Starting phenix.real_space_refine on Mon Mar 25 01:26:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vai_21140/03_2024/6vai_21140.pdb" } resolution = 3.68 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= 0.007 sd= 1.017 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 154 5.16 5 C 29436 2.51 5 N 7964 2.21 5 O 8030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F ARG 233": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 233": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I ARG 144": "NH1" <-> "NH2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J ARG 181": "NH1" <-> "NH2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 233": "NH1" <-> "NH2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K ARG 144": "NH1" <-> "NH2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "K PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K ARG 249": "NH1" <-> "NH2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "L ARG 144": "NH1" <-> "NH2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 175": "OE1" <-> "OE2" Residue "L ARG 181": "NH1" <-> "NH2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L ARG 233": "NH1" <-> "NH2" Residue "L ARG 249": "NH1" <-> "NH2" Residue "L GLU 261": "OE1" <-> "OE2" Residue "L TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M GLU 145": "OE1" <-> "OE2" Residue "M PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 175": "OE1" <-> "OE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 126": "OE1" <-> "OE2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "N PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "N ARG 181": "NH1" <-> "NH2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "N TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N ARG 249": "NH1" <-> "NH2" Residue "N GLU 261": "OE1" <-> "OE2" Residue "N TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 126": "OE1" <-> "OE2" Residue "O ARG 144": "NH1" <-> "NH2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 175": "OE1" <-> "OE2" Residue "O ARG 181": "NH1" <-> "NH2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O ARG 233": "NH1" <-> "NH2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O GLU 261": "OE1" <-> "OE2" Residue "O TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P ARG 144": "NH1" <-> "NH2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 233": "NH1" <-> "NH2" Residue "P ARG 249": "NH1" <-> "NH2" Residue "P GLU 261": "OE1" <-> "OE2" Residue "P TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q GLU 145": "OE1" <-> "OE2" Residue "Q PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 175": "OE1" <-> "OE2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "Q GLU 183": "OE1" <-> "OE2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q ARG 249": "NH1" <-> "NH2" Residue "Q GLU 261": "OE1" <-> "OE2" Residue "Q TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R GLU 145": "OE1" <-> "OE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 175": "OE1" <-> "OE2" Residue "R ARG 181": "NH1" <-> "NH2" Residue "R GLU 183": "OE1" <-> "OE2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 249": "NH1" <-> "NH2" Residue "R GLU 261": "OE1" <-> "OE2" Residue "R TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "S GLU 145": "OE1" <-> "OE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 175": "OE1" <-> "OE2" Residue "S ARG 181": "NH1" <-> "NH2" Residue "S GLU 183": "OE1" <-> "OE2" Residue "S TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 233": "NH1" <-> "NH2" Residue "S ARG 249": "NH1" <-> "NH2" Residue "S GLU 261": "OE1" <-> "OE2" Residue "S TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 126": "OE1" <-> "OE2" Residue "T ARG 144": "NH1" <-> "NH2" Residue "T GLU 145": "OE1" <-> "OE2" Residue "T PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 175": "OE1" <-> "OE2" Residue "T ARG 181": "NH1" <-> "NH2" Residue "T GLU 183": "OE1" <-> "OE2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T ARG 249": "NH1" <-> "NH2" Residue "T GLU 261": "OE1" <-> "OE2" Residue "T TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 126": "OE1" <-> "OE2" Residue "U ARG 144": "NH1" <-> "NH2" Residue "U GLU 145": "OE1" <-> "OE2" Residue "U PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 175": "OE1" <-> "OE2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U GLU 183": "OE1" <-> "OE2" Residue "U TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 233": "NH1" <-> "NH2" Residue "U ARG 249": "NH1" <-> "NH2" Residue "U GLU 261": "OE1" <-> "OE2" Residue "U TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 126": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "V GLU 145": "OE1" <-> "OE2" Residue "V PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 175": "OE1" <-> "OE2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V GLU 183": "OE1" <-> "OE2" Residue "V TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 233": "NH1" <-> "NH2" Residue "V ARG 249": "NH1" <-> "NH2" Residue "V GLU 261": "OE1" <-> "OE2" Residue "V TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45584 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "M" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "N" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "O" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "T" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "U" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "V" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 22.72, per 1000 atoms: 0.50 Number of scatterers: 45584 At special positions: 0 Unit cell: (145.22, 146.28, 191.86, 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 154 16.00 O 8030 8.00 N 7964 7.00 C 29436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.02 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.02 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.02 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.02 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 130 " distance=2.02 