Starting phenix.real_space_refine on Sat Feb 24 15:17:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lom_0938/02_2024/6lom_0938.pdb" } resolution = 3.73 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= 0.015 sd= 0.071 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 280 5.16 5 C 28760 2.51 5 N 7620 2.21 5 O 8060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I ARG 130": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I ARG 283": "NH1" <-> "NH2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 130": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J ARG 283": "NH1" <-> "NH2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 283": "NH1" <-> "NH2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "L ARG 283": "NH1" <-> "NH2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M ARG 130": "NH1" <-> "NH2" Residue "M ARG 133": "NH1" <-> "NH2" Residue "M ARG 283": "NH1" <-> "NH2" Residue "M TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 133": "NH1" <-> "NH2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O ARG 130": "NH1" <-> "NH2" Residue "O ARG 133": "NH1" <-> "NH2" Residue "O ARG 283": "NH1" <-> "NH2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "P ARG 283": "NH1" <-> "NH2" Residue "P TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "Q ARG 133": "NH1" <-> "NH2" Residue "Q ARG 283": "NH1" <-> "NH2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 133": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 91": "NH1" <-> "NH2" Residue "S ARG 130": "NH1" <-> "NH2" Residue "S ARG 133": "NH1" <-> "NH2" Residue "S ARG 283": "NH1" <-> "NH2" Residue "S TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 91": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 133": "NH1" <-> "NH2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44720 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "M" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "N" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "O" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "P" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "Q" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "S" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "T" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2236 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 21.80, per 1000 atoms: 0.49 Number of scatterers: 44720 At special positions: 0 Unit cell: (141, 143, 193, 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 280 16.00 O 8060 8.00 N 7620 7.00 C 28760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=80, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 131 " distance=2.02 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 171 " distance=2.05 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 131 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 171 " distance=2.05 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 131 " distance=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 171 " distance=2.05 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 131 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 171 " distance=2.05 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 131 " distance=2.02 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 171 " distance=2.05 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 131 " distance=2.02 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 176 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 171 " distance=2.05 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 131 " distance=2.02 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 171 " distance=2.05 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 131 " distance=2.02 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 171 " distance=2.05 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 131 " distance=2.02 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 176 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 171 " distance=2.05 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 131 " distance=2.02 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 176 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 146 " - pdb=" SG CYS J 171 " distance=2.05 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 131 " distance=2.02 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 176 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 171 " distance=2.05 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 131 " distance=2.02 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 176 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 146 " - pdb=" SG CYS L 171 " distance=2.05 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 131 " distance=2.02 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 176 " distance=2.03 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 174 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 171 " distance=2.05 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 131 " distance=2.02 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 176 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 174 " distance=2.03 Simple disulfide: pdb=" SG CYS N 146 " - pdb=" SG CYS N 171 " distance=2.05 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 131 " distance=2.02 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 176 " distance=2.03 Simple disulfide: pdb=" SG CYS O 138 " - pdb=" SG CYS O 174 " distance=2.03 Simple disulfide: pdb=" SG CYS O 146 " - pdb=" SG CYS O 171 " distance=2.05 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 131 " distance=2.02 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 176 " distance=2.03 Simple disulfide: pdb=" SG CYS P 138 " - pdb=" SG CYS P 174 " distance=2.03 Simple disulfide: pdb=" SG CYS P 146 " - pdb=" SG CYS P 171 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 131 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 176 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 138 " - pdb=" SG CYS Q 174 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 146 " - pdb=" SG CYS Q 171 " distance=2.05 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 131 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 174 " distance=2.03 Simple disulfide: pdb=" SG CYS R 146 " - pdb=" SG CYS R 171 " distance=2.05 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 131 " distance=2.02 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 138 " - pdb=" SG CYS S 174 " distance=2.03 Simple disulfide: pdb=" SG CYS S 146 " - pdb=" SG CYS S 171 " distance=2.05 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 131 " distance=2.02 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 176 " distance=2.03 Simple disulfide: pdb=" SG CYS T 138 " - pdb=" SG CYS T 174 " distance=2.03 Simple disulfide: pdb=" SG CYS T 146 " - pdb=" SG CYS T 171 " distance=2.05 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: 16.77 Conformation dependent library (CDL) restraints added in 7.8 seconds 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11240 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 19 Processing helix chain 'A' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Proline residue: A 64 - end of helix removed outlier: 3.718A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS A 174 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 212 Processing helix chain 'A' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'B' and resid 2 through 19 Processing helix chain 'B' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 60 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Proline residue: B 64 - end of helix removed outlier: 3.718A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS B 174 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 212 Processing helix chain 'B' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'C' and resid 2 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) Proline residue: C 64 - end of helix removed outlier: 3.718A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS C 174 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 212 Processing helix chain 'C' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP C 238 " --> pdb=" O THR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'D' and resid 2 through 19 Processing helix chain 'D' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA D 30 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) Proline residue: D 64 - end of helix removed outlier: 3.718A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS D 101 " --> pdb=" O TRP D 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.162A pdb=" N CYS D 174 " --> pdb=" O CYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 212 Processing helix chain 'D' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA E 30 " --> pdb=" O GLY E 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 31 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Proline residue: E 64 - end of helix removed outlier: 3.718A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS E 135 " --> pdb=" O CYS E 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS E 174 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 212 Processing helix chain 'E' and resid 219 through 255 removed outlier: 4.412A pdb=" N GLN E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 299 through 307 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA F 30 " --> pdb=" O GLY F 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 31 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE F 60 " --> pdb=" O HIS F 56 " (cutoff:3.500A) Proline residue: F 64 - end of helix removed outlier: 3.718A pdb=" N ASN F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) Proline residue: F 115 - end of helix Processing helix chain 'F' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS F 135 " --> pdb=" O CYS F 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS F 174 " --> pdb=" O CYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 212 Processing helix chain 'F' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 299 through 307 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 25 through 41 removed outlier: 4.007A pdb=" N ALA G 30 " --> pdb=" O GLY G 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 removed outlier: 4.109A pdb=" N ILE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 60 " --> pdb=" O HIS G 56 " (cutoff:3.500A) Proline residue: G 64 - end of helix removed outlier: 3.718A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS G 101 " --> pdb=" O TRP G 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Proline residue: G 115 - end of helix Processing helix chain 'G' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS G 135 " --> pdb=" O CYS G 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS G 174 " --> pdb=" O CYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 212 Processing helix chain 'G' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN G 235 " --> pdb=" O ASN G 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP G 238 " --> pdb=" O THR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 299 through 307 Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE H 60 " --> pdb=" O HIS H 56 " (cutoff:3.500A) Proline residue: H 64 - end of helix removed outlier: 3.718A pdb=" N ASN H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS H 101 " --> pdb=" O TRP H 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA H 114 " --> pdb=" O GLN H 110 " (cutoff:3.500A) Proline residue: H 115 - end of helix Processing helix chain 'H' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS H 135 " --> pdb=" O CYS H 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS H 174 " --> pdb=" O CYS H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 212 Processing helix chain 'H' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN H 235 " --> pdb=" O ASN H 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP H 238 " --> pdb=" O THR H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA I 30 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR I 31 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU I 38 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE I 60 " --> pdb=" O HIS I 56 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.718A pdb=" N ASN I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS I 101 " --> pdb=" O TRP I 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Proline residue: I 115 - end of helix Processing helix chain 'I' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS I 135 " --> pdb=" O CYS I 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 147 Processing helix chain 'I' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS I 174 " --> pdb=" O CYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 212 Processing helix chain 'I' and resid 219 through 255 removed outlier: 4.412A pdb=" N GLN I 235 " --> pdb=" O ASN I 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP I 238 " --> pdb=" O THR I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 286 Processing helix chain 'I' and resid 299 through 307 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU J 38 " --> pdb=" O GLY J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE J 60 " --> pdb=" O HIS J 56 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.718A pdb=" N ASN J 76 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS J 101 " --> pdb=" O TRP J 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Proline residue: J 115 - end of helix Processing helix chain 'J' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS J 135 " --> pdb=" O CYS J 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS J 138 " --> pdb=" O SER J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 175 removed outlier: 4.160A pdb=" N CYS J 174 " --> pdb=" O CYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 212 Processing helix chain 'J' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN J 235 " --> pdb=" O ASN J 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP J 238 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 286 Processing helix chain 'J' and resid 299 through 307 Processing helix chain 'K' and resid 2 through 19 Processing helix chain 'K' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA K 30 " --> pdb=" O GLY K 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR K 31 " --> pdb=" O ILE K 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE K 60 " --> pdb=" O HIS K 56 " (cutoff:3.500A) Proline residue: K 64 - end of helix removed outlier: 3.718A pdb=" N ASN K 76 " --> pdb=" O GLY K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS K 101 " --> pdb=" O TRP K 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA K 114 " --> pdb=" O GLN K 110 " (cutoff:3.500A) Proline residue: K 115 - end of helix Processing helix chain 'K' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS K 135 " --> pdb=" O CYS K 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS K 138 " --> pdb=" O SER K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS K 174 " --> pdb=" O CYS K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 212 Processing helix chain 'K' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN K 235 " --> pdb=" O ASN K 231 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP K 238 " --> pdb=" O THR K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 286 Processing helix chain 'K' and resid 299 through 307 Processing helix chain 'L' and resid 2 through 19 Processing helix chain 'L' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 31 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE L 60 " --> pdb=" O HIS L 56 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.718A pdb=" N ASN L 76 " --> pdb=" O GLY L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS L 101 " --> pdb=" O TRP L 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) Proline residue: L 115 - end of helix Processing helix chain 'L' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS L 135 " --> pdb=" O CYS L 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 147 Processing helix chain 'L' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS L 174 " --> pdb=" O CYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 212 Processing helix chain 'L' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN L 235 " --> pdb=" O ASN L 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP L 238 " --> pdb=" O THR L 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN L 252 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 286 Processing helix chain 'L' and resid 299 through 307 Processing helix chain 'M' and resid 2 through 19 Processing helix chain 'M' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA M 30 " --> pdb=" O GLY M 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR M 31 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU M 38 " --> pdb=" O GLY M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE M 54 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE M 60 " --> pdb=" O HIS M 56 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.717A pdb=" N ASN M 76 " --> pdb=" O GLY M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS M 101 " --> pdb=" O TRP M 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA M 114 " --> pdb=" O GLN M 110 " (cutoff:3.500A) Proline residue: M 115 - end of helix Processing helix chain 'M' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS M 135 " --> pdb=" O CYS M 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS M 138 " --> pdb=" O SER M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 147 Processing helix chain 'M' and resid 149 through 158 removed outlier: 3.744A pdb=" N ASN M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS M 174 " --> pdb=" O CYS M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 212 Processing helix chain 'M' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN M 235 " --> pdb=" O ASN M 231 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP M 238 " --> pdb=" O THR M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 286 Processing helix chain 'M' and resid 299 through 307 Processing helix chain 'N' and resid 2 through 19 Processing helix chain 'N' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 31 " --> pdb=" O ILE N 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE N 54 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE N 60 " --> pdb=" O HIS N 56 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.718A pdb=" N ASN N 76 " --> pdb=" O GLY N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP N 80 " --> pdb=" O ASN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS N 101 " --> pdb=" O TRP N 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA N 114 " --> pdb=" O GLN N 110 " (cutoff:3.500A) Proline residue: N 115 - end of helix Processing helix chain 'N' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS N 135 " --> pdb=" O CYS N 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS N 138 " --> pdb=" O SER N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 147 Processing helix chain 'N' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS N 174 " --> pdb=" O CYS N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 212 Processing helix chain 'N' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN N 235 " --> pdb=" O ASN N 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP N 238 " --> pdb=" O THR N 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 286 Processing helix chain 'N' and resid 299 through 307 Processing helix chain 'O' and resid 2 through 19 Processing helix chain 'O' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR O 31 " --> pdb=" O ILE O 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU O 38 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE O 54 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE O 60 " --> pdb=" O HIS O 56 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.718A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS O 101 " --> pdb=" O TRP O 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA O 114 " --> pdb=" O GLN O 110 " (cutoff:3.500A) Proline residue: O 115 - end of helix Processing helix chain 'O' and resid 129 through 138 removed outlier: 4.825A pdb=" N HIS O 135 " --> pdb=" O CYS O 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 147 Processing helix chain 'O' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 175 removed outlier: 4.162A pdb=" N CYS O 174 " --> pdb=" O CYS O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 212 Processing helix chain 'O' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN O 235 " --> pdb=" O ASN O 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP O 238 " --> pdb=" O THR O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 299 through 307 Processing helix chain 'P' and resid 2 through 19 Processing helix chain 'P' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR P 31 " --> pdb=" O ILE P 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE P 54 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE P 60 " --> pdb=" O HIS P 56 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.718A pdb=" N ASN P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP P 80 " --> pdb=" O ASN P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS P 101 " --> pdb=" O TRP P 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA P 114 " --> pdb=" O GLN P 110 " (cutoff:3.500A) Proline residue: P 115 - end of helix Processing helix chain 'P' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS P 135 " --> pdb=" O CYS P 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS P 138 " --> pdb=" O SER P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 147 Processing helix chain 'P' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS P 174 " --> pdb=" O CYS P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 212 Processing helix chain 'P' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN P 235 " --> pdb=" O ASN P 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP P 238 " --> pdb=" O THR P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 286 Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'Q' and resid 2 through 19 Processing helix chain 'Q' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR Q 31 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU Q 38 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 76 removed outlier: 4.110A pdb=" N ILE Q 54 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE Q 60 " --> pdb=" O HIS Q 56 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.718A pdb=" N ASN Q 76 " --> pdb=" O GLY Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 84 removed outlier: 4.208A pdb=" N TRP Q 80 " --> pdb=" O ASN Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS Q 101 " --> pdb=" O TRP Q 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA Q 114 " --> pdb=" O GLN Q 110 " (cutoff:3.500A) Proline residue: Q 115 - end of helix Processing helix chain 'Q' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS Q 135 " --> pdb=" O CYS Q 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS Q 138 " --> pdb=" O SER Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 147 Processing helix chain 'Q' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN Q 153 " --> pdb=" O SER Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS Q 174 " --> pdb=" O CYS Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 212 Processing helix chain 'Q' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN Q 235 " --> pdb=" O ASN Q 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 286 Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'R' and resid 2 through 19 Processing helix chain 'R' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.109A pdb=" N ILE R 54 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.718A pdb=" N ASN R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS R 101 " --> pdb=" O TRP R 97 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 129 through 138 removed outlier: 4.825A pdb=" N HIS R 135 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS R 174 " --> pdb=" O CYS R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 Processing helix chain 'R' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN R 235 " --> pdb=" O ASN R 231 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN R 252 " --> pdb=" O LEU R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 286 Processing helix chain 'R' and resid 299 through 307 Processing helix chain 'S' and resid 2 through 19 Processing helix chain 'S' and resid 25 through 41 removed outlier: 4.009A pdb=" N ALA S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR S 31 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU S 38 " --> pdb=" O GLY S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE S 54 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE S 60 " --> pdb=" O HIS S 56 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.718A pdb=" N ASN S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 84 removed outlier: 4.210A pdb=" N TRP S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 125 removed outlier: 3.534A pdb=" N CYS S 101 " --> pdb=" O TRP S 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA S 114 " --> pdb=" O GLN S 110 " (cutoff:3.500A) Proline residue: S 115 - end of helix Processing helix chain 'S' and resid 129 through 138 removed outlier: 4.826A pdb=" N HIS S 135 " --> pdb=" O CYS S 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS S 138 " --> pdb=" O SER S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 147 Processing helix chain 'S' and resid 149 through 158 removed outlier: 3.746A pdb=" N ASN S 153 " --> pdb=" O SER S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS S 174 " --> pdb=" O CYS S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 212 Processing helix chain 'S' and resid 219 through 255 removed outlier: 4.411A pdb=" N GLN S 235 " --> pdb=" O ASN S 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP S 238 " --> pdb=" O THR S 234 " (cutoff:3.500A) Processing helix chain 'S' and resid 281 through 286 Processing helix chain 'S' and resid 299 through 307 Processing helix chain 'T' and resid 2 through 19 Processing helix chain 'T' and resid 25 through 41 removed outlier: 4.008A pdb=" N ALA T 30 " --> pdb=" O GLY T 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR T 31 " --> pdb=" O ILE T 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU T 38 " --> pdb=" O GLY T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 76 removed outlier: 4.111A pdb=" N ILE T 54 " --> pdb=" O TYR T 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) Proline residue: T 64 - end of helix removed outlier: 3.718A pdb=" N ASN T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 84 removed outlier: 4.209A pdb=" N TRP T 80 " --> pdb=" O ASN T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 125 removed outlier: 3.533A pdb=" N CYS T 101 " --> pdb=" O TRP T 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA T 114 " --> pdb=" O GLN T 110 " (cutoff:3.500A) Proline residue: T 115 - end of helix Processing helix chain 'T' and resid 129 through 138 removed outlier: 4.827A pdb=" N HIS T 135 " --> pdb=" O CYS T 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS T 138 " --> pdb=" O SER T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 147 Processing helix chain 'T' and resid 149 through 158 removed outlier: 3.745A pdb=" N ASN T 153 " --> pdb=" O SER T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 175 removed outlier: 4.161A pdb=" N CYS T 174 " --> pdb=" O CYS T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 212 Processing helix chain 'T' and resid 219 through 255 removed outlier: 4.410A pdb=" N GLN T 235 " --> pdb=" O ASN T 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP T 238 " --> pdb=" O THR T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 286 Processing helix chain 'T' and resid 299 through 307 2956 hydrogen bonds defined for protein. 