Starting phenix.real_space_refine on Wed Mar 20 14:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/03_2024/6cb8_7449_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 S 216 5.16 5 C 31698 2.51 5 N 8478 2.21 5 O 9342 1.98 5 H 50436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 100224 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO A 233 " pdbres="CDL A 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO B 233 " pdbres="CDL B 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO C 233 " pdbres="CDL C 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO D 233 " pdbres="CDL D 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO E 233 " pdbres="CDL E 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO F 233 " pdbres="CDL F 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO G 233 " pdbres="CDL G 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO H 233 " pdbres="CDL H 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO I 233 " pdbres="CDL I 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO J 233 " pdbres="CDL J 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO K 233 " pdbres="CDL K 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO L 233 " pdbres="CDL L 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO M 233 " pdbres="CDL M 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO N 233 " pdbres="CDL N 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "O" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO O 233 " pdbres="CDL O 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO P 233 " pdbres="CDL P 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Q 233 " pdbres="CDL Q 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO R 233 " pdbres="CDL R 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO S 233 " pdbres="CDL S 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO T 233 " pdbres="CDL T 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "U" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO U 233 " pdbres="CDL U 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "V" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO V 233 " pdbres="CDL V 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "W" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO W 233 " pdbres="CDL W 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO X 233 " pdbres="CDL X 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Y" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Y 233 " pdbres="CDL Y 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Z 233 " pdbres="CDL Z 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "0" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO 0 233 " pdbres="CDL 0 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Residues with excluded nonbonded symmetry interactions: 27 residue: pdb=" CB2 CDL A 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL A 301 " occ=0.00 residue: pdb=" CB2 CDL B 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL B 301 " occ=0.00 residue: pdb=" CB2 CDL C 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL C 301 " occ=0.00 residue: pdb=" CB2 CDL D 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL D 301 " occ=0.00 residue: pdb=" CB2 CDL E 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL E 301 " occ=0.00 residue: pdb=" CB2 CDL F 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL F 301 " occ=0.00 residue: pdb=" CB2 CDL G 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL G 301 " occ=0.00 residue: pdb=" CB2 CDL H 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL H 301 " occ=0.00 residue: pdb=" CB2 CDL I 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL I 301 " occ=0.00 residue: pdb=" CB2 CDL J 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL J 301 " occ=0.00 residue: pdb=" CB2 CDL K 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL K 301 " occ=0.00 residue: pdb=" CB2 CDL L 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL L 301 " occ=0.00 ... (remaining 15 not shown) Time building chain proxies: 32.51, per 1000 atoms: 0.32 Number of scatterers: 100224 At special positions: 0 Unit cell: (295.68, 295.68, 77.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 54 15.00 O 9342 8.00 N 8478 7.00 C 31698 6.00 H 50436 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 65.06 Conformation dependent library (CDL) restraints added in 8.4 seconds 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11880 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 135 helices and 81 sheets defined 22.2% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 19.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP A 6 " --> pdb=" O PRO A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP B 6 " --> pdb=" O PRO B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP C 6 " --> pdb=" O PRO C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP D 6 " --> pdb=" O PRO D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP E 6 " --> pdb=" O PRO E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP F 6 " --> pdb=" O PRO F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP G 6 " --> pdb=" O PRO G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'H' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP H 6 " --> pdb=" O PRO H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 132 Processing helix chain 'H' and resid 138 through 148 Processing helix chain 'I' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP I 6 " --> pdb=" O PRO I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU I 63 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'J' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP J 6 " --> pdb=" O PRO J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 Processing helix chain 'J' and resid 138 through 148 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP K 6 " --> pdb=" O PRO K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 138 through 148 Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP L 6 " --> pdb=" O PRO L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 132 Processing helix chain 'L' and resid 138 through 148 Processing helix chain 'M' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP M 6 " --> pdb=" O PRO M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 132 Processing helix chain 'M' and resid 138 through 148 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 34 Processing helix chain 'N' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU N 63 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 138 through 148 Processing helix chain 'O' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP O 6 " --> pdb=" O PRO O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 34 Processing helix chain 'O' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 132 Processing helix chain 'O' and resid 138 through 148 Processing helix chain 'P' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP P 6 " --> pdb=" O PRO P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 Processing helix chain 'P' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 138 through 148 Processing helix chain 'Q' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Q 6 " --> pdb=" O PRO Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU Q 63 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 132 Processing helix chain 'Q' and resid 138 through 148 Processing helix chain 'R' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP R 6 " --> pdb=" O PRO R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 132 Processing helix chain 'R' and resid 138 through 148 Processing helix chain 'S' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP S 6 " --> pdb=" O PRO S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 34 Processing helix chain 'S' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU S 65 " --> pdb=" O LEU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 132 Processing helix chain 'S' and resid 138 through 148 Processing helix chain 'T' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP T 6 " --> pdb=" O PRO T 2 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 132 Processing helix chain 'T' and resid 138 through 148 Processing helix chain 'U' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP U 6 " --> pdb=" O PRO U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 34 Processing helix chain 'U' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 132 Processing helix chain 'U' and resid 138 through 148 Processing helix chain 'V' and resid 2 through 16 removed outlier: 3.622A pdb=" N ASP V 6 " --> pdb=" O PRO V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 Processing helix chain 'V' and resid 138 through 148 Processing helix chain 'W' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP W 6 " --> pdb=" O PRO W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 34 Processing helix chain 'W' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU W 65 " --> pdb=" O LEU W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 132 Processing helix chain 'W' and resid 138 through 148 Processing helix chain 'X' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP X 6 " --> pdb=" O PRO X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 34 Processing helix chain 'X' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU X 65 " --> pdb=" O LEU X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 138 through 148 Processing helix chain 'Y' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Y 6 " --> pdb=" O PRO Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 138 through 148 Processing helix chain 'Z' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP Z 6 " --> pdb=" O PRO Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 34 Processing helix chain 'Z' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 138 through 148 Processing helix chain '0' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP 0 6 " --> pdb=" O PRO 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU 0 65 " --> pdb=" O LEU 0 61 " (cutoff:3.500A) Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 138 through 148 Processing sheet with id= 1, first strand: chain 'A' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU A 204 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 207 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 155 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 37 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A 112 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 165 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU A 156 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 205 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU B 204 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 207 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 155 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS B 37 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR B 112 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR B 165 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU B 156 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 205 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU C 204 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG C 207 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 155 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 37 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR C 112 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 165 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU C 156 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 205 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU D 204 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 207 " --> pdb=" O