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 130 " distance=2.02 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 130 " distance=2.03 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 130 " distance=2.02 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 130 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 130 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 130 " distance=2.02 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 130 " distance=2.02 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 162 " distance=2.03 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 130 " distance=2.03 Simple disulfide: pdb=" SG CYS U 48 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 46 " - pdb=" SG CYS V 130 " distance=2.02 Simple disulfide: pdb=" SG CYS V 48 " - pdb=" SG CYS V 162 " 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 Time building additional restraints: 15.56 Conformation dependent library (CDL) restraints added in 6.4 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11132 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 removed outlier: 4.210A pdb=" N ALA A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.765A pdb=" N ILE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 252 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 252 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 252 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL E 176 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 252 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 252 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP F 278 " --> pdb=" O PRO F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 Processing helix chain 'G' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL G 176 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 252 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP G 278 " --> pdb=" O PRO G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'H' and resid 26 through 40 Processing helix chain 'H' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 111 removed outlier: 3.711A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 160 Processing helix chain 'H' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 252 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP H 278 " --> pdb=" O PRO H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'I' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL I 176 " --> pdb=" O PHE I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 252 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP I 278 " --> pdb=" O PRO I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 160 Processing helix chain 'J' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU J 174 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL J 176 " --> pdb=" O PHE J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 252 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 302 Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE K 120 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 160 Processing helix chain 'K' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL K 176 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 252 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP K 278 " --> pdb=" O PRO K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 302 Processing helix chain 'L' and resid 26 through 40 Processing helix chain 'L' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'L' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE L 120 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 Processing helix chain 'L' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU L 174 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL L 176 " --> pdb=" O PHE L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 252 Processing helix chain 'L' and resid 257 through 267 Processing helix chain 'L' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP L 278 " --> pdb=" O PRO L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 Processing helix chain 'M' and resid 26 through 40 Processing helix chain 'M' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'M' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU M 174 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL M 176 " --> pdb=" O PHE M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 252 Processing helix chain 'M' and resid 257 through 267 Processing helix chain 'M' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP M 278 " --> pdb=" O PRO M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 302 Processing helix chain 'N' and resid 26 through 40 Processing helix chain 'N' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'N' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP N 80 " --> pdb=" O ASN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE N 120 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 160 Processing helix chain 'N' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU N 175 " --> pdb=" O ASP N 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL N 176 " --> pdb=" O PHE N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 252 Processing helix chain 'N' and resid 257 through 267 Processing helix chain 'N' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP N 278 " --> pdb=" O PRO N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 302 Processing helix chain 'O' and resid 26 through 40 Processing helix chain 'O' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU O 55 " --> pdb=" O ALA O 51 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'O' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE O 120 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY O 125 " --> pdb=" O SER O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 160 Processing helix chain 'O' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU O 174 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU O 175 " --> pdb=" O ASP O 