8808 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: 13.75 Time building geometry restraints manager: 18.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14037 1.34 - 1.47: 12541 1.47 - 1.60: 18942 1.60 - 1.73: 0 1.73 - 1.85: 340 Bond restraints: 45860 Sorted by residual: bond pdb=" C PRO K 172 " pdb=" N PRO K 173 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.08e-02 8.57e+03 7.22e+00 bond pdb=" C PRO R 172 " pdb=" N PRO R 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 7.04e+00 bond pdb=" C PRO S 172 " pdb=" N PRO S 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 7.00e+00 bond pdb=" C PRO A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 6.98e+00 bond pdb=" C PRO O 172 " pdb=" N PRO O 173 " ideal model delta sigma weight residual 1.336 1.364 -0.029 1.08e-02 8.57e+03 6.98e+00 ... (remaining 45855 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.44: 1739 107.44 - 114.14: 25264 114.14 - 120.85: 22055 120.85 - 127.56: 12955 127.56 - 134.26: 507 Bond angle restraints: 62520 Sorted by residual: angle pdb=" N PRO I 172 " pdb=" CA PRO I 172 " pdb=" C PRO I 172 " ideal model delta sigma weight residual 110.70 116.58 -5.88 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO G 172 " pdb=" CA PRO G 172 " pdb=" C PRO G 172 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO F 172 " pdb=" CA PRO F 172 " pdb=" C PRO F 172 " ideal model delta sigma weight residual 110.70 116.56 -5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" N PRO E 172 " pdb=" CA PRO E 172 " pdb=" C PRO E 172 " ideal model delta sigma weight residual 110.70 116.56 -5.86 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N PRO J 172 " pdb=" CA PRO J 172 " pdb=" C PRO J 172 " ideal model delta sigma weight residual 110.70 116.55 -5.85 1.22e+00 6.72e-01 2.30e+01 ... (remaining 62515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 23882 14.96 - 29.92: 2198 29.92 - 44.88: 660 44.88 - 59.84: 200 59.84 - 74.80: 60 Dihedral angle restraints: 27000 sinusoidal: 9620 harmonic: 17380 Sorted by residual: dihedral pdb=" CA CYS T 171 " pdb=" C CYS T 171 " pdb=" N PRO T 172 " pdb=" CA PRO T 172 " ideal model delta harmonic sigma weight residual -180.00 -123.73 -56.27 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS M 171 " pdb=" C CYS M 171 " pdb=" N PRO M 172 " pdb=" CA PRO M 172 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS S 171 " pdb=" C CYS S 171 " pdb=" N PRO S 172 " pdb=" CA PRO S 172 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 26997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4020 0.043 - 0.086: 2084 0.086 - 0.129: 750 0.129 - 0.171: 146 0.171 - 0.214: 60 Chirality restraints: 7060 Sorted by residual: chirality pdb=" CA PHE P 44 " pdb=" N PHE P 44 " pdb=" C PHE P 44 " pdb=" CB PHE P 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE R 44 " pdb=" N PHE R 44 " pdb=" C PHE R 44 " pdb=" CB PHE R 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE N 44 " pdb=" N PHE N 44 " pdb=" C PHE N 44 " pdb=" CB PHE N 44 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 7057 not shown) Planarity restraints: 7940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 311 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO M 312 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO M 312 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 312 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 311 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO F 312 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 312 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 311 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 312 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 312 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 312 " 0.035 5.00e-02 4.00e+02 ... (remaining 7937 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3643 2.73 - 3.27: 46063 3.27 - 3.82: 76275 3.82 - 4.36: 84741 4.36 - 4.90: 144060 Nonbonded interactions: 354782 Sorted by model distance: nonbonded pdb=" OD1 ASN A 304 " pdb=" ND2 ASN B 252 " model vdw 2.191 2.520 nonbonded pdb=" OD1 ASN R 304 " pdb=" ND2 ASN S 252 " model vdw 2.243 2.520 nonbonded pdb=" O ARG C 130 " pdb=" OG SER C 134 " model vdw 2.244 2.440 nonbonded pdb=" O ARG S 130 " pdb=" OG SER S 134 " model vdw 2.244 2.440 nonbonded pdb=" O ARG G 130 " pdb=" OG SER G 134 " model vdw 2.245 2.440 ... (remaining 354777 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' } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.080 Check model and map are aligned: 0.610 Set scattering table: 0.400 Process input model: 104.380 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.360 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.007 0.094 45860 Z= 0.478 Angle : 1.167 10.739 62520 Z= 0.628 Chirality : 0.058 0.214 7060 Planarity : 0.009 0.069 7940 Dihedral : 13.554 74.799 15520 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.81 % Allowed : 9.50 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 27.27 % Twisted General : 0.71 % 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: -4.24 (0.08), residues: 5820 helix: -2.34 (0.06), residues: 4180 sheet: None (None), residues: 0 loop : -3.63 (0.12), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP C 118 HIS 0.006 0.002 HIS B 135 PHE 0.024 0.003 PHE H 44 TYR 0.021 0.003 TYR N 128 ARG 0.024 0.002 ARG T 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 973 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8452 (tt) cc_final: 0.7843 (tt) REVERT: A 135 HIS cc_start: 0.7544 (t-90) cc_final: 0.7102 (t-90) REVERT: A 187 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 287 ILE cc_start: 0.6863 (mt) cc_final: 0.6583 (pt) REVERT: B 135 HIS cc_start: 0.7629 (t-90) cc_final: 0.7220 (t-90) REVERT: B 187 GLU cc_start: 0.8704 (tm-30) cc_final: 0.7979 (tm-30) REVERT: C 82 LEU cc_start: 0.8527 (tt) cc_final: 0.8293 (mt) REVERT: C 98 LYS cc_start: 0.6915 (tttt) cc_final: 0.6655 (tptt) REVERT: C 135 HIS cc_start: 0.7459 (t-90) cc_final: 0.7121 (t-90) REVERT: C 186 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8777 (tp) REVERT: C 187 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8266 (tm-30) REVERT: C 242 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8053 (ttmm) REVERT: D 135 HIS cc_start: 0.7675 (t-90) cc_final: 0.7231 (t-90) REVERT: D 187 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 231 ASN cc_start: 0.8310 (t160) cc_final: 0.8028 (t0) REVERT: D 256 PHE cc_start: 0.8502 (t80) cc_final: 0.8265 (t80) REVERT: D 285 ARG cc_start: 0.7612 (mpt90) cc_final: 0.7296 (ttm110) REVERT: D 286 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8356 (mm) REVERT: E 135 HIS cc_start: 0.7700 (t-90) cc_final: 0.7164 (t-90) REVERT: E 187 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8295 (tm-30) REVERT: E 199 LEU cc_start: 0.8740 (tt) cc_final: 0.8494 (tp) REVERT: E 285 ARG cc_start: 0.7401 (mpt90) cc_final: 0.7137 (ttm110) REVERT: F 82 LEU cc_start: 0.8393 (tt) cc_final: 0.7863 (tt) REVERT: F 98 LYS cc_start: 0.6490 (tttt) cc_final: 0.6285 (tptt) REVERT: F 135 HIS cc_start: 0.7652 (t-90) cc_final: 0.7173 (t-90) REVERT: F 187 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 82 LEU cc_start: 0.8550 (tt) cc_final: 0.8293 (mt) REVERT: G 135 HIS cc_start: 0.7644 (t-90) cc_final: 0.7212 (t-90) REVERT: G 186 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8832 (tp) REVERT: G 187 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8148 (tm-30) REVERT: G 285 ARG cc_start: 0.7431 (mpt90) cc_final: 0.7183 (ttm110) REVERT: H 82 LEU cc_start: 0.8524 (tt) cc_final: 0.8298 (mt) REVERT: H 98 LYS cc_start: 0.6923 (tttt) cc_final: 0.6652 (tptt) REVERT: H 135 HIS cc_start: 0.7477 (t-90) cc_final: 0.7132 (t-90) REVERT: H 186 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8771 (tp) REVERT: H 187 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8276 (tm-30) REVERT: H 242 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7941 (ttmm) REVERT: H 256 PHE cc_start: 0.8587 (t80) cc_final: 0.8384 (t80) REVERT: I 135 HIS cc_start: 0.7688 (t-90) cc_final: 0.7262 (t-90) REVERT: I 187 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8018 (tm-30) REVERT: I 231 ASN cc_start: 0.8318 (t160) cc_final: 0.8028 (t0) REVERT: I 242 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8132 (tttp) REVERT: I 256 PHE cc_start: 0.8508 (t80) cc_final: 0.8295 (t80) REVERT: I 285 ARG cc_start: 0.7630 (mpt90) cc_final: 0.7296 (ttm110) REVERT: J 135 HIS cc_start: 0.7644 (t-90) cc_final: 0.7169 (t-90) REVERT: J 187 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8302 (tm-30) REVERT: J 199 LEU cc_start: 0.8748 (tt) cc_final: 0.8471 (tp) REVERT: J 285 ARG cc_start: 0.7395 (mpt90) cc_final: 0.7139 (ttm110) REVERT: K 82 LEU cc_start: 0.8540 (tt) cc_final: 0.8279 (mt) REVERT: K 135 HIS cc_start: 0.7654 (t-90) cc_final: 0.7130 (t-90) REVERT: K 186 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8813 (tp) REVERT: K 187 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8091 (tm-30) REVERT: K 285 ARG cc_start: 0.7451 (mpt90) cc_final: 0.7133 (ttm110) REVERT: L 82 LEU cc_start: 0.8557 (tt) cc_final: 0.8305 (mt) REVERT: L 98 LYS cc_start: 0.7030 (tttt) cc_final: 0.6753 (tptt) REVERT: L 135 HIS cc_start: 0.7360 (t-90) cc_final: 0.7013 (t-90) REVERT: L 186 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8740 (tp) REVERT: L 187 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8234 (tm-30) REVERT: L 231 ASN cc_start: 0.8216 (t160) cc_final: 0.7978 (t0) REVERT: L 242 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8065 (ttmm) REVERT: L 256 PHE cc_start: 0.8557 (t80) cc_final: 0.8326 (t80) REVERT: M 135 HIS cc_start: 0.7642 (t-90) cc_final: 0.7095 (t-90) REVERT: M 187 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7992 (tm-30) REVERT: M 199 LEU cc_start: 0.8714 (tt) cc_final: 0.8479 (tp) REVERT: M 231 ASN cc_start: 0.8311 (t160) cc_final: 0.8014 (t0) REVERT: M 256 PHE cc_start: 0.8549 (t80) cc_final: 0.8223 (t80) REVERT: M 285 ARG cc_start: 0.7554 (mpt90) cc_final: 0.7187 (ttm110) REVERT: N 135 HIS cc_start: 0.7614 (t-90) cc_final: 0.7129 (t-90) REVERT: N 187 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8291 (tm-30) REVERT: N 199 LEU cc_start: 0.8720 (tt) cc_final: 0.8471 (tp) REVERT: N 285 ARG cc_start: 0.7377 (mpt90) cc_final: 0.7120 (ttm110) REVERT: O 82 LEU cc_start: 0.8444 (tt) cc_final: 0.7884 (tt) REVERT: O 135 HIS cc_start: 0.7565 (t-90) cc_final: 0.7108 (t-90) REVERT: O 187 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8332 (tm-30) REVERT: O 287 ILE cc_start: 0.6825 (mt) cc_final: 0.6587 (pt) REVERT: P 82 LEU cc_start: 0.8556 (tt) cc_final: 0.8303 (mt) REVERT: P 135 HIS cc_start: 0.7676 (t-90) cc_final: 0.7143 (t-90) REVERT: P 186 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8820 (tp) REVERT: P 187 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8099 (tm-30) REVERT: P 285 ARG cc_start: 0.7455 (mpt90) cc_final: 0.7150 (ttm110) REVERT: Q 82 LEU cc_start: 0.8544 (tt) cc_final: 0.8309 (mt) REVERT: Q 98 LYS cc_start: 0.7003 (tttt) cc_final: 0.6721 (tptt) REVERT: Q 135 HIS cc_start: 0.7384 (t-90) cc_final: 0.7034 (t-90) REVERT: Q 186 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (tp) REVERT: Q 187 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8236 (tm-30) REVERT: Q 231 ASN cc_start: 0.8223 (t160) cc_final: 0.7998 (t0) REVERT: Q 242 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8063 (ttmm) REVERT: Q 256 PHE cc_start: 0.8565 (t80) cc_final: 0.8336 (t80) REVERT: R 135 HIS cc_start: 0.7615 (t-90) cc_final: 0.7082 (t-90) REVERT: R 187 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7968 (tm-30) REVERT: R 199 LEU cc_start: 0.8685 (tt) cc_final: 0.8481 (tp) REVERT: R 231 ASN cc_start: 0.8327 (t160) cc_final: 0.8021 (t0) REVERT: R 242 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8113 (tttp) REVERT: R 256 PHE cc_start: 0.8493 (t80) cc_final: 0.8242 (t80) REVERT: R 285 ARG cc_start: 0.7602 (mpt90) cc_final: 0.7270 (ttm110) REVERT: S 98 LYS cc_start: 0.6742 (tttt) cc_final: 0.6440 (tptt) REVERT: S 135 HIS cc_start: 0.7663 (t-90) cc_final: 0.7182 (t-90) REVERT: S 187 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8261 (tm-30) REVERT: S 199 LEU cc_start: 0.8740 (tt) cc_final: 0.8492 (tp) REVERT: S 285 ARG cc_start: 0.7505 (mpt90) cc_final: 0.7184 (ttm110) REVERT: T 82 LEU cc_start: 0.8441 (tt) cc_final: 0.7889 (tt) REVERT: T 135 HIS cc_start: 0.7527 (t-90) cc_final: 0.7128 (t-90) REVERT: T 187 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8321 (tm-30) REVERT: T 287 ILE cc_start: 0.6771 (mt) cc_final: 0.6548 (pt) outliers start: 80 outliers final: 40 residues processed: 1033 average time/residue: 0.6111 time to fit residues: 999.7691 Evaluate side-chains 568 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 520 time to evaluate : 5.