MET D 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 155 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS D 37 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR D 112 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 165 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU D 156 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 205 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU E 204 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG E 207 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 155 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS E 37 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL E 99 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR E 112 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR E 165 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU E 156 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 205 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU F 204 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 207 " --> pdb=" O MET F 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET F 155 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS F 37 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR F 112 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR F 165 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU F 156 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 205 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU G 204 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 207 " --> pdb=" O MET G 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET G 155 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS G 37 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR G 112 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR G 165 " --> pdb=" O THR G 112 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU G 156 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 205 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU H 204 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG H 207 " --> pdb=" O MET H 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET H 155 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS H 37 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR H 112 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR H 165 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU H 156 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 205 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU I 204 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG I 207 " --> pdb=" O MET I 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET I 155 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS I 37 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR I 112 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR I 165 " --> pdb=" O THR I 112 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU I 156 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I 205 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU J 204 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 207 " --> pdb=" O MET J 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET J 155 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS J 37 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL J 99 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR J 112 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR J 165 " --> pdb=" O THR J 112 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU J 156 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 205 " --> pdb=" O VAL J 158 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU K 204 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG K 207 " --> pdb=" O MET K 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET K 155 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS K 37 " --> pdb=" O VAL K 154 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL K 99 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR K 112 " --> pdb=" O THR K 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR K 165 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU K 156 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA K 205 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU L 204 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG L 207 " --> pdb=" O MET L 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET L 155 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS L 37 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL L 99 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR L 112 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR L 165 " --> pdb=" O THR L 112 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU L 156 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 205 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU M 204 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG M 207 " --> pdb=" O MET M 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET M 155 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS M 37 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL M 99 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR M 112 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR M 165 " --> pdb=" O THR M 112 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU M 156 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA M 205 " --> pdb=" O VAL M 158 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU N 204 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG N 207 " --> pdb=" O MET N 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET N 155 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS N 37 " --> pdb=" O VAL N 154 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR N 112 " --> pdb=" O THR N 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR N 165 " --> pdb=" O THR N 112 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU N 156 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA N 205 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU O 204 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG O 207 " --> pdb=" O MET O 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET O 155 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS O 37 " --> pdb=" O VAL O 154 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL O 99 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR O 112 " --> pdb=" O THR O 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR O 165 " --> pdb=" O THR O 112 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU O 156 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA O 205 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU P 204 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG P 207 " --> pdb=" O MET P 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET P 155 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS P 37 " --> pdb=" O VAL P 154 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL P 99 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR P 112 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR P 165 " --> pdb=" O THR P 112 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU P 156 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA P 205 " --> pdb=" O VAL P 158 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Q 204 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Q 207 " --> pdb=" O MET Q 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET Q 155 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Q 37 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Q 99 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Q 112 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Q 165 " --> pdb=" O THR Q 112 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Q' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Q 156 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Q 205 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU R 204 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG R 207 " --> pdb=" O MET R 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET R 155 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS R 37 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL R 99 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR R 112 " --> pdb=" O THR R 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR R 165 " --> pdb=" O THR R 112 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU R 156 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 205 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU S 204 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG S 207 " --> pdb=" O MET S 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET S 155 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS S 37 " --> pdb=" O VAL S 154 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR S 112 " --> pdb=" O THR S 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR S 165 " --> pdb=" O THR S 112 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU S 156 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA S 205 " --> pdb=" O VAL S 158 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU T 204 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG T 207 " --> pdb=" O MET T 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET T 155 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS T 37 " --> pdb=" O VAL T 154 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR T 112 " --> pdb=" O THR T 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR T 165 " --> pdb=" O THR T 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU T 156 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA T 205 " --> pdb=" O VAL T 158 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU U 204 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG U 207 " --> pdb=" O MET U 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET U 155 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS U 37 " --> pdb=" O VAL U 154 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL U 99 " --> pdb=" O VAL U 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR U 112 " --> pdb=" O THR U 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR U 165 " --> pdb=" O THR U 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU U 156 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA U 205 " --> pdb=" O VAL U 158 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU V 204 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG V 207 " --> pdb=" O MET V 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET V 155 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS V 37 " --> pdb=" O VAL V 154 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL V 99 " --> pdb=" O VAL V 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR V 112 " --> pdb=" O THR V 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR V 165 " --> pdb=" O THR V 112 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU V 156 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA V 205 " --> pdb=" O VAL V 158 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU W 204 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG W 207 " --> pdb=" O MET W 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET W 155 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS W 37 " --> pdb=" O VAL W 154 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL W 99 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR W 112 " --> pdb=" O THR W 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR W 165 " --> pdb=" O THR W 112 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU W 156 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA W 205 " --> pdb=" O VAL W 158 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU X 204 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG X 207 " --> pdb=" O MET X 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET X 155 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS X 37 " --> pdb=" O VAL X 154 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL X 99 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR X 112 " --> pdb=" O THR X 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR X 165 " --> pdb=" O THR X 112 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU X 156 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA X 205 " --> pdb=" O VAL X 158 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Y' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Y 204 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Y 207 " --> pdb=" O MET Y 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Y 155 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Y 37 " --> pdb=" O VAL Y 154 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Y' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL Y 99 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR Y 112 " --> pdb=" O THR Y 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Y 165 " --> pdb=" O THR Y 112 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Y' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Y 156 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Y 205 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Z 204 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Z 207 " --> pdb=" O MET Z 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET Z 155 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Z 37 " --> pdb=" O VAL Z 154 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Z 112 " --> pdb=" O THR Z 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR Z 165 " --> pdb=" O THR Z 112 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Z 156 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA Z 205 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '0' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU 0 204 " --> pdb=" O LEU 0 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG 0 207 " --> pdb=" O MET 0 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 0 155 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS 0 37 " --> pdb=" O VAL 0 154 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '0' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL 0 99 " --> pdb=" O VAL 0 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR 0 112 " --> pdb=" O THR 0 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 0 165 " --> pdb=" O THR 0 112 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '0' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU 0 156 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 0 205 " --> pdb=" O VAL 0 158 " (cutoff:3.500A) 2208 hydrogen bonds defined for protein. 6543 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: 37.68 Time building geometry restraints manager: 68.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 50355 1.03 - 1.23: 218 1.23 - 1.42: 20383 1.42 - 1.62: 29781 1.62 - 1.81: 405 Bond restraints: 101142 Sorted by residual: bond pdb=" OB2 CDL K 301 " pdb=" PB2 CDL K 301 " ideal model delta sigma weight residual 1.579 1.651 -0.072 1.50e-02 4.44e+03 2.27e+01 bond pdb=" OB2 CDL R 301 " pdb=" PB2 CDL R 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OA2 CDL U 301 " pdb=" PA1 CDL U 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OB2 CDL D 301 " pdb=" PB2 CDL D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.22e+01 bond pdb=" OA2 CDL S 301 " pdb=" PA1 CDL S 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.22e+01 ... (remaining 101137 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 1549 106.17 - 113.12: 121472 113.12 - 120.08: 28878 120.08 - 127.03: 30891 127.03 - 133.99: 459 Bond angle restraints: 183249 Sorted by residual: angle pdb=" CB2 CDL Z 301 " pdb=" OB2 CDL Z 301 " pdb=" PB2 CDL Z 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.26e+00 angle pdb=" CB2 CDL I 301 " pdb=" OB2 CDL I 301 " pdb=" PB2 CDL I 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.24e+00 angle pdb=" CB2 CDL W 301 " pdb=" OB2 CDL W 301 " pdb=" PB2 CDL W 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.23e+00 angle pdb=" CB2 CDL S 301 " pdb=" OB2 CDL S 301 " pdb=" PB2 CDL S 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" CB2 CDL C 301 " pdb=" OB2 CDL C 301 " pdb=" PB2 CDL C 301 " ideal model delta sigma weight residual 121.27 118.41 2.86 1.00e+00 1.00e+00 8.21e+00 ... (remaining 183244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 43370 14.26 - 28.52: 2827 28.52 - 42.78: 877 42.78 - 57.03: 203 57.03 - 71.29: 54 Dihedral angle restraints: 47331 sinusoidal: 26217 harmonic: 21114 Sorted by residual: dihedral pdb=" CA GLY Y 19 " pdb=" C GLY Y 19 " pdb=" N ASP Y 20 " pdb=" CA ASP Y 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLY C 19 " pdb=" C GLY C 19 " pdb=" N ASP C 20 " pdb=" CA ASP C 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY S 19 " pdb=" C GLY S 19 " pdb=" N ASP S 20 " pdb=" CA ASP S 20 " ideal model delta harmonic sigma weight residual 180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 47328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4397 0.032 - 0.064: 2246 0.064 - 0.096: 937 0.096 - 0.129: 328 0.129 - 0.161: 57 Chirality restraints: 7965 Sorted by residual: chirality pdb=" CA VAL B 39 " pdb=" N VAL B 39 " pdb=" C VAL B 39 " pdb=" CB VAL B 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA VAL M 39 " pdb=" N VAL M 39 " pdb=" C VAL M 39 " pdb=" CB VAL M 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA VAL U 39 " pdb=" N VAL U 39 " pdb=" C VAL U 39 " pdb=" CB VAL U 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 7962 not shown) Planarity restraints: 14553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO H 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 179 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " -0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO C 179 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO L 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 14550 not shown) Histogram of nonbonded interaction distances: 0.43 - 1.26: 270 1.26 - 2.10: 5536 2.10 - 2.93: 280253 2.93 - 3.77: 409455 3.77 - 4.60: 710838 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1406352 Sorted by model distance: nonbonded pdb="HD21 LEU G 27 " pdb=" HE1 PHE H 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU O 27 " pdb=" HE1 PHE P 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU F 27 " pdb=" HE1 PHE G 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU V 27 " pdb=" HE1 PHE W 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU K 27 " pdb=" HE1 PHE L 79 " model vdw 0.429 2.270 ... (remaining 1406347 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 '0' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 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: 1.150 Extract box with map and model: 14.980 Check model and map are aligned: 1.120 Set scattering table: 0.740 Process input model: 261.060 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 50706 Z= 0.384 Angle : 0.842 8.453 68715 Z= 0.442 Chirality : 0.046 0.161 7965 Planarity : 0.006 0.070 8667 Dihedral : 11.709 71.294 18981 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 37.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.58 % Favored : 81.42 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -5.72 (0.09), residues: 6102 helix: -2.46 (0.12), residues: 1269 sheet: -3.41 (0.08), residues: 2592 loop : -4.85 (0.09), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Z 219 HIS 0.008 0.002 HIS U 147 PHE 0.020 0.002 PHE C 30 TYR 0.012 0.002 TYR O 206 ARG 0.009 0.002 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1391 time to evaluate : 6.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 227 ASP cc_start: 0.7497 (p0) cc_final: 0.6974 (p0) REVERT: B 118 LEU cc_start: 0.8301 (mt) cc_final: 0.7974 (mp) REVERT: B 127 ASN cc_start: 0.7463 (m110) cc_final: 0.7184 (t0) REVERT: B 225 CYS cc_start: 0.6601 (p) cc_final: 0.6209 (m) REVERT: B 227 ASP cc_start: 0.7155 (p0) cc_final: 0.6690 (p0) REVERT: C 118 LEU cc_start: 0.7973 (mt) cc_final: 0.7683 (mp) REVERT: D 229 MET cc_start: 0.6880 (mmm) cc_final: 0.5831 (mmm) REVERT: E 37 CYS cc_start: 0.2022 (m) cc_final: 0.1787 (m) REVERT: E 58 TYR cc_start: 0.5839 (m-80) cc_final: 0.5554 (m-80) REVERT: F 34 ARG cc_start: 0.2238 (mmp-170) cc_final: 0.1862 (mmt-90) REVERT: F 144 MET cc_start: 0.7094 (mmm) cc_final: 0.6480 (mmt) REVERT: F 223 TYR cc_start: 0.4430 (t80) cc_final: 0.4127 (t80) REVERT: G 223 TYR cc_start: 0.2699 (t80) cc_final: 0.2394 (t80) REVERT: J 57 ASP cc_start: 0.4085 (m-30) cc_final: 0.3326 (m-30) REVERT: O 117 THR cc_start: -0.0676 (m) cc_final: -0.0915 (m) REVERT: Q 131 GLU cc_start: 0.6624 (pt0) cc_final: 0.6262 (mp0) REVERT: R 129 LYS cc_start: 0.5539 (ptmm) cc_final: 0.5240 (ttpp) REVERT: R 131 GLU cc_start: 0.5973 (pt0) cc_final: 0.5492 (mm-30) REVERT: S 129 LYS cc_start: 0.5850 (ptmm) cc_final: 0.5564 (ttpp) REVERT: S 130 LYS cc_start: 0.6489 (tptt) cc_final: 0.6230 (tptt) REVERT: T 130 LYS cc_start: 0.6787 (tptt) cc_final: 0.6574 (tttm) REVERT: T 229 MET cc_start: 0.3529 (mmm) cc_final: 0.3273 (mmt) REVERT: U 153 VAL cc_start: 0.2422 (t) cc_final: 0.2208 (t) REVERT: W 88 GLN cc_start: 0.6669 (tm130) cc_final: 0.6204 (tm-30) REVERT: W 110 SER cc_start: 0.7625 (t) cc_final: 0.7395 (m) REVERT: X 79 PHE cc_start: 0.1897 (m-80) cc_final: 0.0826 (m-80) REVERT: X 167 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6697 (mp0) REVERT: X 217 ASN cc_start: 0.5116 (p0) cc_final: 0.3993 (t0) REVERT: Y 90 GLN cc_start: 0.7082 (tt0) cc_final: 0.6680 (tm-30) REVERT: Y 167 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6914 (tp30) REVERT: Z 202 CYS cc_start: 0.7915 (t) cc_final: 0.7626 (t) REVERT: 0 227 ASP cc_start: 0.7432 (p0) cc_final: 0.6752 (p0) outliers start: 0 outliers final: 0 residues processed: 1391 average time/residue: 1.3839 time to fit residues: 3032.7022 Evaluate side-chains 859 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 859 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 524 optimal weight: 2.9990 chunk 470 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 chunk 317 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 486 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 563 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 88 GLN F 109 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 HIS K 116 GLN K 187 GLN L 187 GLN M 187 GLN N 187 GLN O 187 GLN P 187 GLN ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 GLN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 GLN S 187 GLN U 150 ASN V 83 ASN W 138 HIS ** X 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN Y 230 GLN ** 0 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4213 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 50706 Z= 0.327 Angle : 0.862 12.145 68715 Z= 0.448 Chirality : 0.050 0.319 7965 Planarity : 0.007 0.080 8667 Dihedral : 7.995 59.868 6831 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 2.27 % Allowed : 11.84 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -4.32 (0.10), residues: 6102 helix: -0.91 (0.15), residues: 1269 sheet: -2.72 (0.09), residues: 2538 loop : -4.04 (0.10), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 219 HIS 0.008 0.002 HIS S 32 PHE 0.030 0.002 PHE A 4 TYR 0.023 0.002 TYR R 152 ARG 0.016 0.002 ARG Y 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1035 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 112 THR cc_start: 0.8195 (t) cc_final: 0.7953 (m) REVERT: B 225 CYS