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL O 176 " --> pdb=" O PHE O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 252 Processing helix chain 'O' and resid 257 through 267 Processing helix chain 'O' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP O 278 " --> pdb=" O PRO O 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 302 Processing helix chain 'P' and resid 26 through 40 Processing helix chain 'P' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'P' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP P 80 " --> pdb=" O ASN P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE P 120 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 125 " --> pdb=" O SER P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 160 Processing helix chain 'P' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU P 174 " --> pdb=" O SER P 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU P 175 " --> pdb=" O ASP P 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 252 Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP P 278 " --> pdb=" O PRO P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 297 through 302 Processing helix chain 'Q' and resid 26 through 40 Processing helix chain 'Q' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'Q' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP Q 80 " --> pdb=" O ASN Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER Q 105 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 125 removed outlier: 3.765A pdb=" N ILE Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY Q 125 " --> pdb=" O SER Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 160 Processing helix chain 'Q' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU Q 174 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU Q 175 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL Q 176 " --> pdb=" O PHE Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 252 Processing helix chain 'Q' and resid 257 through 267 Processing helix chain 'Q' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP Q 278 " --> pdb=" O PRO Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 302 Processing helix chain 'R' and resid 26 through 40 Processing helix chain 'R' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU R 175 " --> pdb=" O ASP R 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL R 176 " --> pdb=" O PHE R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 252 Processing helix chain 'R' and resid 257 through 267 Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP R 278 " --> pdb=" O PRO R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 302 Processing helix chain 'S' and resid 26 through 40 Processing helix chain 'S' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU S 55 " --> pdb=" O ALA S 51 " (cutoff:3.500A) Proline residue: S 64 - end of helix Processing helix chain 'S' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER S 105 " --> pdb=" O LEU S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE S 120 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 160 Processing helix chain 'S' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU S 174 " --> pdb=" O SER S 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU S 175 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 252 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP S 278 " --> pdb=" O PRO S 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 302 Processing helix chain 'T' and resid 26 through 40 Processing helix chain 'T' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU T 55 " --> pdb=" O ALA T 51 " (cutoff:3.500A) Proline residue: T 64 - end of helix Processing helix chain 'T' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP T 80 " --> pdb=" O ASN T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE T 120 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY T 125 " --> pdb=" O SER T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU T 174 " --> pdb=" O SER T 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU T 175 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL T 176 " --> pdb=" O PHE T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 252 Processing helix chain 'T' and resid 257 through 267 Processing helix chain 'T' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP T 278 " --> pdb=" O PRO T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 297 through 302 Processing helix chain 'U' and resid 26 through 40 Processing helix chain 'U' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) Proline residue: U 64 - end of helix Processing helix chain 'U' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP U 80 " --> pdb=" O ASN U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER U 105 " --> pdb=" O LEU U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE U 120 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY U 125 " --> pdb=" O SER U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 Processing helix chain 'U' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU U 174 " --> pdb=" O SER U 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU U 175 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL U 176 " --> pdb=" O PHE U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 252 Processing helix chain 'U' and resid 257 through 267 Processing helix chain 'U' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP U 278 " --> pdb=" O PRO U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 302 Processing helix chain 'V' and resid 26 through 40 Processing helix chain 'V' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU V 55 " --> pdb=" O ALA V 51 " (cutoff:3.500A) Proline residue: V 64 - end of helix Processing helix chain 'V' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP V 80 " --> pdb=" O ASN V 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE V 120 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY V 125 " --> pdb=" O SER V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU V 174 " --> pdb=" O SER V 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU V 175 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL V 176 " --> pdb=" O PHE V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 252 Processing helix chain 'V' and resid 257 through 267 Processing helix chain 'V' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP V 278 " --> pdb=" O PRO V 274 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 302 3014 hydrogen bonds defined for protein. 