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 186 LEU Chi-restraints excluded: chain T residue 209 ILE Chi-restraints excluded: chain T residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 489 optimal weight: 1.9990 chunk 439 optimal weight: 30.0000 chunk 243 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 454 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 526 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN B 53 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN C 53 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN D 53 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN E 53 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN G 53 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN H 53 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 53 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 HIS ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 ASN J 53 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 ASN ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 HIS ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN K 53 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 ASN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN L 53 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 HIS ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN M 53 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 ASN N 53 ASN ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 306 ASN O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 HIS ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN P 53 ASN ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 ASN ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 244 HIS ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 ASN Q 53 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 ASN ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 HIS ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN R 53 ASN ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 HIS ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 ASN S 53 ASN ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 244 HIS ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 ASN T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 148 ASN ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 244 HIS ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 306 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 45860 Z= 0.241 Angle : 0.719 12.480 62520 Z= 0.386 Chirality : 0.044 0.151 7060 Planarity : 0.006 0.049 7940 Dihedral : 8.977 58.825 6456 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 5.88 % Allowed : 18.01 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 18.18 % 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: -2.37 (0.10), residues: 5820 helix: -0.76 (0.07), residues: 4160 sheet: None (None), residues: 0 loop : -3.54 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP T 195 HIS 0.003 0.001 HIS T 95 PHE 0.021 0.001 PHE C 200 TYR 0.014 0.002 TYR D 128 ARG 0.007 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 577 time to evaluate : 5.380 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 135 HIS cc_start: 0.7307 (t-90) cc_final: 0.7062 (t-90) REVERT: A 187 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 287 ILE cc_start: 0.6960 (mt) cc_final: 0.6747 (pt) REVERT: B 135 HIS cc_start: 0.7471 (t-90) cc_final: 0.7204 (t-90) REVERT: B 187 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 195 TRP cc_start: 0.8878 (m100) cc_final: 0.8471 (m100) REVERT: C 186 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8799 (tp) REVERT: C 187 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 242 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8045 (ttmm) REVERT: D 135 HIS cc_start: 0.7485 (t-90) cc_final: 0.7220 (t-90) REVERT: D 187 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 285 ARG cc_start: 0.7725 (mpt90) cc_final: 0.7488 (mtp-110) REVERT: E 61 MET cc_start: 0.7546 (mmm) cc_final: 0.7149 (tpp) REVERT: E 123 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: E 187 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 296 MET cc_start: 0.6215 (mmp) cc_final: 0.6015 (mtt) REVERT: F 135 HIS cc_start: 0.7361 (t-90) cc_final: 0.7105 (t-90) REVERT: F 187 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7689 (tm-30) REVERT: G 135 HIS cc_start: 0.7497 (t-90) cc_final: 0.7178 (t-90) REVERT: G 187 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7629 (tm-30) REVERT: G 285 ARG cc_start: 0.7347 (mpt90) cc_final: 0.7036 (mtp-110) REVERT: H 186 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8792 (tp) REVERT: H 187 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7303 (tm-30) REVERT: H 242 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7921 (ttmm) REVERT: H 256 PHE cc_start: 0.8509 (t80) cc_final: 0.8305 (t80) REVERT: I 135 HIS cc_start: 0.7475 (t-90) cc_final: 0.7214 (t-90) REVERT: I 187 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7476 (tm-30) REVERT: I 256 PHE cc_start: 0.8636 (t80) cc_final: 0.8346 (t80) REVERT: I 285 ARG cc_start: 0.7708 (mpt90) cc_final: 0.7407 (mtp-110) REVERT: J 61 MET cc_start: 0.7505 (mmm) cc_final: 0.7014 (tpp) REVERT: J 123 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: J 135 HIS cc_start: 0.7501 (t-90) cc_final: 0.7173 (t-90) REVERT: J 187 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7472 (tm-30) REVERT: K 135 HIS cc_start: 0.7532 (t-90) cc_final: 0.7199 (t-90) REVERT: K 187 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7646 (tm-30) REVERT: K 195 TRP cc_start: 0.8895 (m100) cc_final: 0.8642 (m100) REVERT: K 285 ARG cc_start: 0.7412 (mpt90) cc_final: 0.7007 (mtp-110) REVERT: L 135 HIS cc_start: 0.7310 (t-90) cc_final: 0.7088 (t-90) REVERT: L 186 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8769 (tp) REVERT: L 187 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7308 (tm-30) REVERT: L 195 TRP cc_start: 0.8872 (m100) cc_final: 0.8662 (m100) REVERT: L 242 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8018 (ttmm) REVERT: L 256 PHE cc_start: 0.8488 (t80) cc_final: 0.8192 (t80) REVERT: M 135 HIS cc_start: 0.7518 (t-90) cc_final: 0.7249 (t-90) REVERT: M 187 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7470 (tm-30) REVERT: M 285 ARG cc_start: 0.7741 (mpt90) cc_final: 0.7385 (mtp-110) REVERT: N 187 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7496 (tm-30) REVERT: O 135 HIS cc_start: 0.7319 (t-90) cc_final: 0.7085 (t-90) REVERT: O 187 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7623 (tm-30) REVERT: P 123 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: P 135 HIS cc_start: 0.7552 (t-90) cc_final: 0.7217 (t-90) REVERT: P 187 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7624 (tm-30) REVERT: P 195 TRP cc_start: 0.8907 (m100) cc_final: 0.8657 (m100) REVERT: P 285 ARG cc_start: 0.7407 (mpt90) cc_final: 0.7023 (mtp-110) REVERT: Q 135 HIS cc_start: 0.7337 (t-90) cc_final: 0.7123 (t-90) REVERT: Q 186 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8768 (tp) REVERT: Q 187 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Q 195 TRP cc_start: 0.8864 (m100) cc_final: 0.8655 (m100) REVERT: Q 242 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8032 (ttmm) REVERT: Q 256 PHE cc_start: 0.8502 (t80) cc_final: 0.8211 (t80) REVERT: R 135 HIS cc_start: 0.7458 (t-90) cc_final: 0.7201 (t-90) REVERT: R 187 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7444 (tm-30) REVERT: R 285 ARG cc_start: 0.7645 (mpt90) cc_final: 0.7251 (mtp-110) REVERT: S 61 MET cc_start: 0.7571 (mmm) cc_final: 0.6949 (tpp) REVERT: S 98 LYS cc_start: 0.6548 (tttt) cc_final: 0.6130 (tptt) REVERT: S 123 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: S 135 HIS cc_start: 0.7507 (t-90) cc_final: 0.7214 (t-90) REVERT: S 187 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7465 (tm-30) REVERT: T 135 HIS cc_start: 0.7336 (t-90) cc_final: 0.7093 (t-90) REVERT: T 187 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 260 outliers final: 137 residues processed: 794 average time/residue: 0.5847 time to fit residues: 746.5230 Evaluate side-chains 584 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 439 time to evaluate : 4.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 217 LYS Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 207 LEU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 219 THR Chi-restraints excluded: chain S residue 287 ILE Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 292 optimal weight: 0.0770 chunk 163 optimal weight: 8.9990 chunk 438 optimal weight: 50.0000 chunk 358 optimal weight: 5.9990 chunk 145 optimal weight: 110.0000 chunk 527 optimal weight: 2.9990 chunk 570 optimal weight: 2.9990 chunk 469 optimal weight: 5.9990 chunk 523 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 423 optimal weight: 0.0020 overall best weight: 2.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45860 Z= 0.247 Angle : 0.676 10.250 62520 Z= 0.364 Chirality : 0.044 0.160 7060 Planarity : 0.005 0.052 7940 Dihedral : 8.070 59.850 6430 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 7.01 % Allowed : 18.94 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 18.18 % 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 (0.11), residues: 5820 helix: -0.02 (0.08), residues: 4180 sheet: None (None), residues: 0 loop : -4.09 (0.12), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 195 HIS 0.005 0.001 HIS A 244 PHE 0.015 0.001 PHE N 44 TYR 0.014 0.001 TYR I 129 ARG 0.009 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 476 time to evaluate : 5.666 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 130 ARG cc_start: 0.8380 (ptt90) cc_final: 0.8111 (ptm-80) REVERT: A 187 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 187 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 195 TRP cc_start: 0.8896 (m100) cc_final: 0.8443 (m100) REVERT: C 130 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8172 (ptm-80) REVERT: C 187 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 242 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8130 (ttmm) REVERT: D 187 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 231 ASN cc_start: 0.8244 (t160) cc_final: 0.8004 (t0) REVERT: D 285 ARG cc_start: 0.7864 (mpt90) cc_final: 0.7537 (mtp-110) REVERT: D 286 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8546 (mm) REVERT: E 53 ASN cc_start: 0.8390 (t0) cc_final: 0.8135 (t0) REVERT: E 130 ARG cc_start: 0.8489 (ptt90) cc_final: 0.8252 (ptm-80) REVERT: E 187 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7717 (tm-30) REVERT: E 199 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8680 (mp) REVERT: E 231 ASN cc_start: 0.8267 (t160) cc_final: 0.8005 (t0) REVERT: F 187 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 187 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7613 (tm-30) REVERT: G 231 ASN cc_start: 0.8283 (t160) cc_final: 0.8082 (t0) REVERT: G 285 ARG cc_start: 0.7450 (mpt90) cc_final: 0.7134 (mtp-110) REVERT: H 130 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8187 (ptm-80) REVERT: H 187 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7544 (tm-30) REVERT: H 242 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8019 (ttmm) REVERT: I 187 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7567 (tm-30) REVERT: I 231 ASN cc_start: 0.8244 (t160) cc_final: 0.7999 (t0) REVERT: I 285 ARG cc_start: 0.7889 (mpt90) cc_final: 0.7607 (mtp-110) REVERT: J 53 ASN cc_start: 0.8308 (t0) cc_final: 0.8000 (t0) REVERT: J 130 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8238 (ptm-80) REVERT: J 187 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7780 (tm-30) REVERT: J 199 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8694 (mp) REVERT: J 231 ASN cc_start: 0.8289 (t160) cc_final: 0.8026 (t0) REVERT: K 187 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7557 (tm-30) REVERT: K 195 TRP cc_start: 0.8911 (m100) cc_final: 0.8328 (m100) REVERT: K 254 ARG cc_start: 0.8326 (mmt90) cc_final: 0.8080 (mmt180) REVERT: K 285 ARG cc_start: 0.7472 (mpt90) cc_final: 0.7109 (mtp-110) REVERT: L 130 ARG cc_start: 0.8416 (ptt90) cc_final: 0.8159 (ptm-80) REVERT: L 187 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7554 (tm-30) REVERT: L 242 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8132 (ttmm) REVERT: L 250 GLU cc_start: 0.7682 (tp30) cc_final: 0.7235 (mm-30) REVERT: M 187 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7585 (tm-30) REVERT: M 231 ASN cc_start: 0.8248 (t160) cc_final: 0.7989 (t0) REVERT: M 285 ARG cc_start: 0.7856 (mpt90) cc_final: 0.7593 (mtp-110) REVERT: N 53 ASN cc_start: 0.8358 (t0) cc_final: 0.8087 (t0) REVERT: N 130 ARG cc_start: 0.8410 (ptt90) cc_final: 0.8162 (ptm-80) REVERT: N 187 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7704 (tm-30) REVERT: N 199 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8659 (mp) REVERT: N 231 ASN cc_start: 0.8250 (t160) cc_final: 0.7991 (t0) REVERT: O 130 ARG cc_start: 0.8383 (ptt90) cc_final: 0.8126 (ptm-80) REVERT: O 187 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7542 (tm-30) REVERT: P 187 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7588 (tm-30) REVERT: P 195 TRP cc_start: 0.8924 (m100) cc_final: 0.8323 (m100) REVERT: P 285 ARG cc_start: 0.7487 (mpt90) cc_final: 0.7109 (mtp-110) REVERT: Q 130 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8169 (ptm-80) REVERT: Q 187 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7570 (tm-30) REVERT: Q 242 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8137 (ttmm) REVERT: R 187 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7591 (tm-30) REVERT: R 231 ASN cc_start: 0.8234 (t160) cc_final: 0.7971 (t0) REVERT: R 285 ARG cc_start: 0.7826 (mpt90) cc_final: 0.7474 (mtp-110) REVERT: S 53 ASN cc_start: 0.8326 (t0) cc_final: 0.8026 (t0) REVERT: S 61 MET cc_start: 0.7407 (mmm) cc_final: 0.6880 (tpp) REVERT: S 123 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: S 130 ARG cc_start: 0.8475 (ptt90) cc_final: 0.8239 (ptm-80) REVERT: S 187 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7768 (tm-30) REVERT: S 189 GLU cc_start: 0.8546 (tp30) cc_final: 0.8099 (tp30) REVERT: S 195 TRP cc_start: 0.9060 (m100) cc_final: 0.8380 (m100) REVERT: S 199 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8554 (mp) REVERT: S 231 ASN cc_start: 0.8301 (t160) cc_final: 0.8040 (t0) REVERT: T 130 ARG cc_start: 0.8378 (ptt90) cc_final: 0.8126 (ptm-80) REVERT: T 187 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7533 (tm-30) outliers start: 310 outliers final: 182 residues processed: 717 average time/residue: 0.5736 time to fit residues: 672.1426 Evaluate side-chains 644 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 456 time to evaluate : 4.