cc_start: 0.7458 (p) cc_final: 0.6883 (m) REVERT: B 229 MET cc_start: 0.7728 (mmm) cc_final: 0.7296 (mmm) REVERT: C 78 ASN cc_start: 0.7300 (p0) cc_final: 0.6867 (p0) REVERT: C 225 CYS cc_start: 0.6921 (p) cc_final: 0.6541 (p) REVERT: C 229 MET cc_start: 0.7477 (mmm) cc_final: 0.6742 (mmm) REVERT: E 229 MET cc_start: 0.5447 (mmm) cc_final: 0.4488 (tpp) REVERT: F 83 ASN cc_start: 0.7889 (t0) cc_final: 0.6468 (m-40) REVERT: F 144 MET cc_start: 0.7097 (mmm) cc_final: 0.6744 (mmt) REVERT: G 83 ASN cc_start: 0.6984 (t0) cc_final: 0.6220 (m-40) REVERT: G 126 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6873 (mm-30) REVERT: G 144 MET cc_start: 0.6667 (mmm) cc_final: 0.6455 (mmm) REVERT: G 190 LEU cc_start: 0.7799 (pp) cc_final: 0.7265 (tt) REVERT: G 194 LYS cc_start: 0.7342 (mttp) cc_final: 0.6871 (mmmt) REVERT: I 83 ASN cc_start: 0.7026 (t0) cc_final: 0.6491 (m-40) REVERT: I 178 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6203 (pp) REVERT: I 223 TYR cc_start: 0.1926 (t80) cc_final: 0.1415 (t80) REVERT: L 226 ASN cc_start: 0.3247 (m110) cc_final: 0.3000 (m110) REVERT: O 144 MET cc_start: 0.1706 (mmm) cc_final: 0.1177 (mmm) REVERT: Q 203 VAL cc_start: -0.1877 (p) cc_final: -0.2195 (p) REVERT: R 131 GLU cc_start: 0.6030 (pt0) cc_final: 0.5710 (mm-30) REVERT: S 232 PHE cc_start: 0.0644 (m-80) cc_final: 0.0392 (m-80) REVERT: T 1 MET cc_start: -0.1243 (tpp) cc_final: -0.1608 (tpt) REVERT: T 78 ASN cc_start: 0.1945 (m-40) cc_final: 0.1707 (p0) REVERT: T 84 MET cc_start: 0.4251 (tmm) cc_final: 0.3782 (tmm) REVERT: U 1 MET cc_start: -0.0828 (tpp) cc_final: -0.1293 (tpp) REVERT: V 84 MET cc_start: 0.6954 (tmm) cc_final: 0.6719 (tmm) REVERT: W 88 GLN cc_start: 0.7028 (tm130) cc_final: 0.6479 (tm-30) REVERT: W 167 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6299 (mp0) REVERT: X 88 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7503 (tm-30) REVERT: X 148 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: X 167 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6829 (mm-30) REVERT: Y 14 GLU cc_start: 0.6121 (mt-10) cc_final: 0.5903 (mt-10) REVERT: Y 88 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7529 (tm-30) REVERT: Y 95 VAL cc_start: 0.4046 (m) cc_final: 0.3716 (m) REVERT: Y 144 MET cc_start: 0.8163 (mmt) cc_final: 0.7825 (mmp) REVERT: Y 159 GLU cc_start: 0.8503 (mp0) cc_final: 0.8276 (mp0) REVERT: Y 167 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7043 (tp30) REVERT: Y 231 THR cc_start: 0.6748 (p) cc_final: 0.6452 (p) REVERT: Z 95 VAL cc_start: 0.2581 (m) cc_final: 0.2373 (m) REVERT: Z 187 GLN cc_start: 0.8187 (tt0) cc_final: 0.7886 (mp10) REVERT: Z 202 CYS cc_start: 0.8407 (t) cc_final: 0.8050 (t) REVERT: 0 154 VAL cc_start: 0.8359 (m) cc_final: 0.7962 (p) outliers start: 127 outliers final: 82 residues processed: 1117 average time/residue: 1.2783 time to fit residues: 2292.0013 Evaluate side-chains 871 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 787 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 PHE Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain K residue 32 HIS Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 189 SER Chi-restraints excluded: chain V residue 226 ASN Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 169 THR Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 148 GLU Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain Y residue 48 PHE Chi-restraints excluded: chain Y residue 79 PHE Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 198 ILE Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 198 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 125 LEU Chi-restraints excluded: chain 0 residue 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 313 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 469 optimal weight: 0.9980 chunk 384 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 564 optimal weight: 3.9990 chunk 610 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 560 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 453 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN D 230 GLN J 116 GLN L 83 ASN ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 GLN O 83 ASN O 109 GLN ** O 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN Q 109 GLN R 109 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN Z 173 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5069 moved from start: 0.8817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 50706 Z= 0.298 Angle : 0.735 8.690 68715 Z= 0.383 Chirality : 0.046 0.239 7965 Planarity : 0.007 0.084 8667 Dihedral : 6.984 59.640 6831 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 3.63 % Allowed : 14.62 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.76 (0.10), residues: 6102 helix: -0.41 (0.15), residues: 1296 sheet: -2.62 (0.09), residues: 2619 loop : -3.41 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 219 HIS 0.006 0.001 HIS R 138 PHE 0.034 0.002 PHE J 48 TYR 0.024 0.002 TYR J 206 ARG 0.013 0.001 ARG Q 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 933 time to evaluate : 6.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: B 84 MET cc_start: 0.9023 (ppp) cc_final: 0.8749 (tmm) REVERT: B 120 VAL cc_start: 0.7528 (p) cc_final: 0.6996 (m) REVERT: B 178 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5593 (pt) REVERT: B 227 ASP cc_start: 0.7926 (p0) cc_final: 0.7148 (p0) REVERT: D 178 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6108 (pt) REVERT: E 229 MET cc_start: 0.5465 (mmm) cc_final: 0.4809 (tpp) REVERT: G 14 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7787 (tm-30) REVERT: G 48 PHE cc_start: 0.7620 (t80) cc_final: 0.7347 (t80) REVERT: G 126 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6935 (mt-10) REVERT: H 57 ASP cc_start: 0.7343 (m-30) cc_final: 0.6698 (m-30) REVERT: H 83 ASN cc_start: 0.7157 (t0) cc_final: 0.6079 (m110) REVERT: I 83 ASN cc_start: 0.6359 (t0) cc_final: 0.5779 (m-40) REVERT: J 223 TYR cc_start: 0.2267 (t80) cc_final: 0.1730 (t80) REVERT: J 229 MET cc_start: -0.4430 (mmt) cc_final: -0.4689 (mmm) REVERT: J 230 GLN cc_start: 0.0959 (mm110) cc_final: 0.0642 (mm-40) REVERT: K 55 ARG cc_start: 0.2651 (OUTLIER) cc_final: 0.1868 (ptm-80) REVERT: M 84 MET cc_start: 0.7771 (tmm) cc_final: 0.7554 (tmm) REVERT: M 114 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: M 168 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6595 (tm-30) REVERT: O 144 MET cc_start: 0.1742 (mmm) cc_final: 0.1305 (mmm) REVERT: P 65 GLU cc_start: 0.3036 (pp20) cc_final: 0.2791 (pm20) REVERT: P 144 MET cc_start: 0.1094 (mmm) cc_final: 0.0320 (mmm) REVERT: P 226 ASN cc_start: 0.4536 (m110) cc_final: 0.4228 (m-40) REVERT: Q 62 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.4945 (t0) REVERT: Q 144 MET cc_start: 0.1429 (tpp) cc_final: 0.0975 (tpp) REVERT: R 130 LYS cc_start: 0.6465 (tptp) cc_final: 0.6190 (tptt) REVERT: R 131 GLU cc_start: 0.4813 (pt0) cc_final: 0.4540 (mm-30) REVERT: S 102 LYS cc_start: 0.5888 (tttt) cc_final: 0.5224 (mptt) REVERT: S 227 ASP cc_start: 0.6897 (t0) cc_final: 0.6127 (t0) REVERT: T 87 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7610 (p) REVERT: T 190 LEU cc_start: 0.6934 (pp) cc_final: 0.6693 (pp) REVERT: T 227 ASP cc_start: 0.7775 (t0) cc_final: 0.7245 (t0) REVERT: U 89 VAL cc_start: 0.6151 (p) cc_final: 0.5908 (t) REVERT: U 227 ASP cc_start: 0.7624 (t0) cc_final: 0.7229 (t0) REVERT: V 59 THR cc_start: 0.7537 (p) cc_final: 0.7301 (p) REVERT: V 117 THR cc_start: 0.6691 (m) cc_final: 0.6410 (m) REVERT: V 167 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6775 (tp30) REVERT: V 227 ASP cc_start: 0.8228 (t0) cc_final: 0.7899 (t0) REVERT: W 58 TYR cc_start: 0.7729 (m-80) cc_final: 0.7515 (m-80) REVERT: W 88 GLN cc_start: 0.7147 (tm130) cc_final: 0.6436 (tm-30) REVERT: W 167 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7201 (tp30) REVERT: X 62 ASP cc_start: 0.8065 (t0) cc_final: 0.7785 (m-30) REVERT: X 92 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5816 (mp) REVERT: X 159 GLU cc_start: 0.8564 (mp0) cc_final: 0.8332 (mp0) REVERT: X 167 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7585 (tp30) REVERT: Y 115 VAL cc_start: 0.7374 (t) cc_final: 0.7105 (t) REVERT: Y 167 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7823 (tp30) REVERT: Y 202 CYS cc_start: 0.7880 (t) cc_final: 0.7657 (t) REVERT: Z 62 ASP cc_start: 0.7945 (m-30) cc_final: 0.7735 (m-30) REVERT: Z 187 GLN cc_start: 0.8140 (tt0) cc_final: 0.6840 (mp10) REVERT: Z 202 CYS cc_start: 0.8380 (t) cc_final: 0.8167 (t) REVERT: Z 227 ASP cc_start: 0.8326 (p0) cc_final: 0.7676 (p0) REVERT: 0 86 ASP cc_start: 0.8549 (t0) cc_final: 0.8301 (m-30) REVERT: 0 163 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8060 (tm-30) REVERT: 0 187 GLN cc_start: 0.8127 (tt0) cc_final: 0.6890 (mp10) outliers start: 203 outliers final: 114 residues processed: 1086 average time/residue: 1.2459 time to fit residues: 2183.0959 Evaluate side-chains 861 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 739 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LYS Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain K residue 32 HIS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 191 ASN Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain Q residue 25 ASP Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 78 ASN Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 34 ARG Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 162 GLN Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 226 ASN Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain Y residue 48 PHE Chi-restraints excluded: chain Y residue 79 PHE Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 198 ILE Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 198 ILE Chi-restraints excluded: chain Z residue 225 CYS Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 127 ASN Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 225 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 558 optimal weight: 2.9990 chunk 424 optimal weight: 0.0370 chunk 293 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 379 optimal weight: 0.7980 chunk 566 optimal weight: 6.9990 chunk 600 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 537 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 230 GLN D 32 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN M 187 GLN N 109 GLN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 16 ASN U 150 ASN V 230 GLN X 150 ASN Y 78 ASN Y 217 ASN Y 226 ASN 0 78 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 1.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 50706 Z= 0.325 Angle : 0.803 12.022 68715 Z= 0.415 Chirality : 0.048 0.242 7965 Planarity : 0.007 0.073 8667 Dihedral : 6.995 59.755 6831 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 4.67 % Allowed : 17.64 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.65 (0.10), residues: 6102 helix: -0.33 (0.15), residues: 1296 sheet: -2.56 (0.10), residues: 2511 loop : -3.32 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 219 HIS 0.014 0.001 HIS H 32 PHE 0.035 0.002 PHE N 81 TYR 0.036 0.002 TYR E 152 ARG 0.019 0.001 ARG U 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 841 time to evaluate : 6.