8910 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: 13.97 Time building geometry restraints manager: 16.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14938 1.34 - 1.46: 10399 1.46 - 1.58: 21303 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 46794 Sorted by residual: bond pdb=" CA VAL D 269 " pdb=" CB VAL D 269 " ideal model delta sigma weight residual 1.550 1.537 0.013 1.03e-02 9.43e+03 1.70e+00 bond pdb=" CA VAL K 269 " pdb=" CB VAL K 269 " ideal model delta sigma weight residual 1.550 1.537 0.013 1.03e-02 9.43e+03 1.69e+00 bond pdb=" CA VAL B 269 " pdb=" CB VAL B 269 " ideal model delta sigma weight residual 1.550 1.538 0.013 1.03e-02 9.43e+03 1.51e+00 bond pdb=" CA VAL A 269 " pdb=" CB VAL A 269 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.47e+00 bond pdb=" CA VAL P 269 " pdb=" CB VAL P 269 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.43e+00 ... (remaining 46789 not shown) Histogram of bond angle deviations from ideal: 101.36 - 107.89: 2015 107.89 - 114.43: 26463 114.43 - 120.96: 23096 120.96 - 127.50: 11660 127.50 - 134.03: 654 Bond angle restraints: 63888 Sorted by residual: angle pdb=" N GLY N 252 " pdb=" CA GLY N 252 " pdb=" C GLY N 252 " ideal model delta sigma weight residual 114.85 110.72 4.13 1.35e+00 5.49e-01 9.37e+00 angle pdb=" N GLY M 252 " pdb=" CA GLY M 252 " pdb=" C GLY M 252 " ideal model delta sigma weight residual 114.85 110.73 4.12 1.35e+00 5.49e-01 9.29e+00 angle pdb=" N GLY R 252 " pdb=" CA GLY R 252 " pdb=" C GLY R 252 " ideal model delta sigma weight residual 114.85 110.75 4.10 1.35e+00 5.49e-01 9.21e+00 angle pdb=" N GLY D 252 " pdb=" CA GLY D 252 " pdb=" C GLY D 252 " ideal model delta sigma weight residual 114.85 110.76 4.09 1.35e+00 5.49e-01 9.20e+00 angle pdb=" N GLY L 252 " pdb=" CA GLY L 252 " pdb=" C GLY L 252 " ideal model delta sigma weight residual 114.85 110.76 4.09 1.35e+00 5.49e-01 9.18e+00 ... (remaining 63883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 24167 17.22 - 34.44: 2739 34.44 - 51.67: 352 51.67 - 68.89: 110 68.89 - 86.11: 88 Dihedral angle restraints: 27456 sinusoidal: 10252 harmonic: 17204 Sorted by residual: dihedral pdb=" CA ARG N 144 " pdb=" C ARG N 144 " pdb=" N GLU N 145 " pdb=" CA GLU N 145 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG I 144 " pdb=" C ARG I 144 " pdb=" N GLU I 145 " pdb=" CA GLU I 145 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG C 144 " pdb=" C ARG C 144 " pdb=" N GLU C 145 " pdb=" CA GLU C 145 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 27453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3948 0.027 - 0.054: 2236 0.054 - 0.081: 628 0.081 - 0.108: 225 0.108 - 0.135: 113 Chirality restraints: 7150 Sorted by residual: chirality pdb=" CA LYS O 163 " pdb=" N LYS O 163 " pdb=" C LYS O 163 " pdb=" CB LYS O 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA LYS D 163 " pdb=" N LYS D 163 " pdb=" C LYS D 163 " pdb=" CB LYS D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA LYS F 163 " pdb=" N LYS F 163 " pdb=" C LYS F 163 " pdb=" CB LYS F 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 7147 not shown) Planarity restraints: 8228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 162 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C CYS P 162 " 0.023 2.00e-02 2.50e+03 pdb=" O CYS P 162 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS P 163 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS S 162 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C CYS S 162 " 0.023 2.00e-02 2.50e+03 pdb=" O CYS S 162 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS S 163 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 162 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C CYS K 162 " -0.023 2.00e-02 2.50e+03 pdb=" O CYS K 162 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS K 163 " 0.008 2.00e-02 2.50e+03 ... (remaining 8225 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 11943 2.79 - 3.32: 46739 3.32 - 3.85: 73198 3.85 - 4.37: 77909 4.37 - 4.90: 134056 Nonbonded interactions: 343845 Sorted by model distance: nonbonded pdb=" NH1 ARG Q 240 " pdb=" OD2 ASP Q 260 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG H 240 " pdb=" OD2 ASP H 260 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG D 240 " pdb=" OD2 ASP D 260 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG B 240 " pdb=" OD2 ASP B 260 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG N 240 " pdb=" OD2 ASP N 260 " model vdw 2.267 2.520 ... (remaining 343840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.040 Extract box with map and model: 10.040 Check model and map are aligned: 0.780 Set scattering table: 0.480 Process input model: 105.840 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.400 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.026 46794 Z= 0.351 Angle : 0.692 5.827 63888 Z= 0.402 Chirality : 0.039 0.135 7150 Planarity : 0.004 0.028 8228 Dihedral : 14.950 86.112 16192 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.96 % Allowed : 8.15 % Favored : 90.89 % 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: -2.39 (0.10), residues: 5786 helix: -0.42 (0.07), residues: 4268 sheet: None (None), residues: 0 loop : -4.96 (0.09), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 302 HIS 0.005 0.001 HIS Q 238 PHE 0.008 0.001 PHE S 187 TYR 0.016 0.002 TYR E 54 ARG 0.002 0.000 ARG I 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 833 