0.6774 (t0) REVERT: M 76 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8733 (mmtm) REVERT: M 87 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7647 (mtt90) REVERT: G 65 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8533 (mmmm) REVERT: G 68 PHE cc_start: 0.8145 (m-10) cc_final: 0.5761 (m-10) REVERT: G 83 MET cc_start: 0.8475 (mpp) cc_final: 0.7807 (mmt) REVERT: H 32 TYR cc_start: 0.8432 (m-10) cc_final: 0.8137 (m-10) REVERT: H 70 ASP cc_start: 0.9097 (t0) cc_final: 0.8835 (m-30) REVERT: P 4 MET cc_start: 0.6937 (mmm) cc_final: 0.6655 (mmm) REVERT: P 61 ARG cc_start: 0.8898 (ptp90) cc_final: 0.8474 (ptp90) REVERT: P 81 GLU cc_start: 0.8211 (pm20) cc_final: 0.7994 (pm20) REVERT: O 34 MET cc_start: 0.8587 (mmt) cc_final: 0.7782 (mmp) REVERT: O 50 THR cc_start: 0.8463 (m) cc_final: 0.8250 (m) REVERT: V 578 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7528 (mm-30) REVERT: X 596 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7417 (ttm110) REVERT: I 25 SER cc_start: 0.7938 (t) cc_final: 0.7582 (p) REVERT: I 32 TYR cc_start: 0.7291 (m-80) cc_final: 0.6801 (m-80) REVERT: I 53 HIS cc_start: 0.8841 (p90) cc_final: 0.8588 (p90) REVERT: I 57 ASP cc_start: 0.8537 (t0) cc_final: 0.8307 (t0) REVERT: I 83 MET cc_start: 0.8496 (mpp) cc_final: 0.8115 (mpp) REVERT: I 95 TYR cc_start: 0.8539 (m-80) cc_final: 0.8086 (m-80) REVERT: I 99 ASN cc_start: 0.8703 (t0) cc_final: 0.8112 (t0) REVERT: J 45 LYS cc_start: 0.8554 (mptt) cc_final: 0.8317 (mmtt) REVERT: J 87 TYR cc_start: 0.7311 (m-80) cc_final: 0.6802 (m-80) REVERT: B 35 ASN cc_start: 0.9141 (t0) cc_final: 0.8805 (t0) REVERT: D 4 MET cc_start: 0.8799 (mmm) cc_final: 0.7442 (mmm) outliers start: 56 outliers final: 49 residues processed: 426 average time/residue: 0.3540 time to fit residues: 234.9428 Evaluate side-chains 431 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 380 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 163 optimal weight: 0.9990 chunk 263 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 219 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN F 27 GLN F 35 ASN ** W 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23158 Z= 0.250 Angle : 0.631 15.846 31437 Z= 0.318 Chirality : 0.044 0.352 3500 Planarity : 0.004 0.068 3986 Dihedral : 7.185 64.724 3646 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 17.41 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2817 helix: 1.02 (0.40), residues: 194 sheet: 0.03 (0.16), residues: 1009 loop : -0.48 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 PHE 0.021 0.001 PHE S 234 TYR 0.025 0.001 TYR T 162 ARG 0.009 0.000 ARG R 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 382 time to evaluate : 2.584 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: A 3 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7910 (tm-30) REVERT: S 221 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: U 221 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8024 (mm-40) REVERT: R 4 MET cc_start: 0.8858 (mmp) cc_final: 0.8582 (mmp) REVERT: R 42 LYS cc_start: 0.8483 (mppt) cc_final: 0.7882 (mppt) REVERT: R 79 GLN cc_start: 0.7874 (mp10) cc_final: 0.7305 (mp10) REVERT: R 105 ILE cc_start: 0.7630 (tp) cc_final: 0.7353 (tp) REVERT: N 3 GLN cc_start: 0.8628 (mp-120) cc_final: 0.8218 (mp10) REVERT: N 37 GLN cc_start: 0.8411 (tt0) cc_final: 0.7999 (tt0) REVERT: N 61 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7357 (ptp90) REVERT: N 89 