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 174 CYS Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain O residue 46 CYS Chi-restraints excluded: chain O residue 104 TRP Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain S residue 46 CYS Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 104 TRP Chi-restraints excluded: chain S residue 113 VAL Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 0.9980 chunk 396 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 58 optimal weight: 110.0000 chunk 251 optimal weight: 2.9990 chunk 354 optimal weight: 0.8980 chunk 529 optimal weight: 4.9990 chunk 560 optimal weight: 0.0770 chunk 276 optimal weight: 9.9990 chunk 501 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 76 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 76 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 76 ASN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN I 76 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN K 76 ASN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN M 76 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 76 ASN ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 231 ASN ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN R 76 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45860 Z= 0.193 Angle : 0.616 8.033 62520 Z= 0.334 Chirality : 0.042 0.202 7060 Planarity : 0.005 0.049 7940 Dihedral : 7.214 56.242 6418 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 7.99 % Allowed : 18.19 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -1.08 (0.11), residues: 5820 helix: 0.43 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.86 (0.12), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 195 HIS 0.004 0.001 HIS L 135 PHE 0.017 0.001 PHE N 44 TYR 0.009 0.001 TYR G 128 ARG 0.008 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 526 time to evaluate : 4.647 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 130 ARG cc_start: 0.8340 (ptt90) cc_final: 0.8090 (ptm-80) REVERT: A 187 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 189 GLU cc_start: 0.8447 (tp30) cc_final: 0.8040 (tp30) REVERT: A 250 GLU cc_start: 0.7608 (tp30) cc_final: 0.7290 (mm-30) REVERT: A 286 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8531 (tm) REVERT: B 187 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 195 TRP cc_start: 0.8851 (m100) cc_final: 0.8429 (m100) REVERT: C 187 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 195 TRP cc_start: 0.8938 (m100) cc_final: 0.8317 (m100) REVERT: C 242 LYS cc_start: 0.8282 (ttmt) cc_final: 0.8034 (ttmm) REVERT: D 187 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 286 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8412 (mm) REVERT: E 53 ASN cc_start: 0.8267 (t0) cc_final: 0.8067 (t0) REVERT: E 130 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8244 (ptm-80) REVERT: E 187 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 189 GLU cc_start: 0.8521 (tp30) cc_final: 0.8076 (tp30) REVERT: E 195 TRP cc_start: 0.9009 (m100) cc_final: 0.8399 (m100) REVERT: F 130 ARG cc_start: 0.8378 (ptt90) cc_final: 0.8107 (ptm-80) REVERT: F 187 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 281 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: G 187 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7506 (tm-30) REVERT: G 195 TRP cc_start: 0.8910 (m100) cc_final: 0.8392 (m100) REVERT: G 285 ARG cc_start: 0.7413 (mpt90) cc_final: 0.7133 (mtp-110) REVERT: G 286 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8348 (tm) REVERT: H 130 ARG cc_start: 0.8402 (ptt90) cc_final: 0.8199 (ptt90) REVERT: H 187 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7547 (tm-30) REVERT: H 195 TRP cc_start: 0.8935 (m100) cc_final: 0.8328 (m100) REVERT: H 242 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7902 (ttmm) REVERT: I 187 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7538 (tm-30) REVERT: I 285 ARG cc_start: 0.7801 (mpt90) cc_final: 0.7589 (mtp-110) REVERT: J 53 ASN cc_start: 0.8182 (t0) cc_final: 0.7871 (t0) REVERT: J 187 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7653 (tm-30) REVERT: J 189 GLU cc_start: 0.8503 (tp30) cc_final: 0.8057 (tp30) REVERT: J 195 TRP cc_start: 0.8996 (m100) cc_final: 0.8426 (m100) REVERT: K 130 ARG cc_start: 0.8288 (ptt90) cc_final: 0.8074 (ptm-80) REVERT: K 187 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7556 (tm-30) REVERT: K 195 TRP cc_start: 0.8866 (m100) cc_final: 0.8348 (m100) REVERT: K 254 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7945 (mmt180) REVERT: K 285 ARG cc_start: 0.7397 (mpt90) cc_final: 0.7055 (mtp-110) REVERT: L 187 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7437 (tm-30) REVERT: L 195 TRP cc_start: 0.8926 (m100) cc_final: 0.8302 (m100) REVERT: L 242 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8127 (ttmm) REVERT: L 250 GLU cc_start: 0.7599 (tp30) cc_final: 0.7201 (mm-30) REVERT: M 187 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7477 (tm-30) REVERT: M 250 GLU cc_start: 0.7857 (tp30) cc_final: 0.7617 (tt0) REVERT: M 285 ARG cc_start: 0.7779 (mpt90) cc_final: 0.7536 (mtp-110) REVERT: N 53 ASN cc_start: 0.8210 (t0) cc_final: 0.7944 (t0) REVERT: N 187 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7633 (tm-30) REVERT: N 189 GLU cc_start: 0.8528 (tp30) cc_final: 0.8076 (tp30) REVERT: O 130 ARG cc_start: 0.8339 (ptt90) cc_final: 0.8088 (ptm-80) REVERT: O 187 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7618 (tm-30) REVERT: O 250 GLU cc_start: 0.7638 (tp30) cc_final: 0.7367 (mm-30) REVERT: O 281 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: P 187 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7513 (tm-30) REVERT: P 195 TRP cc_start: 0.8865 (m100) cc_final: 0.8324 (m100) REVERT: P 285 ARG cc_start: 0.7420 (mpt90) cc_final: 0.7114 (mtp-110) REVERT: Q 187 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7421 (tm-30) REVERT: Q 195 TRP cc_start: 0.8918 (m100) cc_final: 0.8286 (m100) REVERT: Q 242 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8107 (ttmm) REVERT: R 187 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7536 (tm-30) REVERT: R 285 ARG cc_start: 0.7749 (mpt90) cc_final: 0.7520 (mtp-110) REVERT: S 53 ASN cc_start: 0.8217 (t0) cc_final: 0.7909 (t0) REVERT: S 187 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7633 (tm-30) REVERT: T 130 ARG cc_start: 0.8329 (ptt90) cc_final: 0.8086 (ptm-80) REVERT: T 187 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7610 (tm-30) REVERT: T 250 GLU cc_start: 0.7681 (tp30) cc_final: 0.7272 (mm-30) REVERT: T 281 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7289 (m-80) outliers start: 353 outliers final: 197 residues processed: 795 average time/residue: 0.5889 time to fit residues: 757.9348 Evaluate side-chains 622 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 419 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 219 THR Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 466 optimal weight: 5.9990 chunk 318 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 417 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 478 optimal weight: 7.9990 chunk 387 optimal weight: 1.9990 chunk 0 optimal weight: 120.0000 chunk 286 optimal weight: 1.9990 chunk 503 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45860 Z= 0.231 Angle : 0.642 8.284 62520 Z= 0.347 Chirality : 0.044 0.234 7060 Planarity : 0.005 0.047 7940 Dihedral : 6.747 58.829 6412 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.71 % Allowed : 17.60 % Favored : 74.68 % 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: -0.72 (0.11), residues: 5820 helix: 0.69 (0.08), residues: 4180 sheet: None (None), residues: 0 loop : -3.66 (0.13), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 195 HIS 0.004 0.001 HIS L 135 PHE 0.021 0.001 PHE O 200 TYR 0.013 0.001 TYR L 129 ARG 0.005 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 441 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 189 GLU cc_start: 0.8438 (tp30) cc_final: 0.8018 (tp30) REVERT: A 281 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 135 HIS cc_start: 0.7398 (t-90) cc_final: 0.7041 (t-90) REVERT: B 187 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 286 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8241 (tm) REVERT: B 297 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.4258 (p90) REVERT: C 187 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7616 (tm-30) REVERT: C 195 TRP cc_start: 0.8976 (m100) cc_final: 0.8339 (m100) REVERT: C 242 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8121 (ttmm) REVERT: D 135 HIS cc_start: 0.7303 (t-90) cc_final: 0.7062 (t-90) REVERT: D 187 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 281 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: D 297 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.3820 (p90) REVERT: E 53 ASN cc_start: 0.8412 (t0) cc_final: 0.8025 (t0) REVERT: E 187 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8018 (tm-30) REVERT: E 189 GLU cc_start: 0.8471 (tp30) cc_final: 0.8050 (tp30) REVERT: E 195 TRP cc_start: 0.8990 (m100) cc_final: 0.8248 (m100) REVERT: E 199 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8593 (mp) REVERT: E 250 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: F 187 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7566 (tm-30) REVERT: F 189 GLU cc_start: 0.8375 (tp30) cc_final: 0.7994 (tp30) REVERT: F 281 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: G 135 HIS cc_start: 0.7256 (t-90) cc_final: 0.6915 (t-90) REVERT: G 187 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7549 (tm-30) REVERT: G 195 TRP cc_start: 0.8917 (m100) cc_final: 0.8258 (m100) REVERT: G 199 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8512 (mp) REVERT: G 285 ARG cc_start: 0.7504 (mpt90) cc_final: 0.7251 (mtp-110) REVERT: G 297 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4227 (p90) REVERT: H 130 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8224 (ptm-80) REVERT: H 187 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7611 (tm-30) REVERT: H 195 TRP cc_start: 0.8979 (m100) cc_final: 0.8350 (m100) REVERT: H 242 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7970 (ttmm) REVERT: I 135 HIS cc_start: 0.7293 (t-90) cc_final: 0.6979 (t-90) REVERT: I 187 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7660 (tm-30) REVERT: I 281 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: I 285 ARG cc_start: 0.7843 (mpt90) cc_final: 0.7574 (mtp-110) REVERT: I 297 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.3771 (p90) REVERT: J 53 ASN cc_start: 0.8432 (t0) cc_final: 0.7922 (t0) REVERT: J 187 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7725 (tm-30) REVERT: J 189 GLU cc_start: 0.8498 (tp30) cc_final: 0.8072 (tp30) REVERT: J 195 TRP cc_start: 0.9000 (m100) cc_final: 0.8306 (m100) REVERT: J 199 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8602 (mp) REVERT: K 135 HIS cc_start: 0.7336 (t-90) cc_final: 0.6993 (t-90) REVERT: K 187 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7558 (tm-30) REVERT: K 286 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8191 (tm) REVERT: K 297 TYR cc_start: 0.4964 (OUTLIER) cc_final: 0.4295 (p90) REVERT: K 302 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7628 (mt) REVERT: L 187 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7646 (tm-30) REVERT: L 195 TRP cc_start: 0.8953 (m100) cc_final: 0.8317 (m100) REVERT: L 242 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8141 (ttmm) REVERT: L 250 GLU cc_start: 0.7603 (tp30) cc_final: 0.7278 (mm-30) REVERT: M 135 HIS cc_start: 0.7304 (t-90) cc_final: 0.6947 (t-90) REVERT: M 187 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7591 (tm-30) REVERT: M 195 TRP cc_start: 0.8998 (m100) cc_final: 0.8797 (m100) REVERT: M 281 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: M 285 ARG cc_start: 0.7848 (mpt90) cc_final: 0.7597 (mtp-110) REVERT: N 53 ASN cc_start: 0.8386 (t0) cc_final: 0.7970 (t0) REVERT: N 135 HIS cc_start: 0.7379 (t-90) cc_final: 0.7164 (t-90) REVERT: N 187 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7743 (tm-30) REVERT: N 189 GLU cc_start: 0.8441 (tp30) cc_final: 0.8024 (tp30) REVERT: O 187 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7578 (tm-30) REVERT: O 189 GLU cc_start: 0.8366 (tp30) cc_final: 0.7971 (tp30) REVERT: O 281 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: P 187 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7547 (tm-30) REVERT: P 286 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8187 (tm) REVERT: P 297 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4314 (p90) REVERT: Q 187 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7655 (tm-30) REVERT: Q 195 TRP cc_start: 0.8951 (m100) cc_final: 0.8306 (m100) REVERT: Q 242 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8114 (ttmm) REVERT: R 135 HIS cc_start: 0.7229 (t-90) cc_final: 0.6894 (t-90) REVERT: R 187 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7662 (tm-30) REVERT: R 281 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: R 285 ARG cc_start: 0.7866 (mpt90) cc_final: 0.7557 (mtp-110) REVERT: R 297 TYR cc_start: 0.5366 (OUTLIER) cc_final: 0.3824 (p90) REVERT: S 53 ASN cc_start: 0.8482 (t0) cc_final: 0.7990 (t0) REVERT: S 187 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7727 (tm-30) REVERT: S 189 GLU cc_start: 0.8548 (tp30) cc_final: 0.8033 (tp30) REVERT: S 195 TRP cc_start: 0.8989 (m100) cc_final: 0.8272 (m100) REVERT: S 199 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8581 (mp) REVERT: S 250 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: T 187 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7568 (tm-30) REVERT: T 