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8706 (tp40) cc_final: 0.8464 (tp40) REVERT: E 232 GLN cc_start: 0.8674 (tp40) cc_final: 0.8410 (tp40) REVERT: I 291 GLN cc_start: 0.7819 (pp30) cc_final: 0.7537 (pp30) REVERT: K 203 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8248 (tttm) REVERT: L 232 GLN cc_start: 0.8709 (tp40) cc_final: 0.8456 (tp40) REVERT: P 232 GLN cc_start: 0.8666 (tp40) cc_final: 0.8350 (mm-40) REVERT: S 291 GLN cc_start: 0.7795 (pp30) cc_final: 0.7569 (pp30) REVERT: V 203 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8263 (tttm) outliers start: 44 outliers final: 27 residues processed: 855 average time/residue: 0.6009 time to fit residues: 822.0277 Evaluate side-chains 566 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 539 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 2.9990 chunk 433 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 448 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 333 optimal weight: 0.5980 chunk 519 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 216 GLN A 238 HIS A 246 ASN B 53 ASN B 216 GLN B 238 HIS B 246 ASN C 53 ASN C 216 GLN C 238 HIS C 246 ASN D 53 ASN D 216 GLN D 238 HIS D 246 ASN E 53 ASN E 216 GLN E 238 HIS E 246 ASN F 53 ASN F 216 GLN F 232 GLN F 238 HIS F 246 ASN G 53 ASN G 216 GLN G 238 HIS G 246 ASN H 53 ASN H 216 GLN H 232 GLN H 238 HIS H 246 ASN I 53 ASN I 216 GLN I 232 GLN I 238 HIS I 246 ASN J 53 ASN J 216 GLN J 238 HIS J 246 ASN K 53 ASN K 216 GLN K 238 HIS K 246 ASN L 53 ASN L 216 GLN L 238 HIS L 246 ASN M 53 ASN M 216 GLN M 238 HIS M 246 ASN N 53 ASN N 216 GLN N 238 HIS N 246 ASN O 53 ASN O 216 GLN O 238 HIS O 246 ASN P 53 ASN P 216 GLN P 238 HIS P 246 ASN Q 53 ASN Q 216 GLN Q 238 HIS Q 246 ASN R 53 ASN R 216 GLN R 238 HIS R 246 ASN S 53 ASN S 216 GLN S 232 GLN S 238 HIS S 246 ASN T 53 ASN T 216 GLN T 238 HIS T 246 ASN T 291 GLN U 53 ASN U 216 GLN U 238 HIS U 246 ASN V 53 ASN V 216 GLN V 238 HIS V 246 ASN V 291 GLN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46794 Z= 0.210 Angle : 0.587 6.688 63888 Z= 0.299 Chirality : 0.037 0.142 7150 Planarity : 0.004 0.034 8228 Dihedral : 6.034 51.929 6500 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.85 % Allowed : 15.41 % Favored : 79.74 % 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 (0.11), residues: 5786 helix: 1.10 (0.08), residues: 4312 sheet: None (None), residues: 0 loop : -4.35 (0.11), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 80 HIS 0.005 0.001 HIS Q 238 PHE 0.007 0.001 PHE R 100 TYR 0.018 0.002 TYR M 285 ARG 0.006 0.000 ARG M 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 653 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8655 (tp40) cc_final: 0.8322 (tp40) REVERT: E 232 GLN cc_start: 0.8677 (tp40) cc_final: 0.8404 (tp40) REVERT: H 201 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8792 (mm) REVERT: J 201 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8930 (mm) REVERT: L 232 GLN cc_start: 0.8651 (tp40) cc_final: 0.8362 (tp40) REVERT: S 291 GLN cc_start: 0.7622 (pp30) cc_final: 0.7345 (pp30) REVERT: T 183 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7041 (mt-10) REVERT: U 201 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8753 (mm) outliers start: 222 outliers final: 161 residues processed: 748 average time/residue: 0.5248 time to fit residues: 654.2247 Evaluate side-chains 730 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 566 time to evaluate : 5.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 54 TYR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 202 THR Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain T residue 291 GLN Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain V residue 259 ASP Chi-restraints excluded: chain V residue 291 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 0.0030 chunk 161 optimal weight: 3.9990 chunk 432 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 520 optimal weight: 50.0000 chunk 562 optimal weight: 1.9990 chunk 463 optimal weight: 8.9990 chunk 516 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 417 optimal weight: 0.0010 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 46794 Z= 0.194 Angle : 0.555 5.868 63888 Z= 0.284 Chirality : 0.036 0.130 7150 Planarity : 0.004 0.034 8228 Dihedral : 5.454 42.518 6480 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.68 % Allowed : 18.62 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5786 helix: 1.67 (0.08), residues: 4312 sheet: None (None), residues: 0 loop : -4.06 (0.12), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 278 HIS 0.003 0.000 HIS P 238 PHE 0.010 0.001 PHE L 100 TYR 0.019 0.002 TYR O 285 ARG 0.004 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 631 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8650 (tp40) cc_final: 0.8321 (tp40) REVERT: E 232 GLN cc_start: 0.8653 (tp40) cc_final: 0.8381 (tp40) REVERT: L 232 GLN cc_start: 0.8641 (tp40) cc_final: 0.8314 (tp40) REVERT: P 232 GLN cc_start: 0.8587 (tp40) cc_final: 0.8313 (tp40) REVERT: T 102 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8131 (mm) REVERT: T 183 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7181 (mt-10) REVERT: V 291 GLN cc_start: 0.7881 (pp30) cc_final: 0.7680 (pp30) outliers start: 260 outliers final: 188 residues processed: 784 average time/residue: 0.5441 time to fit residues: 722.4093 Evaluate side-chains 757 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 568 time to evaluate : 5.