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: B 169 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 178 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5436 (pt) REVERT: C 33 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6385 (t80) REVERT: C 178 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5918 (pt) REVERT: D 178 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6256 (pt) REVERT: E 65 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: E 78 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7881 (p0) REVERT: E 125 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6961 (tt) REVERT: E 137 ASP cc_start: 0.6817 (t70) cc_final: 0.6494 (t0) REVERT: E 178 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5820 (pt) REVERT: F 65 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6011 (pp20) REVERT: G 126 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7089 (mt-10) REVERT: G 147 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5215 (t-170) REVERT: H 109 GLN cc_start: 0.7846 (tt0) cc_final: 0.7097 (tm-30) REVERT: I 14 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7699 (tt0) REVERT: I 147 HIS cc_start: 0.3322 (OUTLIER) cc_final: 0.3081 (t-170) REVERT: J 14 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7683 (mt-10) REVERT: K 55 ARG cc_start: 0.3978 (OUTLIER) cc_final: 0.2242 (ptm-80) REVERT: K 100 LYS cc_start: 0.3728 (OUTLIER) cc_final: 0.3327 (ptmm) REVERT: K 190 LEU cc_start: 0.8666 (pp) cc_final: 0.7955 (tt) REVERT: L 159 GLU cc_start: 0.6495 (mt-10) cc_final: 0.5878 (mp0) REVERT: M 55 ARG cc_start: 0.1341 (OUTLIER) cc_final: 0.1065 (ttp-110) REVERT: M 114 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: O 144 MET cc_start: 0.1861 (mmm) cc_final: 0.1325 (mmm) REVERT: O 168 GLN cc_start: 0.7648 (tm-30) cc_final: 0.6574 (pt0) REVERT: P 55 ARG cc_start: -0.1335 (OUTLIER) cc_final: -0.2720 (ttp-110) REVERT: Q 131 GLU cc_start: 0.5828 (pt0) cc_final: 0.5475 (mm-30) REVERT: Q 144 MET cc_start: 0.2312 (tpp) cc_final: 0.1764 (tpp) REVERT: R 102 LYS cc_start: 0.5626 (tttt) cc_final: 0.5295 (mmtt) REVERT: R 131 GLU cc_start: 0.4968 (pt0) cc_final: 0.4565 (mm-30) REVERT: T 78 ASN cc_start: 0.5266 (m-40) cc_final: 0.4952 (m-40) REVERT: T 89 VAL cc_start: 0.6892 (OUTLIER) cc_final: 0.6649 (p) REVERT: T 178 LEU cc_start: 0.2045 (OUTLIER) cc_final: 0.1357 (pt) REVERT: T 187 GLN cc_start: 0.7779 (pm20) cc_final: 0.7462 (mp10) REVERT: T 227 ASP cc_start: 0.7660 (t0) cc_final: 0.7225 (t0) REVERT: U 89 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7044 (p) REVERT: U 227 ASP cc_start: 0.8195 (t0) cc_final: 0.7849 (t0) REVERT: V 59 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8510 (p) REVERT: V 78 ASN cc_start: 0.8392 (m-40) cc_final: 0.8191 (m110) REVERT: V 82 LYS cc_start: 0.8328 (tttt) cc_final: 0.8103 (tptp) REVERT: V 89 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.6927 (p) REVERT: V 117 THR cc_start: 0.7450 (m) cc_final: 0.7105 (m) REVERT: V 167 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7919 (tp30) REVERT: V 227 ASP cc_start: 0.8309 (t0) cc_final: 0.7943 (t0) REVERT: W 178 LEU cc_start: 0.1999 (OUTLIER) cc_final: 0.1156 (pt) REVERT: W 183 LEU cc_start: 0.7768 (mp) cc_final: 0.7245 (tt) REVERT: W 227 ASP cc_start: 0.8440 (p0) cc_final: 0.8013 (p0) REVERT: X 84 MET cc_start: 0.8731 (tmm) cc_final: 0.8455 (tmm) REVERT: X 167 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8187 (tp30) REVERT: X 187 GLN cc_start: 0.8134 (tt0) cc_final: 0.7170 (mp10) REVERT: X 192 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7614 (t0) REVERT: X 227 ASP cc_start: 0.8390 (p0) cc_final: 0.7938 (p0) REVERT: Y 84 MET cc_start: 0.8899 (tmm) cc_final: 0.8553 (tmm) REVERT: Y 186 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5186 (pp) REVERT: Z 112 THR cc_start: 0.8015 (t) cc_final: 0.7754 (p) REVERT: Z 147 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7108 (t-170) REVERT: Z 178 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4332 (pt) REVERT: Z 186 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5284 (pp) REVERT: Z 221 ILE cc_start: 0.8718 (pt) cc_final: 0.8368 (pt) REVERT: 0 154 VAL cc_start: 0.8793 (m) cc_final: 0.8413 (p) REVERT: 0 163 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8407 (tm-30) outliers start: 261 outliers final: 152 residues processed: 1048 average time/residue: 1.2546 time to fit residues: 2163.0195 Evaluate side-chains 849 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 668 time to evaluate : 6.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 32 HIS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 100 LYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 193 ASN Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 191 ASN Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain P residue 55 ARG Chi-restraints excluded: chain P residue 147 HIS Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 191 ASN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 34 ARG Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 226 ASN Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain W residue 82 LYS Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain Y residue 48 PHE Chi-restraints excluded: chain Y residue 79 PHE Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 147 HIS Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 33 PHE Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 79 PHE Chi-restraints excluded: chain 0 residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 499 optimal weight: 0.7980 chunk 340 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 446 optimal weight: 0.5980 chunk 247 optimal weight: 5.9990 chunk 512 optimal weight: 3.9990 chunk 414 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 538 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 HIS G 78 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 HIS O 109 GLN P 109 GLN P 147 HIS Q 109 GLN W 168 GLN Y 217 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 1.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 50706 Z= 0.218 Angle : 0.629 12.458 68715 Z= 0.325 Chirality : 0.043 0.168 7965 Planarity : 0.005 0.071 8667 Dihedral : 6.500 59.152 6831 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.86 % Allowed : 20.29 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.36 (0.10), residues: 6102 helix: 0.11 (0.15), residues: 1296 sheet: -2.45 (0.10), residues: 2538 loop : -3.20 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 219 HIS 0.008 0.001 HIS N 138 PHE 0.031 0.001 PHE O 81 TYR 0.016 0.001 TYR L 206 ARG 0.008 0.001 ARG 0 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 721 time to evaluate : 6.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: B 84 MET cc_start: 0.9102 (ppp) cc_final: 0.8696 (tmm) REVERT: B 186 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6573 (pp) REVERT: C 88 GLN cc_start: 0.7942 (pp30) cc_final: 0.7625 (pp30) REVERT: C 137 ASP cc_start: 0.8290 (p0) cc_final: 0.7811 (t70) REVERT: C 178 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5934 (pt) REVERT: E 78 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7454 (p0) REVERT: E 229 MET cc_start: 0.5503 (mmm) cc_final: 0.4719 (tpp) REVERT: F 137 ASP cc_start: 0.6326 (t70) cc_final: 0.6090 (t0) REVERT: F 214 PHE cc_start: 0.6000 (m-10) cc_final: 0.5693 (m-10) REVERT: G 57 ASP cc_start: 0.8712 (m-30) cc_final: 0.8476 (m-30) REVERT: G 81 PHE cc_start: 0.7746 (m-80) cc_final: 0.7511 (m-80) REVERT: G 147 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.5206 (t-170) REVERT: H 14 GLU cc_start: 0.8609 (tt0) cc_final: 0.8375 (tm-30) REVERT: H 109 GLN cc_start: 0.8111 (tt0) cc_final: 0.7764 (mt0) REVERT: H 147 HIS cc_start: 0.4857 (OUTLIER) cc_final: 0.4586 (t-170) REVERT: I 14 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8000 (tt0) REVERT: J 14 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8184 (tt0) REVERT: K 140 PHE cc_start: 0.4641 (OUTLIER) cc_final: 0.4016 (m-80) REVERT: L 34 ARG cc_start: 0.6324 (mmp-170) cc_final: 0.5712 (ptm160) REVERT: L 55 ARG cc_start: 0.1776 (OUTLIER) cc_final: 0.0136 (ptm160) REVERT: O 144 MET cc_start: 0.1842 (mmm) cc_final: 0.1422 (mmm) REVERT: O 155 MET cc_start: 0.2717 (mmt) cc_final: 0.2467 (tpt) REVERT: P 144 MET cc_start: 0.2513 (tpp) cc_final: 0.2079 (tpt) REVERT: Q 144 MET cc_start: 0.2472 (tpp) cc_final: 0.1846 (tpp) REVERT: R 55 ARG cc_start: 0.1296 (OUTLIER) cc_final: 0.0758 (tmm-80) REVERT: R 130 LYS cc_start: 0.7245 (tptp) cc_final: 0.7016 (tptt) REVERT: R 131 GLU cc_start: 0.5147 (pt0) cc_final: 0.4674 (mm-30) REVERT: R 187 GLN cc_start: 0.7997 (pm20) cc_final: 0.7684 (mp10) REVERT: S 55 ARG cc_start: 0.3076 (OUTLIER) cc_final: 0.2716 (tmm-80) REVERT: S 178 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1467 (pt) REVERT: S 227 ASP cc_start: 0.7512 (t0) cc_final: 0.6813 (t0) REVERT: T 178 LEU cc_start: 0.2107 (OUTLIER) cc_final: 0.1341 (pt) REVERT: T 187 GLN cc_start: 0.8001 (pm20) cc_final: 0.7564 (mp10) REVERT: T 190 LEU cc_start: 0.7933 (pp) cc_final: 0.7611 (pp) REVERT: T 227 ASP cc_start: 0.7954 (t0) cc_final: 0.7528 (t0) REVERT: U 89 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7091 (p) REVERT: U 227 ASP cc_start: 0.8303 (t0) cc_final: 0.7971 (t0) REVERT: V 82 LYS cc_start: 0.8505 (tttt) cc_final: 0.8251 (tptp) REVERT: V 89 VAL cc_start: 0.7409 (OUTLIER) cc_final: 0.7086 (p) REVERT: V 167 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8056 (tp30) REVERT: V 176 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.5384 (m-80) REVERT: V 227 ASP cc_start: 0.8394 (t0) cc_final: 0.8081 (t0) REVERT: W 178 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.2008 (pt) REVERT: W 183 LEU cc_start: 0.7593 (mp) cc_final: 0.7157 (tt) REVERT: W 227 ASP cc_start: 0.8385 (p0) cc_final: 0.7948 (p0) REVERT: X 84 MET cc_start: 0.8642 (tmm) cc_final: 0.8375 (tmm) REVERT: X 167 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8404 (tp30) REVERT: X 227 ASP cc_start: 0.8217 (p0) cc_final: 0.7796 (p0) REVERT: Y 84 MET cc_start: 0.8808 (tmm) cc_final: 0.8452 (tmm) REVERT: Y 147 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.7056 (t-170) REVERT: Y 163 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8096 (tp30) REVERT: Y 186 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5506 (pp) REVERT: Z 109 GLN cc_start: 0.8270 (tm130) cc_final: 0.7962 (tm-30) REVERT: Z 147 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7332 (t-170) REVERT: Z 181 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4786 (mp) REVERT: Z 221 ILE cc_start: 0.8784 (pt) cc_final: 0.8420 (pt) REVERT: 0 147 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7128 (t-170) REVERT: 0 154 VAL cc_start: 0.8524 (m) cc_final: 0.8122 (p) REVERT: 0 163 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8521 (tm-30) outliers start: 216 outliers final: 138 residues processed: 898 average time/residue: 1.2828 time to fit residues: 1871.5224 Evaluate side-chains 772 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 613 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 146 TYR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 192 ASN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 32 HIS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 100 LYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 140 PHE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 191 ASN Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain P residue 55 ARG Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 87 VAL Chi-restraints excluded: chain P residue 147 HIS Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 116 GLN Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 189 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 25 ASP Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain S residue 176 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain T residue 29 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 147 HIS Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 79 PHE Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 201 optimal weight: 0.3980 chunk 540 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 600 optimal weight: 0.9990 chunk 498 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS D 32 HIS ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN ** N 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN V 90 GLN Y 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 1.