189 GLU cc_start: 0.8348 (tp30) cc_final: 0.7980 (tp30) REVERT: T 250 GLU cc_start: 0.7750 (tp30) cc_final: 0.7246 (mm-30) REVERT: T 281 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7434 (m-80) outliers start: 341 outliers final: 208 residues processed: 684 average time/residue: 0.5632 time to fit residues: 631.1750 Evaluate side-chains 656 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 423 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 250 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 188 optimal weight: 10.0000 chunk 504 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 561 optimal weight: 6.9990 chunk 465 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 45860 Z= 0.312 Angle : 0.704 9.722 62520 Z= 0.378 Chirality : 0.046 0.216 7060 Planarity : 0.005 0.054 7940 Dihedral : 6.311 54.876 6384 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 8.80 % Allowed : 16.74 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -0.73 (0.11), residues: 5820 helix: 0.59 (0.08), residues: 4240 sheet: None (None), residues: 0 loop : -3.50 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 195 HIS 0.007 0.002 HIS T 244 PHE 0.017 0.001 PHE B 123 TYR 0.017 0.002 TYR D 129 ARG 0.009 0.001 ARG S 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 490 time to evaluate : 5.380 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 187 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 189 GLU cc_start: 0.8354 (tp30) cc_final: 0.7824 (tp30) REVERT: A 281 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: B 135 HIS cc_start: 0.7389 (t-90) cc_final: 0.7180 (t-90) REVERT: B 187 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 286 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8514 (tm) REVERT: B 297 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.4910 (p90) REVERT: B 301 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7438 (mt0) REVERT: C 187 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 187 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 195 TRP cc_start: 0.9006 (m100) cc_final: 0.8800 (m100) REVERT: D 250 GLU cc_start: 0.7889 (tp30) cc_final: 0.7603 (tt0) REVERT: D 281 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: D 297 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.3949 (p90) REVERT: E 53 ASN cc_start: 0.8582 (t0) cc_final: 0.8109 (t0) REVERT: E 123 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6876 (m-10) REVERT: E 187 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8060 (tm-30) REVERT: E 189 GLU cc_start: 0.8496 (tp30) cc_final: 0.8008 (tp30) REVERT: E 195 TRP cc_start: 0.9044 (m100) cc_final: 0.8261 (m100) REVERT: E 199 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8593 (mp) REVERT: E 250 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: F 131 CYS cc_start: 0.6887 (t) cc_final: 0.6646 (t) REVERT: F 187 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 189 GLU cc_start: 0.8441 (tp30) cc_final: 0.7979 (tp30) REVERT: F 281 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: G 91 ARG cc_start: 0.7532 (tpp-160) cc_final: 0.7270 (tpp80) REVERT: G 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 285 ARG cc_start: 0.7529 (mpt90) cc_final: 0.7222 (mtp-110) REVERT: G 297 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.4604 (p90) REVERT: H 187 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7669 (tm-30) REVERT: H 242 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8106 (tttp) REVERT: I 135 HIS cc_start: 0.7138 (t-90) cc_final: 0.6872 (t-90) REVERT: I 187 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7693 (tm-30) REVERT: I 195 TRP cc_start: 0.9012 (m100) cc_final: 0.8750 (m100) REVERT: I 250 GLU cc_start: 0.7995 (tp30) cc_final: 0.7658 (tt0) REVERT: I 281 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: I 285 ARG cc_start: 0.7921 (mpt90) cc_final: 0.7638 (mtp-110) REVERT: I 297 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.3926 (p90) REVERT: J 53 ASN cc_start: 0.8415 (t0) cc_final: 0.7931 (t0) REVERT: J 123 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: J 187 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7742 (tm-30) REVERT: J 189 GLU cc_start: 0.8527 (tp30) cc_final: 0.7967 (tp30) REVERT: J 195 TRP cc_start: 0.9065 (m100) cc_final: 0.8344 (m100) REVERT: J 199 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8598 (mp) REVERT: J 250 GLU cc_start: 0.7979 (tp30) cc_final: 0.7720 (tt0) REVERT: K 61 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7307 (tpp) REVERT: K 187 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7594 (tm-30) REVERT: K 286 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8486 (tm) REVERT: K 297 TYR cc_start: 0.5252 (OUTLIER) cc_final: 0.4636 (p90) REVERT: L 187 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7684 (tm-30) REVERT: M 187 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7719 (tm-30) REVERT: M 195 TRP cc_start: 0.9028 (m100) cc_final: 0.8744 (m100) REVERT: M 250 GLU cc_start: 0.7961 (tp30) cc_final: 0.7649 (tt0) REVERT: M 281 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: M 285 ARG cc_start: 0.7891 (mpt90) cc_final: 0.7612 (mtp-110) REVERT: M 297 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.4052 (p90) REVERT: N 53 ASN cc_start: 0.8453 (t0) cc_final: 0.7967 (t0) REVERT: N 123 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: N 187 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7786 (tm-30) REVERT: N 189 GLU cc_start: 0.8510 (tp30) cc_final: 0.8257 (tp30) REVERT: N 195 TRP cc_start: 0.9068 (m100) cc_final: 0.8382 (m100) REVERT: N 250 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: O 187 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7610 (tm-30) REVERT: O 189 GLU cc_start: 0.8419 (tp30) cc_final: 0.7985 (tp30) REVERT: O 281 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: P 91 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.7202 (tpp80) REVERT: P 135 HIS cc_start: 0.7219 (t-90) cc_final: 0.7018 (t-90) REVERT: P 187 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7586 (tm-30) REVERT: P 286 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8516 (tm) REVERT: P 297 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4680 (p90) REVERT: P 301 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7160 (mm110) REVERT: Q 187 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7676 (tm-30) REVERT: R 187 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7697 (tm-30) REVERT: R 195 TRP cc_start: 0.8994 (m100) cc_final: 0.8775 (m100) REVERT: R 250 GLU cc_start: 0.7881 (tp30) cc_final: 0.7583 (tt0) REVERT: R 281 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: R 285 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7704 (mtp-110) REVERT: R 297 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.3911 (p90) REVERT: S 53 ASN cc_start: 0.8459 (t0) cc_final: 0.7982 (t0) REVERT: S 123 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: S 187 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7737 (tm-30) REVERT: S 189 GLU cc_start: 0.8539 (tp30) cc_final: 0.7936 (tp30) REVERT: S 250 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: T 187 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7610 (tm-30) REVERT: T 189 GLU cc_start: 0.8426 (tp30) cc_final: 0.7993 (tp30) REVERT: T 281 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7842 (m-80) outliers start: 389 outliers final: 269 residues processed: 772 average time/residue: 0.5709 time to fit residues: 733.4670 Evaluate side-chains 776 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 478 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 146 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 146 CYS Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 146 CYS Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 146 CYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 146 CYS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 146 CYS Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 104 TRP Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 CYS Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 TRP Chi-restraints excluded: chain R residue 146 CYS Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 146 CYS Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 250 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 104 TRP Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 319 optimal weight: 120.0000 chunk 409 optimal weight: 50.0000 chunk 317 optimal weight: 8.9990 chunk 472 optimal weight: 7.9990 chunk 313 optimal weight: 0.7980 chunk 559 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 340 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45860 Z= 0.241 Angle : 0.661 11.280 62520 Z= 0.353 Chirality : 0.044 0.213 7060 Planarity : 0.005 0.051 7940 Dihedral : 6.036 52.462 6380 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 7.76 % Allowed : 18.21 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5820 helix: 0.82 (0.08), residues: 4240 sheet: None (None), residues: 0 loop : -3.52 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 195 HIS 0.006 0.001 HIS L 135 PHE 0.021 0.001 PHE D 200 TYR 0.014 0.001 TYR M 50 ARG 0.006 0.001 ARG J 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 465 time to evaluate : 5.403 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: A 140 ILE cc_start: 0.4549 (OUTLIER) cc_final: 0.4304 (pp) REVERT: A 187 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 189 GLU cc_start: 0.8312 (tp30) cc_final: 0.7907 (tp30) REVERT: A 281 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 187 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 286 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8460 (tm) REVERT: B 297 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.4494 (p90) REVERT: C 187 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7691 (tm-30) REVERT: D 187 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 195 TRP cc_start: 0.9012 (m100) cc_final: 0.8716 (m100) REVERT: D 250 GLU cc_start: 0.7830 (tp30) cc_final: 0.7568 (tt0) REVERT: D 281 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: D 297 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.4022 (p90) REVERT: E 53 ASN cc_start: 0.8557 (t0) cc_final: 0.8119 (t0) REVERT: E 123 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: E 187 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7995 (tm-30) REVERT: E 189 GLU cc_start: 0.8443 (tp30) cc_final: 0.7972 (tp30) REVERT: E 195 TRP cc_start: 0.9045 (m100) cc_final: 0.8281 (m100) REVERT: E 199 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8568 (mp) REVERT: E 250 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: F 187 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7551 (tm-30) REVERT: F 189 GLU cc_start: 0.8386 (tp30) cc_final: 0.7942 (tp30) REVERT: F 281 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: G 52 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8743 (mm) REVERT: G 91 ARG cc_start: 0.7372 (tpp-160) cc_final: 0.7114 (tpp80) REVERT: G 187 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7615 (tm-30) REVERT: G 297 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4557 (p90) REVERT: H 187 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7682 (tm-30) REVERT: H 242 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8006 (ttmm) REVERT: I 187 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7682 (tm-30) REVERT: I 195 TRP cc_start: 0.9013 (m100) cc_final: 0.8738 (m100) REVERT: I 250 GLU cc_start: 0.7941 (tp30) cc_final: 0.7627 (tt0) REVERT: I 281 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: I 285 ARG cc_start: 0.7856 (mpt90) cc_final: 0.7447 (mtp-110) REVERT: I 297 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.4081 (p90) REVERT: J 53 ASN cc_start: 0.8390 (t0) cc_final: 0.7857 (t0) REVERT: J 123 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7111 (m-10) REVERT: J 187 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7687 (tm-30) REVERT: J 189 GLU cc_start: 0.8534 (tp30) cc_final: 0.8047 (tp30) REVERT: J 195 TRP cc_start: 0.9030 (m100) cc_final: 0.8429 (m100) REVERT: J 250 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: K 187 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7614 (tm-30) REVERT: K 297 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.4587 (p90) REVERT: L 187 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7725 (tm-30) REVERT: M 187 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7618 (tm-30) REVERT: M 195 TRP cc_start: 0.9034 (m100) cc_final: 0.8755 (m100) REVERT: M 250 GLU cc_start: 0.7906 (tp30) cc_final: 0.7609 (tt0) REVERT: M 281 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: M 285 ARG cc_start: 0.7863 (mpt90) cc_final: 0.7493 (mtp-110) REVERT: M 297 TYR cc_start: 0.5578 (OUTLIER) cc_final: 0.4121 (p90) REVERT: N 53 ASN cc_start: 0.8395 (t0) cc_final: 0.7948 (t0) REVERT: N 135 HIS cc_start: 0.7178 (t-90) cc_final: 0.6941 (t-90) REVERT: N 187 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7727 (tm-30) REVERT: N 189 GLU cc_start: 0.8511 (tp30) cc_final: 0.8062 (tp30) REVERT: N 195 TRP cc_start: 0.9019 (m100) cc_final: 0.8344 (m100) REVERT: N 250 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: O 140 ILE cc_start: 0.4566 (OUTLIER) cc_final: 0.4267 (pp) REVERT: O 187 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7512 (tm-30) REVERT: O 189 GLU cc_start: 0.8321 (tp30) cc_final: 0.7928 (tp30) REVERT: O 281 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: P 187 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7593 (tm-30) REVERT: P 297 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4640 (p90) REVERT: Q 187 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7726 (tm-30) REVERT: R 187 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7699 (tm-30) REVERT: R 195 TRP cc_start: 0.9000 (m100) cc_final: 0.8746 (m100) REVERT: R 250 GLU cc_start: 0.7817 (tp30) cc_final: 0.7559 (tt0) REVERT: R 281 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: R 285 ARG cc_start: 0.7884 (mpt90) cc_final: 0.7558 (mtp-110) REVERT: R 297 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.4083 (p90) REVERT: S 53 ASN cc_start: 0.8428 (t0) cc_final: 0.7906 (t0) REVERT: S 123 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: S 187 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7705 (tm-30) REVERT: S 189 GLU cc_start: 0.8542 (tp30) cc_final: 0.7943 (tp30) REVERT: S 195 TRP cc_start: 0.9037 (m100) cc_final: 0.8425 (m100) REVERT: S 250 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: T 187 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7533 (tm-30) REVERT: T 189 GLU cc_start: 0.8347 (tp30) cc_final: 0.7950 (tp30) REVERT: T 281 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7746 (m-80) outliers start: 343 outliers final: 276 residues processed: 708 average time/residue: 0.5288 time to fit residues: 624.3808 Evaluate side-chains 755 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 451 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 146 CYS Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 CYS Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 250 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 146 CYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 CYS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 146 CYS Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 CYS Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 146 CYS Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 146 CYS Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 250 GLU Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 287 ILE Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 345 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 439 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 153 ASN ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 45860 Z= 0.275 Angle : 0.687 17.062 62520 Z= 0.362 Chirality : 0.045 0.251 7060 Planarity : 0.005 0.052 7940 Dihedral : 6.054 52.940 6380 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 7.81 % Allowed : 18.24 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5820 helix: 0.71 (0.08), residues: 4360 sheet: None (None), residues: 0 loop : -3.40 (0.14), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 195 HIS 0.006 0.002 HIS Q 135 PHE 0.018 0.001 PHE D 200 TYR 0.015 0.002 TYR I 129 ARG 0.007 0.001 ARG N 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 470 time to evaluate : 4.824 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: A 187 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 189 GLU cc_start: 0.8374 (tp30) cc_final: 0.7839 (tp30) REVERT: A 281 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: B 187 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 286 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8456 (tm) REVERT: B 297 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.4661 (p90) REVERT: C 187 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 53 ASN cc_start: 0.8409 (t0) cc_final: 0.8146 (t0) REVERT: D 187 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 195 TRP cc_start: 0.9064 (m100) cc_final: 0.8740 (m100) REVERT: D 250 GLU cc_start: 0.7876 (tp30) cc_final: 0.7566 (tt0) REVERT: D 281 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: D 297 TYR cc_start: 0.5515 (OUTLIER) cc_final: 0.4153 (p90) REVERT: E 53 ASN cc_start: 0.8558 (t0) cc_final: 0.8082 (t0) REVERT: E 61 MET cc_start: 0.7507 (tpp) cc_final: 0.7058 (tpp) REVERT: E 123 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: E 187 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8031 (tm-30) REVERT: E 189 GLU cc_start: 0.8476 (tp30) cc_final: 0.7976 (tp30) REVERT: E 195 TRP cc_start: 0.9074 (m100) cc_final: 0.8328 (m100) REVERT: E 199 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8581 (mp) REVERT: E 250 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: F 187 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 189 GLU cc_start: 0.8389 (tp30) cc_final: 0.7909 (tp30) REVERT: F 281 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: G 52 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8833 (mm) REVERT: G 187 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7646 (tm-30) REVERT: G 297 TYR cc_start: 0.5295 (OUTLIER) cc_final: 0.4683 (p90) REVERT: H 130 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8429 (ptt90) REVERT: H 187 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7756 (tm-30) REVERT: H 242 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8084 (tttp) REVERT: I 187 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7695 (tm-30) REVERT: I 195 TRP cc_start: 0.9067 (m100) cc_final: 0.8775 (m100) REVERT: I 250 GLU cc_start: 0.7973 (tp30) cc_final: 0.7665 (tt0) REVERT: I 281 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: I 285 ARG cc_start: 0.7860 (mpt90) cc_final: 0.7353 (mtp-110) REVERT: I 297 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4015 (p90) REVERT: J 53 ASN cc_start: 0.8402 (t0) cc_final: 0.7889 (t0) REVERT: J 123 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: J 187 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7712 (tm-30) REVERT: J 189 GLU cc_start: 0.8529 (tp30) cc_final: 0.7955 (tp30) REVERT: K 187 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7653 (tm-30) REVERT: K 297 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.4580 (p90) REVERT: L 187 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7744 (tm-30) REVERT: L 250 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7473 (mm-30) REVERT: M 187 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7608 (tm-30) REVERT: M 195 TRP cc_start: 0.9053 (m100) cc_final: 0.8757 (m100) REVERT: M 250 GLU cc_start: 0.7948 (tp30) cc_final: 0.7650 (tt0) REVERT: M 281 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: M 285 ARG cc_start: 0.7904 (mpt90) cc_final: 0.7461 (mtp-110) REVERT: M 297 TYR cc_start: 0.5509 (OUTLIER) cc_final: 0.4058 (p90) REVERT: N 53 ASN cc_start: 0.8431 (t0) cc_final: 0.7944 (t0) REVERT: N 123 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: N 187 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7742 (tm-30) REVERT: N 189 GLU cc_start: 0.8526 (tp30) cc_final: 0.7966 (tp30) REVERT: N 195 TRP cc_start: 0.9049 (m100) cc_final: 0.8372 (m100) REVERT: N 250 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: N 296 MET cc_start: 0.6038 (mmp) cc_final: 0.5778 (mtt) REVERT: O 187 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7567 (tm-30) REVERT: O 189 GLU cc_start: 0.8342 (tp30) cc_final: 0.7956 (tp30) REVERT: O 281 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: P 187 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7651 (tm-30) REVERT: P 297 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.4585 (p90) REVERT: P 301 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7244 (mm110) REVERT: Q 187 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7765 (tm-30) REVERT: R 187 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7741 (tm-30) REVERT: R 195 TRP cc_start: 0.9039 (m100) cc_final: 0.8742 (m100) REVERT: R 250 GLU cc_start: 0.7860 (tp30) cc_final: 0.7558 (tt0) REVERT: R 281 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: R 285 ARG cc_start: 0.7890 (mpt90) cc_final: 0.7548 (mtp-110) REVERT: R 297 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.3998 (p90) REVERT: S 53 ASN cc_start: 0.8436 (t0) cc_final: 0.7943 (t0) REVERT: S 123 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: S 187 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7618 (tm-30) REVERT: S 189 GLU cc_start: 0.8529 (tp30) cc_final: 0.7911 (tp30) REVERT: T 135 HIS cc_start: 0.6699 (t-90) cc_final: 0.6384 (t-90) REVERT: T 187 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7583 (tm-30) REVERT: T 189 GLU cc_start: 0.8367 (tp30) cc_final: 0.7966 (tp30) REVERT: T 281 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7789 (m-80) outliers start: 345 outliers final: 272 residues processed: 715 average time/residue: 0.5408 time to fit residues: 643.0150 Evaluate side-chains 758 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 461 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 CYS Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 146 CYS Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 146 CYS Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain J residue 297 TYR Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 104 TRP Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 104 TRP Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 146 CYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 146 CYS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 287 ILE Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 104 TRP Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 146 CYS Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 146 CYS Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain P residue 297 TYR Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 104 TRP Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 201 SER Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 146 CYS Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 234 THR Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 146 CYS Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 234 THR Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 287 ILE Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 508 optimal weight: 30.0000 chunk 535 optimal weight: 0.8980 chunk 488 optimal weight: 1.9990 chunk 520 optimal weight: 0.1980 chunk 313 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 409 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 470 optimal weight: 3.9990 chunk 492 optimal weight: 2.9990 chunk 519 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 76 ASN ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 45860 Z= 0.194 Angle : 0.650 16.677 62520 Z= 0.338 Chirality : 0.043 0.255 7060 Planarity : 0.005 0.052 7940 Dihedral : 5.764 51.927 6378 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.54 % Allowed : 19.57 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5820 helix: 1.08 (0.08), residues: 4240 sheet: None (None), residues: 0 loop : -3.48 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 195 HIS 0.004 0.001 HIS L 135 PHE 0.019 0.001 PHE I 200 TYR 0.018 0.001 TYR I 50 ARG 0.007 0.001 ARG N 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 467 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 189 GLU cc_start: 0.8335 (tp30) cc_final: 0.8005 (tp30) REVERT: A 281 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: A 286 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8499 (tm) REVERT: B 187 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 192 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8421 (pp) REVERT: B 286 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (tm) REVERT: C 187 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 254 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8232 (mmt90) REVERT: D 53 ASN cc_start: 0.8157 (t0) cc_final: 0.7957 (t0) REVERT: D 187 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 195 TRP cc_start: 0.9060 (m100) cc_final: 0.8721 (m100) REVERT: D 250 GLU cc_start: 0.7764 (tp30) cc_final: 0.7499 (tt0) REVERT: D 281 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: E 53 ASN cc_start: 0.8384 (t0) cc_final: 0.7934 (t0) REVERT: E 61 MET cc_start: 0.7359 (tpp) cc_final: 0.6799 (tpp) REVERT: E 123 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6785 (m-10) REVERT: E 187 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 189 GLU cc_start: 0.8434 (tp30) cc_final: 0.7993 (tp30) REVERT: E 250 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: F 187 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 189 GLU cc_start: 0.8336 (tp30) cc_final: 0.7914 (tp30) REVERT: F 281 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: G 52 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8768 (mm) REVERT: G 187 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7573 (tm-30) REVERT: H 130 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.8041 (ptt90) REVERT: H 187 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7638 (tm-30) REVERT: H 242 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7944 (ttmm) REVERT: I 187 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7676 (tm-30) REVERT: I 195 TRP cc_start: 0.9050 (m100) cc_final: 0.8748 (m100) REVERT: I 250 GLU cc_start: 0.7890 (tp30) cc_final: 0.7582 (tt0) REVERT: I 281 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: I 285 ARG cc_start: 0.7754 (mpt90) cc_final: 0.7266 (mtp-110) REVERT: I 297 TYR cc_start: 0.5459 (OUTLIER) cc_final: 0.4041 (p90) REVERT: J 53 ASN cc_start: 0.8254 (t0) cc_final: 0.7773 (t0) REVERT: J 61 MET cc_start: 0.7143 (tpp) cc_final: 0.6497 (tpp) REVERT: J 123 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: J 187 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7554 (tm-30) REVERT: J 189 GLU cc_start: 0.8532 (tp30) cc_final: 0.8060 (tp30) REVERT: J 195 TRP cc_start: 0.9007 (m100) cc_final: 0.8349 (m100) REVERT: J 305 ASP cc_start: 0.7577 (t0) cc_final: 0.7157 (m-30) REVERT: K 187 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7613 (tm-30) REVERT: K 297 TYR cc_start: 0.5025 (OUTLIER) cc_final: 0.4479 (p90) REVERT: K 301 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7098 (mm110) REVERT: L 187 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7647 (tm-30) REVERT: M 187 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7583 (tm-30) REVERT: M 195 TRP cc_start: 0.9028 (m100) cc_final: 0.8718 (m100) REVERT: M 250 GLU cc_start: 0.7860 (tp30) cc_final: 0.7565 (tt0) REVERT: M 281 