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 54 TYR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 THR Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 2.9990 chunk 391 optimal weight: 0.6980 chunk 270 optimal weight: 0.0050 chunk 57 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 522 optimal weight: 0.0270 chunk 552 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 494 optimal weight: 50.0000 chunk 149 optimal weight: 8.9990 overall best weight: 0.9254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 46794 Z= 0.146 Angle : 0.524 7.526 63888 Z= 0.267 Chirality : 0.036 0.143 7150 Planarity : 0.004 0.036 8228 Dihedral : 4.636 28.837 6446 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.59 % Allowed : 22.47 % Favored : 72.95 % 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: 1.03 (0.11), residues: 5786 helix: 2.04 (0.08), residues: 4334 sheet: None (None), residues: 0 loop : -3.85 (0.12), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 278 HIS 0.002 0.000 HIS P 238 PHE 0.006 0.001 PHE U 44 TYR 0.016 0.001 TYR A 285 ARG 0.005 0.000 ARG Q 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 654 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8578 (tp40) cc_final: 0.8278 (tp40) REVERT: D 102 LEU cc_start: 0.8226 (mt) cc_final: 0.7948 (mm) REVERT: D 232 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: E 223 TYR cc_start: 0.8663 (t80) cc_final: 0.8225 (t80) REVERT: E 232 GLN cc_start: 0.8635 (tp40) cc_final: 0.8391 (tp40) REVERT: G 103 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8629 (mm) REVERT: K 154 THR cc_start: 0.8118 (t) cc_final: 0.7828 (t) REVERT: L 232 GLN cc_start: 0.8588 (tp40) cc_final: 0.8298 (tp40) REVERT: O 102 LEU cc_start: 0.8112 (mt) cc_final: 0.7825 (mm) REVERT: P 285 TYR cc_start: 0.6849 (t80) cc_final: 0.6208 (t80) REVERT: Q 154 THR cc_start: 0.7770 (t) cc_final: 0.7365 (t) REVERT: S 223 TYR cc_start: 0.8667 (t80) cc_final: 0.8400 (t80) REVERT: T 102 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7997 (mm) REVERT: T 154 THR cc_start: 0.7721 (t) cc_final: 0.7368 (t) REVERT: T 183 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7032 (mt-10) REVERT: U 154 THR cc_start: 0.7771 (t) cc_final: 0.7414 (t) REVERT: U 201 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8816 (mm) REVERT: V 154 THR cc_start: 0.8150 (t) cc_final: 0.7925 (t) REVERT: V 291 GLN cc_start: 0.7732 (pp30) cc_final: 0.7180 (pp30) outliers start: 210 outliers final: 155 residues processed: 769 average time/residue: 0.5362 time to fit residues: 684.2708 Evaluate side-chains 734 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 575 time to evaluate : 6.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 144 ARG Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 9.9990 chunk 313 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 411 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 471 optimal weight: 6.9990 chunk 382 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 chunk 496 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 232 GLN L 45 HIS V 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46794 Z= 0.188 Angle : 0.528 5.996 63888 Z= 0.269 Chirality : 0.036 0.134 7150 Planarity : 0.004 0.036 8228 Dihedral : 4.607 27.824 6446 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.33 % Allowed : 24.04 % Favored : 71.63 % 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: 1.17 (0.11), residues: 5786 helix: 2.03 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.58 (0.12), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP V 302 HIS 0.005 0.001 HIS L 45 PHE 0.006 0.001 PHE R 100 TYR 0.020 0.001 TYR Q 223 ARG 0.007 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 570 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 LEU cc_start: 0.8251 (mt) cc_final: 0.7970 (mm) REVERT: E 232 GLN cc_start: 0.8630 (tp40) cc_final: 0.8378 (tp40) REVERT: O 144 ARG cc_start: 0.7134 (ptm160) cc_final: 0.6905 (ptt90) REVERT: P 285 TYR cc_start: 0.7123 (t80) cc_final: 0.6598 (t80) REVERT: T 102 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8134 (mm) REVERT: T 183 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7010 (mt-10) outliers start: 198 outliers final: 160 residues processed: 692 average time/residue: 0.5431 time to fit residues: 621.9544 Evaluate side-chains 696 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 535 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 100 PHE Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 0.9990 chunk 497 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 553 optimal weight: 7.9990 chunk 459 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 46794 Z= 0.184 Angle : 0.516 5.968 63888 Z= 0.263 Chirality : 0.036 0.135 7150 Planarity : 0.004 0.035 8228 Dihedral : 4.551 27.899 6446 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.63 % Allowed : 23.84 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 5786 helix: 2.09 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.47 (0.12), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 80 HIS 0.004 0.000 HIS L 45 PHE 0.005 0.001 PHE R 100 TYR 0.015 0.001 TYR A 285 ARG 0.006 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 548 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.8638 (tp40) cc_final: 0.8401 (tp40) REVERT: D 102 LEU cc_start: 0.8246 (mt) cc_final: 0.7915 (mm) REVERT: E 232 GLN cc_start: 0.8625 (tp40) cc_final: 0.8371 (tp40) REVERT: K 154 THR cc_start: 0.8207 (t) cc_final: 0.7906 (t) REVERT: L 232 GLN cc_start: 0.8629 (tp40) cc_final: 0.8400 (tp40) REVERT: O 102 LEU cc_start: 0.8112 (mt) cc_final: 0.7781 (mm) REVERT: P 232 GLN cc_start: 0.8594 (tp40) cc_final: 0.8381 (tp40) REVERT: P 285 TYR cc_start: 0.7206 (t80) cc_final: 0.6800 (t80) REVERT: V 154 THR cc_start: 0.8213 (t) cc_final: 0.7950 (t) outliers start: 212 outliers final: 183 residues processed: 674 average time/residue: 0.5391 time to fit residues: 602.5584 Evaluate side-chains 711 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 528 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain O residue 284 VAL Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain U residue 272 THR Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 100 PHE Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 404 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 551 optimal weight: 0.6980 chunk 345 optimal weight: 0.7980 chunk 336 optimal weight: 0.2980 chunk 254 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: B 246 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 ASN N 300 HIS ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 46794 Z= 0.137 Angle : 0.492 5.946 63888 Z= 0.249 Chirality : 0.035 0.148 7150 Planarity : 0.004 0.035 8228 Dihedral : 4.391 26.983 6446 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.02 % Allowed : 24.28 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 5786 helix: 2.23 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.32 (0.12), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 80 HIS 0.003 0.000 HIS F 238 PHE 0.008 0.001 PHE T 100 TYR 0.021 0.001 TYR P 223 ARG 0.007 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 630 time to evaluate : 5.