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 50706 Z= 0.210 Angle : 0.628 12.362 68715 Z= 0.325 Chirality : 0.044 0.210 7965 Planarity : 0.005 0.070 8667 Dihedral : 6.302 59.193 6831 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.21 % Favored : 88.77 % Rotamer: Outliers : 4.26 % Allowed : 21.02 % Favored : 74.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.21 (0.11), residues: 6102 helix: 0.28 (0.15), residues: 1294 sheet: -2.41 (0.10), residues: 2518 loop : -3.05 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 219 HIS 0.050 0.001 HIS P 147 PHE 0.017 0.001 PHE F 30 TYR 0.032 0.001 TYR P 146 ARG 0.005 0.000 ARG 0 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 674 time to evaluate : 6.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 84 MET cc_start: 0.9113 (ppp) cc_final: 0.8707 (tmm) REVERT: B 186 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6644 (pp) REVERT: C 33 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6618 (t80) REVERT: C 88 GLN cc_start: 0.8051 (pp30) cc_final: 0.7819 (pp30) REVERT: C 137 ASP cc_start: 0.8512 (p0) cc_final: 0.8026 (t70) REVERT: C 178 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5779 (pt) REVERT: D 58 TYR cc_start: 0.8565 (m-80) cc_final: 0.8058 (m-80) REVERT: D 229 MET cc_start: 0.7416 (mmm) cc_final: 0.6957 (mmm) REVERT: E 178 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6046 (pt) REVERT: E 229 MET cc_start: 0.5452 (mmm) cc_final: 0.4892 (tpp) REVERT: F 40 LEU cc_start: 0.8944 (mt) cc_final: 0.8729 (mp) REVERT: F 178 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6023 (pt) REVERT: F 214 PHE cc_start: 0.6188 (m-10) cc_final: 0.5820 (m-10) REVERT: F 229 MET cc_start: 0.6533 (mmm) cc_final: 0.5682 (mmm) REVERT: G 147 HIS cc_start: 0.6284 (OUTLIER) cc_final: 0.5219 (t-170) REVERT: G 176 PHE cc_start: 0.6319 (m-80) cc_final: 0.6101 (m-10) REVERT: G 178 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6504 (pt) REVERT: H 109 GLN cc_start: 0.8237 (tt0) cc_final: 0.7360 (tm-30) REVERT: H 147 HIS cc_start: 0.5875 (OUTLIER) cc_final: 0.5442 (t-170) REVERT: I 14 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8665 (tt0) REVERT: J 14 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8624 (tt0) REVERT: K 53 TYR cc_start: 0.1817 (m-80) cc_final: 0.1582 (m-80) REVERT: L 34 ARG cc_start: 0.6440 (mmp-170) cc_final: 0.5715 (ptm160) REVERT: M 55 ARG cc_start: 0.1920 (OUTLIER) cc_final: -0.0387 (ttp-110) REVERT: M 159 GLU cc_start: 0.4785 (mt-10) cc_final: 0.3929 (mp0) REVERT: N 55 ARG cc_start: 0.0376 (OUTLIER) cc_final: -0.1519 (ttp-110) REVERT: O 144 MET cc_start: 0.2416 (mmm) cc_final: 0.1980 (mmm) REVERT: O 208 VAL cc_start: -0.1442 (OUTLIER) cc_final: -0.1706 (m) REVERT: P 55 ARG cc_start: 0.0778 (OUTLIER) cc_final: -0.0420 (ttp-110) REVERT: Q 1 MET cc_start: -0.0907 (mmt) cc_final: -0.1139 (mmt) REVERT: Q 84 MET cc_start: 0.8500 (tpp) cc_final: 0.8296 (tmm) REVERT: Q 144 MET cc_start: 0.2674 (tpp) cc_final: 0.2199 (tpp) REVERT: R 55 ARG cc_start: 0.3147 (OUTLIER) cc_final: 0.2531 (tmm-80) REVERT: R 102 LYS cc_start: 0.6411 (tttt) cc_final: 0.5882 (mmtt) REVERT: R 187 GLN cc_start: 0.7864 (pm20) cc_final: 0.7310 (mp10) REVERT: S 89 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7087 (p) REVERT: S 227 ASP cc_start: 0.7685 (t0) cc_final: 0.6958 (t0) REVERT: T 21 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (tp) REVERT: T 89 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6729 (p) REVERT: T 178 LEU cc_start: 0.2087 (OUTLIER) cc_final: 0.1340 (pt) REVERT: T 227 ASP cc_start: 0.8315 (t0) cc_final: 0.7879 (t0) REVERT: U 79 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: U 84 MET cc_start: 0.8622 (tmm) cc_final: 0.8359 (tmm) REVERT: U 86 ASP cc_start: 0.8968 (t0) cc_final: 0.8523 (m-30) REVERT: U 89 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7255 (p) REVERT: U 227 ASP cc_start: 0.8560 (t0) cc_final: 0.8176 (t0) REVERT: V 82 LYS cc_start: 0.8653 (tttt) cc_final: 0.8320 (tptp) REVERT: V 89 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.6984 (p) REVERT: V 163 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8024 (tm-30) REVERT: V 176 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: V 227 ASP cc_start: 0.8415 (t0) cc_final: 0.8105 (t0) REVERT: W 112 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8026 (p) REVERT: W 178 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2225 (pt) REVERT: W 183 LEU cc_start: 0.7650 (mp) cc_final: 0.7321 (tt) REVERT: W 227 ASP cc_start: 0.8295 (p0) cc_final: 0.7873 (p0) REVERT: X 84 MET cc_start: 0.8798 (tmm) cc_final: 0.8524 (tmm) REVERT: X 167 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8553 (tp30) REVERT: X 227 ASP cc_start: 0.8193 (p0) cc_final: 0.7711 (p0) REVERT: Y 84 MET cc_start: 0.8908 (tmm) cc_final: 0.8533 (tmm) REVERT: Y 147 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6847 (t-170) REVERT: Y 163 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8381 (tp30) REVERT: Y 186 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5373 (pp) REVERT: Y 187 GLN cc_start: 0.8122 (tt0) cc_final: 0.7183 (mp10) REVERT: Z 109 GLN cc_start: 0.8404 (tm130) cc_final: 0.8046 (tm-30) REVERT: Z 112 THR cc_start: 0.8050 (t) cc_final: 0.7714 (p) REVERT: Z 181 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5012 (mp) REVERT: Z 186 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5674 (pp) REVERT: 0 147 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7623 (t-170) REVERT: 0 154 VAL cc_start: 0.8746 (m) cc_final: 0.8317 (p) REVERT: 0 163 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 238 outliers final: 159 residues processed: 875 average time/residue: 1.2609 time to fit residues: 1789.0592 Evaluate side-chains 787 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 599 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 25 ASP Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 32 HIS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 100 LYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 193 ASN Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 187 GLN Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 109 GLN Chi-restraints excluded: chain O residue 186 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain P residue 55 ARG Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 116 GLN Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 178 LEU Chi-restraints excluded: chain Q residue 219 TRP Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 20 ASP Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 90 GLN Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 175 ILE Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 55 ARG Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 79 PHE Chi-restraints excluded: chain 0 residue 107 LEU Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 156 GLU Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 579 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 438 optimal weight: 0.5980 chunk 339 optimal weight: 0.0980 chunk 505 optimal weight: 6.9990 chunk 335 optimal weight: 3.9990 chunk 598 optimal weight: 0.6980 chunk 374 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 192 ASN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN O 109 GLN R 109 GLN S 230 GLN V 78 ASN Y 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 1.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 50706 Z= 0.172 Angle : 0.577 11.259 68715 Z= 0.295 Chirality : 0.042 0.176 7965 Planarity : 0.005 0.078 8667 Dihedral : 6.087 58.796 6831 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.58 % Allowed : 22.06 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.11), residues: 6102 helix: 0.46 (0.16), residues: 1292 sheet: -2.22 (0.10), residues: 2497 loop : -2.70 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 219 HIS 0.015 0.001 HIS P 147 PHE 0.020 0.001 PHE D 79 TYR 0.010 0.001 TYR O 206 ARG 0.010 0.000 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 657 time to evaluate : 7.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: A 186 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6204 (pp) REVERT: B 84 MET cc_start: 0.9014 (ppp) cc_final: 0.8595 (tmm) REVERT: B 186 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6561 (pp) REVERT: C 88 GLN cc_start: 0.7936 (pp30) cc_final: 0.7727 (pp30) REVERT: C 137 ASP cc_start: 0.8522 (p0) cc_final: 0.8053 (t70) REVERT: D 58 TYR cc_start: 0.8603 (m-80) cc_final: 0.8227 (m-80) REVERT: E 178 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6110 (pt) REVERT: E 229 MET cc_start: 0.5777 (mmm) cc_final: 0.4701 (tpp) REVERT: F 40 LEU cc_start: 0.9040 (mt) cc_final: 0.8790 (mp) REVERT: F 167 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8814 (tm-30) REVERT: F 229 MET cc_start: 0.6547 (mmm) cc_final: 0.5848 (mmm) REVERT: G 147 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5133 (t-170) REVERT: G 176 PHE cc_start: 0.6419 (m-80) cc_final: 0.6193 (m-10) REVERT: G 178 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6533 (pt) REVERT: H 109 GLN cc_start: 0.8231 (tt0) cc_final: 0.7342 (tm-30) REVERT: H 147 HIS cc_start: 0.5800 (OUTLIER) cc_final: 0.5273 (t-170) REVERT: N 55 ARG cc_start: 0.0390 (OUTLIER) cc_final: -0.1496 (ttp-110) REVERT: O 144 MET cc_start: 0.2414 (mmm) cc_final: 0.2064 (mmm) REVERT: P 55 ARG cc_start: 0.1921 (OUTLIER) cc_final: 0.1334 (tmm-80) REVERT: P 144 MET cc_start: 0.2972 (tpp) cc_final: 0.2666 (tpt) REVERT: Q 144 MET cc_start: 0.2992 (tpp) cc_final: 0.2519 (tpp) REVERT: S 178 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.1801 (pt) REVERT: T 178 LEU cc_start: 0.2152 (OUTLIER) cc_final: 0.1500 (pt) REVERT: T 183 LEU cc_start: 0.7826 (mp) cc_final: 0.7344 (tt) REVERT: T 187 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: T 227 ASP cc_start: 0.8347 (t0) cc_final: 0.7922 (t0) REVERT: U 86 ASP cc_start: 0.8922 (t0) cc_final: 0.8451 (m-30) REVERT: U 227 ASP cc_start: 0.8443 (t0) cc_final: 0.8055 (t0) REVERT: V 14 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8038 (mt-10) REVERT: V 82 LYS cc_start: 0.8731 (tttt) cc_final: 0.8402 (tptp) REVERT: V 89 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7252 (p) REVERT: V 163 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8252 (tm-30) REVERT: V 176 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5708 (m-10) REVERT: V 227 ASP cc_start: 0.8304 (t0) cc_final: 0.8026 (t0) REVERT: W 14 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8071 (mt-10) REVERT: W 62 ASP cc_start: 0.8666 (t0) cc_final: 0.8451 (m-30) REVERT: W 112 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8096 (p) REVERT: W 227 ASP cc_start: 0.8270 (p0) cc_final: 0.7873 (p0) REVERT: X 84 MET cc_start: 0.8688 (tmm) cc_final: 0.8370 (tmm) REVERT: X 167 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8614 (tp30) REVERT: X 227 ASP cc_start: 0.8123 (p0) cc_final: 0.7638 (p0) REVERT: Y 14 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8288 (mt-10) REVERT: Y 84 MET cc_start: 0.8815 (tmm) cc_final: 0.8421 (tmm) REVERT: Y 147 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6916 (t-170) REVERT: Y 163 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8432 (tp30) REVERT: Y 186 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5694 (pp) REVERT: Z 109 GLN cc_start: 0.8501 (tm130) cc_final: 0.8110 (tm-30) REVERT: Z 181 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5615 (mp) REVERT: Z 186 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5690 (pp) REVERT: 0 147 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7426 (t-170) REVERT: 0 154 VAL cc_start: 0.8675 (m) cc_final: 0.8270 (p) REVERT: 0 163 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8604 (tm-30) REVERT: 0 186 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6015 (pp) outliers start: 200 outliers final: 142 residues processed: 822 average time/residue: 1.2836 time to fit residues: 1708.0065 Evaluate side-chains 763 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 600 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 176 PHE Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain M residue 187 GLN Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 108 SER Chi-restraints excluded: chain O residue 109 GLN Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain P residue 55 ARG Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 116 GLN Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 219 TRP Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 176 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 187 GLN Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 55 ARG Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 79 PHE Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 186 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 198 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 370 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 357 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 380 optimal weight: 0.7980 chunk 407 optimal weight: 0.9990 chunk 295 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 470 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN P 109 GLN T 230 GLN V 168 GLN Y 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 1.