GLN cc_start: 0.8353 (tt0) cc_final: 0.7528 (tt0) REVERT: N 90 GLN cc_start: 0.8418 (pp30) cc_final: 0.8037 (pp30) REVERT: F 17 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7793 (mt-10) REVERT: F 24 LYS cc_start: 0.9059 (ttpp) cc_final: 0.8839 (ttmm) REVERT: W 548 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8101 (mtt) REVERT: M 13 GLN cc_start: 0.8881 (mm110) cc_final: 0.8358 (mm-40) REVERT: M 50 THR cc_start: 0.8779 (t) cc_final: 0.8552 (t) REVERT: M 73 ASP cc_start: 0.7677 (t0) cc_final: 0.6803 (t0) REVERT: M 76 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8719 (mmtm) REVERT: M 87 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: G 65 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8560 (mmmm) REVERT: G 68 PHE cc_start: 0.8155 (m-10) cc_final: 0.6595 (m-10) REVERT: G 83 MET cc_start: 0.8471 (mpp) cc_final: 0.7936 (mmp) REVERT: H 32 TYR cc_start: 0.8417 (m-10) cc_final: 0.8073 (m-10) REVERT: H 70 ASP cc_start: 0.9123 (t0) cc_final: 0.8841 (m-30) REVERT: P 4 MET cc_start: 0.6896 (mmm) cc_final: 0.6651 (mmm) REVERT: P 61 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8476 (ptp90) REVERT: O 34 MET cc_start: 0.8624 (mmt) cc_final: 0.7821 (mmp) REVERT: V 578 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7585 (mm-30) REVERT: X 596 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7441 (ttm110) REVERT: I 25 SER cc_start: 0.7943 (t) cc_final: 0.7540 (p) REVERT: I 32 TYR cc_start: 0.7303 (m-80) cc_final: 0.6804 (m-80) REVERT: I 53 HIS cc_start: 0.8835 (p90) cc_final: 0.8586 (p90) REVERT: I 57 ASP cc_start: 0.8552 (t0) cc_final: 0.8320 (t0) REVERT: I 83 MET cc_start: 0.8718 (mpp) cc_final: 0.8243 (mpp) REVERT: I 95 TYR cc_start: 0.8547 (m-80) cc_final: 0.8083 (m-80) REVERT: I 99 ASN cc_start: 0.8675 (t0) cc_final: 0.8087 (t0) REVERT: J 45 LYS cc_start: 0.8557 (mptt) cc_final: 0.8318 (mmtt) REVERT: J 87 TYR cc_start: 0.7367 (m-80) cc_final: 0.6865 (m-80) REVERT: B 35 ASN cc_start: 0.9159 (t0) cc_final: 0.8827 (t0) REVERT: D 4 MET cc_start: 0.8808 (mmm) cc_final: 0.7434 (mmm) outliers start: 56 outliers final: 47 residues processed: 416 average time/residue: 0.3544 time to fit residues: 230.0670 Evaluate side-chains 425 residues out of total 2407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 375 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 47 ASP Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 192 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 548 MET Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 35 ASN ** W 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.086218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059142 restraints weight = 67211.048| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.61 r_work: 0.2881 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23158 Z= 0.271 Angle : 0.636 15.790 31437 Z= 0.321 Chirality : 0.044 0.336 3500 Planarity : 0.004 0.063 3986 Dihedral : 7.092 64.347 3646 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.24 % Allowed : 17.62 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2817 helix: 1.02 (0.40), residues: 194 sheet: 0.03 (0.16), residues: 981 loop : -0.50 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP U 288 HIS 0.007 0.001 HIS E 35 PHE 0.021 0.001 PHE S 234 TYR 0.025 0.001 TYR T 162 ARG 0.009 0.000 ARG R 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5993.84 seconds wall clock time: 111 minutes 2.55 seconds (6662.55 seconds total)