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 THR cc_start: 0.7835 (t) cc_final: 0.7459 (t) REVERT: A 232 GLN cc_start: 0.8595 (tp40) cc_final: 0.8385 (tp40) REVERT: D 102 LEU cc_start: 0.8141 (mt) cc_final: 0.7816 (mm) REVERT: D 154 THR cc_start: 0.7681 (t) cc_final: 0.7287 (t) REVERT: E 154 THR cc_start: 0.7793 (t) cc_final: 0.7582 (t) REVERT: E 223 TYR cc_start: 0.8692 (t80) cc_final: 0.8330 (t80) REVERT: E 232 GLN cc_start: 0.8604 (tp40) cc_final: 0.8365 (tp40) REVERT: F 154 THR cc_start: 0.7654 (t) cc_final: 0.7299 (t) REVERT: H 223 TYR cc_start: 0.8720 (t80) cc_final: 0.8457 (t80) REVERT: I 154 THR cc_start: 0.7700 (t) cc_final: 0.7321 (t) REVERT: J 154 THR cc_start: 0.7781 (t) cc_final: 0.7396 (t) REVERT: L 154 THR cc_start: 0.7870 (t) cc_final: 0.7523 (t) REVERT: O 102 LEU cc_start: 0.7999 (mt) cc_final: 0.7633 (mm) REVERT: O 154 THR cc_start: 0.7664 (t) cc_final: 0.7248 (t) REVERT: Q 154 THR cc_start: 0.7550 (t) cc_final: 0.7188 (t) REVERT: S 223 TYR cc_start: 0.8665 (t80) cc_final: 0.8425 (t80) REVERT: T 154 THR cc_start: 0.7607 (t) cc_final: 0.7254 (t) REVERT: U 154 THR cc_start: 0.7693 (t) cc_final: 0.7335 (t) outliers start: 184 outliers final: 155 residues processed: 729 average time/residue: 0.5537 time to fit residues: 665.5259 Evaluate side-chains 738 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 583 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 100 PHE Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 5.9990 chunk 220 optimal weight: 0.6980 chunk 329 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 375 optimal weight: 0.0170 chunk 272 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 chunk 433 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 ASN L 300 HIS ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 46794 Z= 0.130 Angle : 0.492 6.479 63888 Z= 0.248 Chirality : 0.035 0.208 7150 Planarity : 0.004 0.035 8228 Dihedral : 4.252 29.241 6446 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.21 % Allowed : 25.39 % Favored : 71.39 % 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: 1.71 (0.12), residues: 5786 helix: 2.35 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.09 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 80 HIS 0.003 0.000 HIS T 238 PHE 0.007 0.001 PHE B 250 TYR 0.042 0.001 TYR K 223 ARG 0.007 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 640 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 THR cc_start: 0.7724 (t) cc_final: 0.7372 (t) REVERT: A 223 TYR cc_start: 0.8538 (t80) cc_final: 0.8307 (t80) REVERT: C 223 TYR cc_start: 0.8602 (t80) cc_final: 0.8283 (t80) REVERT: D 102 LEU cc_start: 0.8123 (mt) cc_final: 0.7787 (mm) REVERT: D 154 THR cc_start: 0.7692 (t) cc_final: 0.7339 (t) REVERT: D 232 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: E 154 THR cc_start: 0.7427 (t) cc_final: 0.7205 (t) REVERT: E 223 TYR cc_start: 0.8603 (t80) cc_final: 0.8255 (t80) REVERT: E 232 GLN cc_start: 0.8602 (tp40) cc_final: 0.8362 (tp40) REVERT: F 102 LEU cc_start: 0.8334 (mt) cc_final: 0.7957 (mm) REVERT: F 154 THR cc_start: 0.7416 (t) cc_final: 0.7059 (t) REVERT: H 223 TYR cc_start: 0.8628 (t80) cc_final: 0.8385 (t80) REVERT: I 154 THR cc_start: 0.7453 (t) cc_final: 0.7107 (t) REVERT: J 154 THR cc_start: 0.7545 (t) cc_final: 0.7199 (t) REVERT: L 154 THR cc_start: 0.7817 (t) cc_final: 0.7475 (t) REVERT: L 223 TYR cc_start: 0.8547 (t80) cc_final: 0.8293 (t80) REVERT: N 223 TYR cc_start: 0.8540 (t80) cc_final: 0.8238 (t80) REVERT: O 102 LEU cc_start: 0.8017 (mt) cc_final: 0.7652 (mm) REVERT: O 154 THR cc_start: 0.7389 (t) cc_final: 0.7002 (t) REVERT: P 223 TYR cc_start: 0.8388 (t80) cc_final: 0.8166 (t80) REVERT: Q 154 THR cc_start: 0.7379 (t) cc_final: 0.7025 (t) REVERT: S 223 TYR cc_start: 0.8526 (t80) cc_final: 0.8296 (t80) REVERT: T 154 THR cc_start: 0.7322 (t) cc_final: 0.6955 (t) REVERT: U 154 THR cc_start: 0.7403 (t) cc_final: 0.7063 (t) outliers start: 147 outliers final: 127 residues processed: 715 average time/residue: 0.5495 time to fit residues: 642.9877 Evaluate side-chains 720 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 592 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 144 ARG Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 291 GLN Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 0.9990 chunk 528 optimal weight: 0.9980 chunk 481 optimal weight: 5.9990 chunk 513 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 403 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 464 optimal weight: 0.0370 chunk 485 optimal weight: 9.9990 chunk 511 optimal weight: 7.