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: M 285 ARG cc_start: 0.7819 (mpt90) cc_final: 0.7406 (mtp-110) REVERT: M 297 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.4065 (p90) REVERT: N 53 ASN cc_start: 0.8299 (t0) cc_final: 0.7827 (t0) REVERT: N 123 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: N 187 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7565 (tm-30) REVERT: N 189 GLU cc_start: 0.8520 (tp30) cc_final: 0.8066 (tp30) REVERT: N 195 TRP cc_start: 0.9041 (m100) cc_final: 0.8382 (m100) REVERT: N 250 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: N 305 ASP cc_start: 0.7626 (t0) cc_final: 0.7298 (m-30) REVERT: O 187 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7475 (tm-30) REVERT: O 281 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: P 187 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7609 (tm-30) REVERT: P 301 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7207 (mm110) REVERT: Q 187 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7666 (tm-30) REVERT: Q 231 ASN cc_start: 0.8179 (t0) cc_final: 0.7956 (t0) REVERT: R 187 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7701 (tm-30) REVERT: R 195 TRP cc_start: 0.9063 (m100) cc_final: 0.8725 (m100) REVERT: R 250 GLU cc_start: 0.7758 (tp30) cc_final: 0.7497 (tt0) REVERT: R 281 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: R 285 ARG cc_start: 0.7776 (mpt90) cc_final: 0.7347 (mtp-110) REVERT: R 297 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4065 (p90) REVERT: S 53 ASN cc_start: 0.8319 (t0) cc_final: 0.7839 (t0) REVERT: S 123 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7159 (m-10) REVERT: S 187 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7560 (tm-30) REVERT: S 189 GLU cc_start: 0.8540 (tp30) cc_final: 0.7950 (tp30) REVERT: S 195 TRP cc_start: 0.9020 (m100) cc_final: 0.8363 (m100) REVERT: S 250 GLU cc_start: 0.7782 (tt0) cc_final: 0.7538 (tt0) REVERT: T 187 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7530 (tm-30) REVERT: T 281 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7534 (m-80) outliers start: 289 outliers final: 225 residues processed: 672 average time/residue: 0.5382 time to fit residues: 603.9836 Evaluate side-chains 710 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 463 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 146 CYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 234 THR Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 234 THR Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 214 MET Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 342 optimal weight: 0.9980 chunk 550 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 382 optimal weight: 5.9990 chunk 577 optimal weight: 1.9990 chunk 531 optimal weight: 1.9990 chunk 460 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 153 ASN ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45860 Z= 0.202 Angle : 0.685 19.273 62520 Z= 0.351 Chirality : 0.043 0.285 7060 Planarity : 0.005 0.051 7940 Dihedral : 5.620 52.912 6376 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.02 % Allowed : 19.59 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5820 helix: 1.25 (0.08), residues: 4200 sheet: None (None), residues: 0 loop : -3.51 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 195 HIS 0.004 0.001 HIS L 135 PHE 0.018 0.001 PHE I 200 TYR 0.015 0.001 TYR I 50 ARG 0.007 0.000 ARG J 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 469 time to evaluate : 4.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6636 (t-90) cc_final: 0.6389 (t-90) REVERT: A 187 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 189 GLU cc_start: 0.8345 (tp30) cc_final: 0.8012 (tp30) REVERT: A 195 TRP cc_start: 0.9047 (m100) cc_final: 0.8581 (m100) REVERT: A 281 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: B 130 ARG cc_start: 0.8352 (ptm160) cc_final: 0.8096 (ptm-80) REVERT: B 187 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 192 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8436 (pp) REVERT: B 254 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.8029 (mmt180) REVERT: B 286 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (tm) REVERT: C 187 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 187 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 195 TRP cc_start: 0.9076 (m100) cc_final: 0.8749 (m100) REVERT: D 229 TYR cc_start: 0.8773 (t80) cc_final: 0.8530 (t80) REVERT: D 250 GLU cc_start: 0.7788 (tp30) cc_final: 0.7545 (tt0) REVERT: D 281 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: E 53 ASN cc_start: 0.8389 (t0) cc_final: 0.7945 (t0) REVERT: E 61 MET cc_start: 0.7352 (tpp) cc_final: 0.6711 (tpp) REVERT: E 123 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: E 187 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 189 GLU cc_start: 0.8448 (tp30) cc_final: 0.7991 (tp30) REVERT: E 250 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: F 187 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7512 (tm-30) REVERT: F 189 GLU cc_start: 0.8359 (tp30) cc_final: 0.7921 (tp30) REVERT: F 195 TRP cc_start: 0.9040 (m100) cc_final: 0.8589 (m100) REVERT: F 281 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: G 52 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8778 (mm) REVERT: G 82 LEU cc_start: 0.8803 (tt) cc_final: 0.8529 (tt) REVERT: G 187 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7575 (tm-30) REVERT: G 301 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7227 (mm110) REVERT: H 187 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7658 (tm-30) REVERT: H 242 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7954 (ttmm) REVERT: I 187 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7697 (tm-30) REVERT: I 195 TRP cc_start: 0.9071 (m100) cc_final: 0.8729 (m100) REVERT: I 250 GLU cc_start: 0.7930 (tp30) cc_final: 0.7643 (tt0) REVERT: I 281 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: I 285 ARG cc_start: 0.7803 (mpt90) cc_final: 0.7355 (mtp-110) REVERT: I 297 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.4111 (p90) REVERT: J 53 ASN cc_start: 0.8308 (t0) cc_final: 0.7812 (t0) REVERT: J 61 MET cc_start: 0.7223 (tpp) cc_final: 0.6620 (tpp) REVERT: J 123 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: J 187 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7570 (tm-30) REVERT: J 189 GLU cc_start: 0.8543 (tp30) cc_final: 0.8123 (tp30) REVERT: J 195 TRP cc_start: 0.9036 (m100) cc_final: 0.8396 (m100) REVERT: J 250 GLU cc_start: 0.7794 (tt0) cc_final: 0.7582 (tt0) REVERT: K 82 LEU cc_start: 0.8766 (tt) cc_final: 0.8459 (tp) REVERT: K 187 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7649 (tm-30) REVERT: K 297 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4712 (p90) REVERT: K 301 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7236 (mm110) REVERT: L 187 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7645 (tm-30) REVERT: M 187 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7596 (tm-30) REVERT: M 195 TRP cc_start: 0.9061 (m100) cc_final: 0.8712 (m100) REVERT: M 250 GLU cc_start: 0.7897 (tp30) cc_final: 0.7577 (tt0) REVERT: M 281 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: M 285 ARG cc_start: 0.7859 (mpt90) cc_final: 0.7476 (mtp-110) REVERT: N 53 ASN cc_start: 0.8323 (t0) cc_final: 0.7851 (t0) REVERT: N 123 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: N 187 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7583 (tm-30) REVERT: N 189 GLU cc_start: 0.8533 (tp30) cc_final: 0.8039 (tp30) REVERT: N 195 TRP cc_start: 0.9060 (m100) cc_final: 0.8443 (m100) REVERT: N 250 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: N 305 ASP cc_start: 0.7662 (t0) cc_final: 0.7242 (m-30) REVERT: O 135 HIS cc_start: 0.6570 (t-90) cc_final: 0.6362 (t-90) REVERT: O 187 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7556 (tm-30) REVERT: O 195 TRP cc_start: 0.9059 (m100) cc_final: 0.8555 (m100) REVERT: O 281 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: P 82 LEU cc_start: 0.8843 (tt) cc_final: 0.8586 (tt) REVERT: P 187 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7644 (tm-30) REVERT: P 301 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7210 (mm110) REVERT: Q 187 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7669 (tm-30) REVERT: R 187 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7712 (tm-30) REVERT: R 195 TRP cc_start: 0.9082 (m100) cc_final: 0.8764 (m100) REVERT: R 250 GLU cc_start: 0.7749 (tp30) cc_final: 0.7497 (tt0) REVERT: R 281 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: R 285 ARG cc_start: 0.7879 (mpt90) cc_final: 0.7451 (mtp-110) REVERT: R 297 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.4135 (p90) REVERT: S 53 ASN cc_start: 0.8361 (t0) cc_final: 0.7863 (t0) REVERT: S 123 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: S 130 ARG cc_start: 0.8548 (ptt90) cc_final: 0.8239 (ptt90) REVERT: S 187 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7554 (tm-30) REVERT: S 189 GLU cc_start: 0.8528 (tp30) cc_final: 0.7911 (tp30) REVERT: S 195 TRP cc_start: 0.8993 (m100) cc_final: 0.8332 (m100) REVERT: S 250 GLU cc_start: 0.7839 (tt0) cc_final: 0.7622 (tt0) REVERT: T 187 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7532 (tm-30) REVERT: T 195 TRP cc_start: 0.9051 (m100) cc_final: 0.8577 (m100) REVERT: T 250 GLU cc_start: 0.7746 (tp30) cc_final: 0.7380 (mm-30) REVERT: T 281 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7616 (m-80) outliers start: 266 outliers final: 230 residues processed: 659 average time/residue: 0.5264 time to fit residues: 581.0123 Evaluate side-chains 707 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 457 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 162 ASN Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 296 MET Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 233 GLU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 286 LEU Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 214 MET Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 123 PHE Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 146 CYS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 233 GLU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 297 TYR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 123 PHE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 174 CYS Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain N residue 233 GLU Chi-restraints excluded: chain N residue 234 THR Chi-restraints excluded: chain N residue 250 GLU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 284 LEU Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 297 TYR Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 174 CYS Chi-restraints excluded: chain O residue 181 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 174 CYS Chi-restraints excluded: chain P residue 181 THR Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 214 MET Chi-restraints excluded: chain P residue 233 GLU Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 287 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 123 PHE Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 162 ASN Chi-restraints excluded: chain Q residue 181 THR Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 281 PHE Chi-restraints excluded: chain Q residue 286 LEU Chi-restraints excluded: chain Q residue 296 MET Chi-restraints excluded: chain Q residue 297 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 162 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain R residue 234 THR Chi-restraints excluded: chain R residue 281 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 297 TYR Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 123 PHE Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 234 THR Chi-restraints excluded: chain S residue 281 PHE Chi-restraints excluded: chain S residue 284 LEU Chi-restraints excluded: chain S residue 286 LEU Chi-restraints excluded: chain S residue 297 TYR Chi-restraints excluded: chain S residue 302 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 162 ASN Chi-restraints excluded: chain T residue 174 CYS Chi-restraints excluded: chain T residue 181 THR Chi-restraints excluded: chain T residue 201 SER Chi-restraints excluded: chain T residue 219 THR Chi-restraints excluded: chain T residue 233 GLU Chi-restraints excluded: chain T residue 281 PHE Chi-restraints excluded: chain T residue 286 LEU Chi-restraints excluded: chain T residue 296 MET Chi-restraints excluded: chain T residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 365 optimal weight: 2.9990 chunk 490 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 424 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 460 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 473 optimal weight: 7.9990 chunk 58 optimal weight: 120.0000 chunk 84 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.197039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151470 restraints weight = 78650.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155294 restraints weight = 43271.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.157917 restraints weight = 29656.671| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45860 Z= 0.217 Angle : 0.684 18.903 62520 Z= 0.351 Chirality : 0.043 0.307 7060 Planarity : 0.005 0.051 7940 Dihedral : 5.640 53.218 6376 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.11 % Allowed : 19.62 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.05 (0.11), residues: 5820 helix: 1.20 (0.08), residues: 4240 sheet: None (None), residues: 0 loop : -3.36 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 195 HIS 0.005 0.001 HIS L 244 PHE 0.018 0.001 PHE D 200 TYR 0.012 0.001 TYR Q 50 ARG 0.007 0.001 ARG C 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11037.73 seconds wall clock time: 201 minutes 41.21 seconds (12101.21 seconds total)