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 50706 Z= 0.184 Angle : 0.586 8.004 68715 Z= 0.304 Chirality : 0.043 0.219 7965 Planarity : 0.005 0.067 8667 Dihedral : 5.882 59.043 6831 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 3.74 % Allowed : 22.10 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.11), residues: 6102 helix: 0.54 (0.16), residues: 1292 sheet: -2.20 (0.10), residues: 2477 loop : -2.66 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 219 HIS 0.004 0.001 HIS L 138 PHE 0.027 0.001 PHE F 214 TYR 0.011 0.001 TYR M 206 ARG 0.007 0.000 ARG J 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 632 time to evaluate : 6.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: A 186 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6293 (pp) REVERT: B 84 MET cc_start: 0.9039 (ppp) cc_final: 0.8631 (tmm) REVERT: B 186 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6593 (pp) REVERT: C 33 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6659 (t80) REVERT: C 88 GLN cc_start: 0.7992 (pp30) cc_final: 0.7771 (pp30) REVERT: C 137 ASP cc_start: 0.8562 (p0) cc_final: 0.8098 (t70) REVERT: D 58 TYR cc_start: 0.8878 (m-80) cc_final: 0.8444 (m-80) REVERT: D 137 ASP cc_start: 0.6979 (t70) cc_final: 0.6730 (t70) REVERT: D 229 MET cc_start: 0.7602 (mmm) cc_final: 0.7183 (mmm) REVERT: E 178 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6115 (pt) REVERT: E 229 MET cc_start: 0.5518 (mmm) cc_final: 0.4792 (tpp) REVERT: F 40 LEU cc_start: 0.9331 (mt) cc_final: 0.9052 (mp) REVERT: F 137 ASP cc_start: 0.7210 (t0) cc_final: 0.6703 (m-30) REVERT: F 156 GLU cc_start: 0.9013 (pp20) cc_final: 0.8806 (pp20) REVERT: F 167 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8829 (tm-30) REVERT: F 178 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6086 (pt) REVERT: F 214 PHE cc_start: 0.5693 (m-10) cc_final: 0.5210 (m-10) REVERT: F 229 MET cc_start: 0.6369 (mmm) cc_final: 0.5625 (mmm) REVERT: G 118 LEU cc_start: 0.8211 (mm) cc_final: 0.7822 (mp) REVERT: G 147 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.5408 (t-170) REVERT: G 176 PHE cc_start: 0.6577 (m-80) cc_final: 0.6358 (m-80) REVERT: G 178 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6489 (pt) REVERT: H 43 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7031 (mtp180) REVERT: H 109 GLN cc_start: 0.8259 (tt0) cc_final: 0.7312 (tm-30) REVERT: H 147 HIS cc_start: 0.6313 (OUTLIER) cc_final: 0.5652 (t-170) REVERT: L 34 ARG cc_start: 0.6654 (mmp-170) cc_final: 0.6042 (ptm160) REVERT: M 55 ARG cc_start: 0.1771 (OUTLIER) cc_final: -0.0124 (ttp-110) REVERT: M 84 MET cc_start: 0.8417 (tmm) cc_final: 0.7956 (tmm) REVERT: O 144 MET cc_start: 0.2703 (mmm) cc_final: 0.2396 (mmm) REVERT: O 155 MET cc_start: 0.3392 (mmt) cc_final: 0.3169 (tpt) REVERT: P 55 ARG cc_start: 0.1674 (OUTLIER) cc_final: 0.0640 (tmm-80) REVERT: P 144 MET cc_start: 0.2795 (tpp) cc_final: 0.2480 (tpt) REVERT: Q 144 MET cc_start: 0.3012 (tpp) cc_final: 0.2611 (tpp) REVERT: R 147 HIS cc_start: 0.4807 (OUTLIER) cc_final: 0.4574 (t70) REVERT: S 1 MET cc_start: 0.4073 (mmt) cc_final: 0.3722 (mmm) REVERT: S 227 ASP cc_start: 0.7903 (t0) cc_final: 0.7327 (t0) REVERT: T 178 LEU cc_start: 0.2300 (OUTLIER) cc_final: 0.1622 (pt) REVERT: T 183 LEU cc_start: 0.8021 (mp) cc_final: 0.7463 (tt) REVERT: T 187 GLN cc_start: 0.8153 (pm20) cc_final: 0.7662 (mp10) REVERT: T 227 ASP cc_start: 0.8476 (t0) cc_final: 0.8001 (t0) REVERT: U 20 ASP cc_start: 0.8592 (m-30) cc_final: 0.8194 (p0) REVERT: U 86 ASP cc_start: 0.8938 (t0) cc_final: 0.8464 (m-30) REVERT: U 89 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7573 (p) REVERT: U 227 ASP cc_start: 0.8599 (t0) cc_final: 0.8241 (t0) REVERT: V 82 LYS cc_start: 0.8874 (tttt) cc_final: 0.8522 (tptp) REVERT: V 89 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7288 (p) REVERT: V 163 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8531 (tm-30) REVERT: V 176 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5808 (m-10) REVERT: V 227 ASP cc_start: 0.8425 (t0) cc_final: 0.8086 (t0) REVERT: W 14 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8137 (mt-10) REVERT: W 227 ASP cc_start: 0.8537 (p0) cc_final: 0.8169 (p0) REVERT: X 84 MET cc_start: 0.8802 (tmm) cc_final: 0.8493 (tmm) REVERT: X 167 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8731 (tp30) REVERT: X 227 ASP cc_start: 0.8289 (p0) cc_final: 0.7846 (p0) REVERT: Y 14 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8314 (mt-10) REVERT: Y 84 MET cc_start: 0.8836 (tmm) cc_final: 0.8487 (tmm) REVERT: Y 186 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5199 (pp) REVERT: Y 187 GLN cc_start: 0.8070 (tt0) cc_final: 0.7030 (mp10) REVERT: Z 109 GLN cc_start: 0.8516 (tm130) cc_final: 0.8126 (tm-30) REVERT: Z 112 THR cc_start: 0.8236 (t) cc_final: 0.7877 (p) REVERT: Z 144 MET cc_start: 0.8920 (mmp) cc_final: 0.8633 (mmt) REVERT: Z 162 GLN cc_start: 0.8579 (pp30) cc_final: 0.8345 (pp30) REVERT: Z 186 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5633 (pp) REVERT: 0 147 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7792 (t-170) REVERT: 0 154 VAL cc_start: 0.8476 (m) cc_final: 0.8129 (p) REVERT: 0 163 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8635 (tm-30) REVERT: 0 186 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6182 (pp) outliers start: 209 outliers final: 164 residues processed: 805 average time/residue: 1.2443 time to fit residues: 1616.3018 Evaluate side-chains 773 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 589 time to evaluate : 6.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 25 ASP Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 100 LYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 193 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 176 PHE Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 187 GLN Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 55 ARG Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 116 GLN Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 219 TRP Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 176 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 29 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 202 CYS Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 79 PHE Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 137 ASP Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 186 LEU Chi-restraints excluded: chain 0 residue 190 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 544 optimal weight: 2.9990 chunk 573 optimal weight: 2.9990 chunk 523 optimal weight: 4.9990 chunk 557 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 437 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 504 optimal weight: 0.9990 chunk 527 optimal weight: 1.9990 chunk 555 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 HIS ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN M 147 HIS ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 230 GLN Y 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 1.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 50706 Z= 0.250 Angle : 0.683 10.836 68715 Z= 0.352 Chirality : 0.045 0.226 7965 Planarity : 0.006 0.161 8667 Dihedral : 6.316 59.471 6831 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.85 % Allowed : 22.60 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.02 (0.11), residues: 6102 helix: 0.35 (0.15), residues: 1292 sheet: -2.38 (0.10), residues: 2490 loop : -2.77 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 219 HIS 0.007 0.001 HIS W 0 PHE 0.101 0.002 PHE G 79 TYR 0.027 0.001 TYR T 58 ARG 0.019 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 638 time to evaluate : 6.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: A 186 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6147 (pp) REVERT: B 84 MET cc_start: 0.9075 (ppp) cc_final: 0.8657 (tmm) REVERT: B 186 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6410 (pp) REVERT: C 33 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.6856 (t80) REVERT: C 88 GLN cc_start: 0.8290 (pp30) cc_final: 0.7950 (pp30) REVERT: C 137 ASP cc_start: 0.8745 (p0) cc_final: 0.8229 (t70) REVERT: E 137 ASP cc_start: 0.7995 (t0) cc_final: 0.7735 (t70) REVERT: E 229 MET cc_start: 0.6173 (mmm) cc_final: 0.5114 (tpp) REVERT: F 147 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.6926 (t-170) REVERT: F 178 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5911 (pt) REVERT: F 214 PHE cc_start: 0.6416 (m-10) cc_final: 0.5962 (m-10) REVERT: F 229 MET cc_start: 0.6332 (mmm) cc_final: 0.5642 (mmm) REVERT: G 118 LEU cc_start: 0.8435 (mm) cc_final: 0.7988 (mp) REVERT: G 147 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6155 (t-170) REVERT: G 214 PHE cc_start: 0.6437 (t80) cc_final: 0.6098 (t80) REVERT: H 43 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7575 (mmm-85) REVERT: H 109 GLN cc_start: 0.8114 (tt0) cc_final: 0.7596 (tm-30) REVERT: H 137 ASP cc_start: 0.8308 (p0) cc_final: 0.7868 (t0) REVERT: H 147 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6258 (t-170) REVERT: K 49 TRP cc_start: 0.4279 (m100) cc_final: 0.3904 (m100) REVERT: M 84 MET cc_start: 0.8437 (tmm) cc_final: 0.7973 (tmm) REVERT: N 55 ARG cc_start: 0.2234 (OUTLIER) cc_final: 0.0558 (ttp-110) REVERT: O 13 ARG cc_start: 0.3193 (ptp-170) cc_final: 0.1262 (tmm160) REVERT: O 144 MET cc_start: 0.3557 (mmm) cc_final: 0.3201 (mmm) REVERT: P 53 TYR cc_start: 0.7618 (m-10) cc_final: 0.7363 (m-10) REVERT: P 144 MET cc_start: 0.2859 (tpp) cc_final: 0.2572 (tpt) REVERT: Q 94 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.3449 (pt0) REVERT: Q 144 MET cc_start: 0.4032 (tpp) cc_final: 0.3547 (tpp) REVERT: R 147 HIS cc_start: 0.4356 (OUTLIER) cc_final: 0.3052 (t70) REVERT: R 155 MET cc_start: 0.8259 (mmm) cc_final: 0.7928 (mmm) REVERT: S 1 MET cc_start: 0.5189 (mmt) cc_final: 0.4874 (mmm) REVERT: S 25 ASP cc_start: 0.8936 (p0) cc_final: 0.8656 (m-30) REVERT: S 227 ASP cc_start: 0.7947 (t0) cc_final: 0.7352 (t0) REVERT: T 165 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8583 (t) REVERT: T 178 LEU cc_start: 