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 GLN ** T 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 46794 Z= 0.200 Angle : 0.522 5.357 63888 Z= 0.265 Chirality : 0.036 0.207 7150 Planarity : 0.004 0.034 8228 Dihedral : 4.394 29.097 6446 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.69 % Allowed : 25.37 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5786 helix: 2.29 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.09 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 80 HIS 0.004 0.001 HIS E 45 PHE 0.007 0.001 PHE T 100 TYR 0.019 0.001 TYR F 223 ARG 0.008 0.000 ARG H 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 549 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 THR cc_start: 0.8060 (t) cc_final: 0.7674 (t) REVERT: B 107 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8517 (mt) REVERT: B 285 TYR cc_start: 0.7124 (t80) cc_final: 0.6871 (t80) REVERT: D 102 LEU cc_start: 0.8213 (mt) cc_final: 0.7894 (mm) REVERT: D 154 THR cc_start: 0.7920 (t) cc_final: 0.7553 (t) REVERT: E 154 THR cc_start: 0.7856 (t) cc_final: 0.7614 (t) REVERT: E 183 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: E 232 GLN cc_start: 0.8620 (tp40) cc_final: 0.8369 (tp40) REVERT: F 154 THR cc_start: 0.7741 (t) cc_final: 0.7398 (t) REVERT: I 154 THR cc_start: 0.7793 (t) cc_final: 0.7429 (t) REVERT: J 154 THR cc_start: 0.7874 (t) cc_final: 0.7503 (t) REVERT: K 154 THR cc_start: 0.8025 (t) cc_final: 0.7800 (t) REVERT: L 154 THR cc_start: 0.8091 (t) cc_final: 0.7706 (t) REVERT: M 107 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8520 (mt) REVERT: M 285 TYR cc_start: 0.7138 (t80) cc_final: 0.6906 (t80) REVERT: O 102 LEU cc_start: 0.8089 (mt) cc_final: 0.7765 (mm) REVERT: O 154 THR cc_start: 0.7725 (t) cc_final: 0.7330 (t) REVERT: P 223 TYR cc_start: 0.8570 (t80) cc_final: 0.8270 (t80) REVERT: Q 154 THR cc_start: 0.7680 (t) cc_final: 0.7320 (t) REVERT: T 154 THR cc_start: 0.7661 (t) cc_final: 0.7303 (t) REVERT: U 154 THR cc_start: 0.7808 (t) cc_final: 0.7416 (t) outliers start: 169 outliers final: 149 residues processed: 640 average time/residue: 0.5440 time to fit residues: 573.1432 Evaluate side-chains 693 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 541 time to evaluate : 5.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 291 GLN Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain O residue 284 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 126 GLU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 4.9990 chunk 543 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 377 optimal weight: 4.9990 chunk 569 optimal weight: 6.9990 chunk 524 optimal weight: 0.9990 chunk 453 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 350 optimal weight: 0.3980 chunk 278 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 46794 Z= 0.180 Angle : 0.512 5.359 63888 Z= 0.260 Chirality : 0.036 0.125 7150 Planarity : 0.004 0.033 8228 Dihedral : 4.357 28.962 6446 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.56 % Allowed : 25.61 % Favored : 70.83 % 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: 1.64 (0.11), residues: 5786 helix: 2.28 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.05 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.003 0.000 HIS E 238 PHE 0.008 0.001 PHE U 100 TYR 0.015 0.001 TYR F 223 ARG 0.007 0.000 ARG H 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 534 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 TYR cc_start: 0.7183 (t80) cc_final: 0.6899 (t80) REVERT: D 102 LEU cc_start: 0.8124 (mt) cc_final: 0.7792 (mm) REVERT: D 154 THR cc_start: 0.7967 (t) cc_final: 0.7621 (t) REVERT: E 154 THR cc_start: 0.7860 (t) cc_final: 0.7632 (t) REVERT: E 183 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: E 232 GLN cc_start: 0.8610 (tp40) cc_final: 0.8361 (tp40) REVERT: F 154 THR cc_start: 0.7743 (t) cc_final: 0.7421 (t) REVERT: I 154 THR cc_start: 0.7816 (t) cc_final: 0.7474 (t) REVERT: J 154 THR cc_start: 0.7918 (t) cc_final: 0.7552 (t) REVERT: K 154 THR cc_start: 0.8083 (t) cc_final: 0.7846 (t) REVERT: M 285 TYR cc_start: 0.7209 (t80) cc_final: 0.6964 (t80) REVERT: O 102 LEU cc_start: 0.8062 (mt) cc_final: 0.7712 (mm) REVERT: O 154 THR cc_start: 0.7725 (t) cc_final: 0.7329 (t) REVERT: P 223 TYR cc_start: 0.8573 (t80) cc_final: 0.8257 (t80) REVERT: P 232 GLN cc_start: 0.8568 (tp40) cc_final: 0.8314 (tp40) REVERT: Q 154 THR cc_start: 0.7745 (t) cc_final: 0.7383 (t) REVERT: T 154 THR cc_start: 0.7707 (t) cc_final: 0.7365 (t) REVERT: U 154 THR cc_start: 0.7836 (t) cc_final: 0.7472 (t) outliers start: 163 outliers final: 150 residues processed: 626 average time/residue: 0.5497 time to fit residues: 565.7796 Evaluate side-chains 677 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 526 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 291 GLN Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 259 ASP Chi-restraints excluded: chain O residue 284 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 259 ASP Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 259 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 126 GLU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 259 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 259 ASP Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 259 ASP Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 259 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 2.9990 chunk 483 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 418 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 454 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 466 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 HIS ** L 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099176 restraints weight = 82429.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102300 restraints weight = 45480.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104542 restraints weight = 30982.006| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 46794 Z= 0.189 Angle : 0.515 5.364 63888 Z= 0.261 Chirality : 0.036 0.124 7150 Planarity : 0.004 0.032 8228 Dihedral : 4.408 28.731 6446 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.63 % Allowed : 25.66 % Favored : 70.72 % 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: 1.64 (0.11), residues: 5786 helix: 2.27 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.01 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 80 HIS 0.004 0.000 HIS C 45 PHE 0.009 0.001 PHE N 100 TYR 0.046 0.001 TYR K 223 ARG 0.007 0.000 ARG H 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10628.47 seconds wall clock time: 190 minutes 43.70 seconds (11443.70 seconds total)