0.2426 (OUTLIER) cc_final: 0.1670 (pt) REVERT: T 227 ASP cc_start: 0.8730 (t0) cc_final: 0.8302 (t0) REVERT: U 20 ASP cc_start: 0.8660 (m-30) cc_final: 0.8378 (p0) REVERT: U 89 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (p) REVERT: U 94 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6509 (mp0) REVERT: U 109 GLN cc_start: 0.8639 (tm130) cc_final: 0.8369 (tm-30) REVERT: U 141 LEU cc_start: 0.7857 (tt) cc_final: 0.7583 (tp) REVERT: U 147 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6707 (t70) REVERT: U 227 ASP cc_start: 0.8469 (t0) cc_final: 0.8068 (t0) REVERT: V 20 ASP cc_start: 0.8840 (m-30) cc_final: 0.8596 (p0) REVERT: V 82 LYS cc_start: 0.8958 (tttt) cc_final: 0.8692 (tmtt) REVERT: V 89 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7601 (p) REVERT: V 176 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: V 227 ASP cc_start: 0.8591 (t0) cc_final: 0.8238 (t0) REVERT: W 147 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7217 (t-90) REVERT: W 227 ASP cc_start: 0.8588 (p0) cc_final: 0.8251 (p0) REVERT: X 84 MET cc_start: 0.8913 (tmm) cc_final: 0.8599 (tmm) REVERT: X 147 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7861 (t-170) REVERT: X 227 ASP cc_start: 0.8444 (p0) cc_final: 0.8048 (p0) REVERT: Y 84 MET cc_start: 0.9010 (tmm) cc_final: 0.8645 (tmm) REVERT: Y 147 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7205 (t-170) REVERT: Y 186 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5391 (pp) REVERT: Y 187 GLN cc_start: 0.7938 (tt0) cc_final: 0.6812 (mp10) REVERT: Z 109 GLN cc_start: 0.8643 (tm130) cc_final: 0.8227 (tm-30) REVERT: Z 186 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5826 (pp) REVERT: 0 147 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.8049 (t-170) REVERT: 0 154 VAL cc_start: 0.8533 (m) cc_final: 0.8193 (p) REVERT: 0 186 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6369 (pp) outliers start: 215 outliers final: 152 residues processed: 810 average time/residue: 1.2271 time to fit residues: 1598.2808 Evaluate side-chains 737 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 561 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 176 PHE Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 146 TYR Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 152 TYR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain Q residue 219 TRP Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 78 ASN Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 176 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 29 ASP Chi-restraints excluded: chain T residue 79 PHE Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 165 THR Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 189 SER Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 147 HIS Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 147 HIS Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 147 HIS Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain Z residue 202 CYS Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 107 LEU Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 186 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 366 optimal weight: 2.9990 chunk 589 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 chunk 410 optimal weight: 1.9990 chunk 618 optimal weight: 3.9990 chunk 569 optimal weight: 0.1980 chunk 492 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 380 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS C 32 HIS ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN M 226 ASN ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN Y 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 1.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50706 Z= 0.168 Angle : 0.597 11.046 68715 Z= 0.305 Chirality : 0.043 0.212 7965 Planarity : 0.005 0.070 8667 Dihedral : 5.990 58.671 6831 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.83 % Allowed : 24.30 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.11), residues: 6102 helix: 0.54 (0.16), residues: 1295 sheet: -2.23 (0.10), residues: 2484 loop : -2.67 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 219 HIS 0.007 0.001 HIS M 147 PHE 0.025 0.001 PHE P 79 TYR 0.027 0.001 TYR T 58 ARG 0.017 0.000 ARG R 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 595 time to evaluate : 6.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: A 186 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6130 (pp) REVERT: B 84 MET cc_start: 0.9015 (ppp) cc_final: 0.8590 (tmm) REVERT: B 186 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6529 (pp) REVERT: C 14 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8331 (tm-30) REVERT: C 33 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6941 (t80) REVERT: C 88 GLN cc_start: 0.8068 (pp30) cc_final: 0.7833 (pp30) REVERT: C 137 ASP cc_start: 0.8551 (p0) cc_final: 0.7971 (t70) REVERT: D 58 TYR cc_start: 0.8963 (m-10) cc_final: 0.8493 (m-80) REVERT: E 137 ASP cc_start: 0.7972 (t0) cc_final: 0.7712 (t70) REVERT: E 229 MET cc_start: 0.5860 (mmm) cc_final: 0.5129 (tpp) REVERT: F 178 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5913 (pt) REVERT: F 214 PHE cc_start: 0.6301 (m-10) cc_final: 0.5821 (m-10) REVERT: F 229 MET cc_start: 0.6580 (mmm) cc_final: 0.5894 (mmm) REVERT: G 118 LEU cc_start: 0.8383 (mm) cc_final: 0.7984 (mp) REVERT: G 147 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.5949 (t-170) REVERT: H 43 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7691 (mmm-85) REVERT: H 109 GLN cc_start: 0.8110 (tt0) cc_final: 0.7608 (tm-30) REVERT: H 137 ASP cc_start: 0.8389 (p0) cc_final: 0.7943 (t0) REVERT: H 147 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6289 (t-170) REVERT: L 144 MET cc_start: 0.5354 (mmm) cc_final: 0.4793 (mmm) REVERT: M 25 ASP cc_start: 0.4405 (t0) cc_final: 0.3834 (m-30) REVERT: M 133 LYS cc_start: 0.7011 (mtmm) cc_final: 0.6756 (mtpp) REVERT: O 13 ARG cc_start: 0.3231 (ptp-170) cc_final: 0.1455 (tmm160) REVERT: O 144 MET cc_start: 0.3485 (mmm) cc_final: 0.3224 (mmm) REVERT: Q 94 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.3334 (pt0) REVERT: Q 144 MET cc_start: 0.4060 (tpp) cc_final: 0.3619 (tpp) REVERT: R 109 GLN cc_start: 0.8427 (tm130) cc_final: 0.8148 (tm-30) REVERT: R 147 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.3154 (t70) REVERT: R 155 MET cc_start: 0.8140 (mmm) cc_final: 0.7723 (mmm) REVERT: R 167 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8599 (tm-30) REVERT: S 1 MET cc_start: 0.5359 (mmt) cc_final: 0.4978 (mmm) REVERT: S 25 ASP cc_start: 0.8904 (p0) cc_final: 0.8665 (m-30) REVERT: S 227 ASP cc_start: 0.7774 (t0) cc_final: 0.7163 (t0) REVERT: T 130 LYS cc_start: 0.7650 (tppt) cc_final: 0.6984 (tptt) REVERT: T 178 LEU cc_start: 0.2546 (OUTLIER) cc_final: 0.1796 (pt) REVERT: T 227 ASP cc_start: 0.8821 (t0) cc_final: 0.8372 (t0) REVERT: U 58 TYR cc_start: 0.8970 (m-80) cc_final: 0.8737 (m-80) REVERT: U 86 ASP cc_start: 0.8702 (t0) cc_final: 0.8292 (m-30) REVERT: U 89 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7724 (p) REVERT: U 109 GLN cc_start: 0.8452 (tm130) cc_final: 0.8159 (tm-30) REVERT: U 141 LEU cc_start: 0.7853 (tt) cc_final: 0.7575 (tp) REVERT: U 227 ASP cc_start: 0.8430 (t0) cc_final: 0.8098 (t0) REVERT: V 20 ASP cc_start: 0.8700 (m-30) cc_final: 0.8500 (p0) REVERT: V 82 LYS cc_start: 0.8911 (tttt) cc_final: 0.8660 (tmtt) REVERT: V 176 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: W 227 ASP cc_start: 0.8673 (p0) cc_final: 0.8366 (p0) REVERT: X 84 MET cc_start: 0.8830 (tmm) cc_final: 0.8513 (tmm) REVERT: X 147 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7736 (t-170) REVERT: Y 84 MET cc_start: 0.8948 (tmm) cc_final: 0.8589 (tmm) REVERT: Y 186 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5875 (pp) REVERT: Z 109 GLN cc_start: 0.8633 (tm130) cc_final: 0.8215 (tm-30) REVERT: Z 186 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5920 (pp) REVERT: 0 147 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7912 (t-170) REVERT: 0 154 VAL cc_start: 0.8465 (m) cc_final: 0.8157 (p) REVERT: 0 186 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6516 (pp) outliers start: 158 outliers final: 120 residues processed: 723 average time/residue: 1.2843 time to fit residues: 1507.1459 Evaluate side-chains 693 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 556 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 176 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 192 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 193 ASN Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 146 TYR Chi-restraints excluded: chain L residue 176 PHE Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 193 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 55 ARG Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 193 ASN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 146 TYR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 109 GLN Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 147 HIS Chi-restraints excluded: chain Q residue 152 TYR Chi-restraints excluded: chain Q residue 219 TRP Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 147 HIS Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 147 HIS Chi-restraints excluded: chain S residue 176 PHE Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 79 PHE Chi-restraints excluded: chain T residue 147 HIS Chi-restraints excluded: chain T residue 176 PHE Chi-restraints excluded: chain T residue 178 LEU Chi-restraints excluded: chain T residue 193 ASN Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 178 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 147 HIS Chi-restraints excluded: chain V residue 176 PHE Chi-restraints excluded: chain V residue 178 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 171 ASN Chi-restraints excluded: chain W residue 178 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 147 HIS Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 192 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 112 THR Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 79 PHE Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 190 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 74 THR Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 147 HIS Chi-restraints excluded: chain 0 residue 178 LEU Chi-restraints excluded: chain 0 residue 186 LEU Chi-restraints excluded: chain 0 residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 391 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 454 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 206 optimal weight: 0.0980 chunk 506 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.172185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.142185 restraints weight = 258575.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.144935 restraints weight = 178217.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.145755 restraints weight = 122854.999| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 1.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.280 50706 Z= 0.198 Angle : 0.661 59.197 68715 Z= 0.352 Chirality : 0.042 0.192 7965 Planarity : 0.005 0.067 8667 Dihedral : 5.989 58.675 6831 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.68 % Allowed : 24.51 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 6102 helix: 0.53 (0.16), residues: 1295 sheet: -2.22 (0.10), residues: 2484 loop : -2.66 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 219 HIS 0.005 0.001 HIS M 147 PHE 0.027 0.001 PHE P 33 TYR 0.043 0.001 TYR K 53 ARG 0.021 0.000 ARG G 209 =============================================================================== Job complete usr+sys time: 27127.50 seconds wall clock time: 468 minutes 55.19 seconds (28135.19 seconds total)