Starting phenix.real_space_refine on Mon Mar 18 03:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwd_29502/03_2024/8fwd_29502.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 27528 2.51 5 N 7200 2.21 5 O 8256 1.98 5 H 40200 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83280 Number of models: 1 Model: "" Number of chains: 48 Chain: "0" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "1" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "2" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "3" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "4" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "6" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "7" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "8" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "9" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "J" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "N" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "T" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "V" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "X" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "Z" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "b" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "c" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "d" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "f" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "i" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "j" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "k" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1962 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "l" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1508 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 27.32, per 1000 atoms: 0.33 Number of scatterers: 83280 At special positions: 0 Unit cell: (179.655, 180.54, 179.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 8256 8.00 N 7200 7.00 C 27528 6.00 H 40200 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: 52.12 Conformation dependent library (CDL) restraints added in 7.5 seconds 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10896 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain '0' and resid 1 through 16 removed outlier: 3.575A pdb=" N LEU 0 5 " --> pdb=" O GLU 0 1 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 0 7 " --> pdb=" O ALA 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 31 removed outlier: 4.151A pdb=" N ARG 0 24 " --> pdb=" O ARG 0 20 " (cutoff:3.500A) Processing helix chain '0' and resid 36 through 51 removed outlier: 3.880A pdb=" N GLN 0 50 " --> pdb=" O ALA 0 46 " (cutoff:3.500A) Processing helix chain '0' and resid 52 through 67 removed outlier: 4.924A pdb=" N GLU 0 58 " --> pdb=" O ASP 0 54 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR 0 59 " --> pdb=" O GLU 0 55 " (cutoff:3.500A) Processing helix chain '0' and resid 70 through 85 Processing helix chain '0' and resid 86 through 100 Processing helix chain '1' and resid 2 through 17 removed outlier: 3.691A pdb=" N TYR 1 7 " --> pdb=" O SER 1 3 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL 1 8 " --> pdb=" O ALA 1 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET 1 9 " --> pdb=" O LEU 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 19 through 34 removed outlier: 4.115A pdb=" N GLU 1 25 " --> pdb=" O SER 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 51 Processing helix chain '1' and resid 53 through 68 removed outlier: 3.558A pdb=" N LEU 1 67 " --> pdb=" O LYS 1 63 " (cutoff:3.500A) Processing helix chain '1' and resid 71 through 86 removed outlier: 3.621A pdb=" N TRP 1 75 " --> pdb=" O ASP 1 71 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 102 Processing helix chain '1' and resid 105 through 120 removed outlier: 3.737A pdb=" N ALA 1 109 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 136 Processing helix chain '2' and resid 3 through 16 Processing helix chain '2' and resid 18 through 33 removed outlier: 3.733A pdb=" N ILE 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 51 Processing helix chain '2' and resid 52 through 67 removed outlier: 3.698A pdb=" N ARG 2 62 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 Processing helix chain '2' and resid 86 through 100 Processing helix chain '3' and resid 2 through 17 removed outlier: 3.686A pdb=" N TYR 3 7 " --> pdb=" O SER 3 3 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL 3 8 " --> pdb=" O ALA 3 4 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 34 removed outlier: 4.074A pdb=" N GLU 3 25 " --> pdb=" O SER 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 51 removed outlier: 3.573A pdb=" N TRP 3 41 " --> pdb=" O ASP 3 37 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 3 42 " --> pdb=" O ALA 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 68 removed outlier: 4.261A pdb=" N GLU 3 59 " --> pdb=" O ASP 3 55 " (cutoff:3.500A) Processing helix chain '3' and resid 71 through 86 removed outlier: 3.921A pdb=" N TRP 3 75 " --> pdb=" O ASP 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 102 Processing helix chain '3' and resid 105 through 120 removed outlier: 3.944A pdb=" N ALA 3 109 " --> pdb=" O ASP 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 136 Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 33 removed outlier: 3.880A pdb=" N ILE 4 28 " --> pdb=" O ARG 4 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA 4 29 " --> pdb=" O ALA 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 36 through 50 Processing helix chain '4' and resid 52 through 67 removed outlier: 4.659A pdb=" N GLU 4 58 " --> pdb=" O ASP 4 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR 4 59 " --> pdb=" O GLU 4 55 " (cutoff:3.500A) Processing helix chain '4' and resid 70 through 84 Processing helix chain '4' and resid 86 through 100 Processing helix chain '5' and resid 2 through 17 removed outlier: 3.865A pdb=" N TYR 5 7 " --> pdb=" O SER 5 3 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL 5 8 " --> pdb=" O ALA 5 4 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET 5 9 " --> pdb=" O LEU 5 5 " (cutoff:3.500A) Processing helix chain '5' and resid 19 through 34 removed outlier: 4.124A pdb=" N GLU 5 25 " --> pdb=" O SER 5 21 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 51 removed outlier: 3.623A pdb=" N TRP 5 41 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU 5 42 " --> pdb=" O ALA 5 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS 5 50 " --> pdb=" O SER 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 68 Processing helix chain '5' and resid 71 through 86 Processing helix chain '5' and resid 87 through 102 Processing helix chain '5' and resid 105 through 120 removed outlier: 3.805A pdb=" N ALA 5 109 " --> pdb=" O ASP 5 105 " (cutoff:3.500A) Processing helix chain '5' and resid 121 through 136 Processing helix chain '6' and resid 2 through 16 removed outlier: 4.111A pdb=" N TYR 6 7 " --> pdb=" O ALA 6 3 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 33 removed outlier: 3.965A pdb=" N ILE 6 28 " --> pdb=" O ARG 6 24 " (cutoff:3.500A) Processing helix chain '6' and resid 36 through 51 Processing helix chain '6' and resid 52 through 67 removed outlier: 3.623A pdb=" N ARG 6 62 " --> pdb=" O GLU 6 58 " (cutoff:3.500A) Processing helix chain '6' and resid 70 through 84 Processing helix chain '6' and resid 86 through 100 Processing helix chain '7' and resid 2 through 17 removed outlier: 3.776A pdb=" N TYR 7 7 " --> pdb=" O SER 7 3 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL 7 8 " --> pdb=" O ALA 7 4 " (cutoff:3.500A) Processing helix chain '7' and resid 19 through 34 removed outlier: 4.038A pdb=" N GLU 7 25 " --> pdb=" O SER 7 21 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 51 removed outlier: 3.570A pdb=" N TRP 7 41 " --> pdb=" O ASP 7 37 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 7 42 " --> pdb=" O ALA 7 38 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 68 removed outlier: 4.019A pdb=" N GLU 7 59 " --> pdb=" O ASP 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 86 Processing helix chain '7' and resid 87 through 102 Processing helix chain '7' and resid 105 through 120 removed outlier: 3.715A pdb=" N ALA 7 109 " --> pdb=" O ASP 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 121 through 136 Processing helix chain '8' and resid 2 through 16 Processing helix chain '8' and resid 18 through 31 removed outlier: 3.589A pdb=" N ARG 8 27 " --> pdb=" O ILE 8 23 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE 8 28 " --> pdb=" O ARG 8 24 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 8 29 " --> pdb=" O ALA 8 25 " (cutoff:3.500A) Processing helix chain '8' and resid 36 through 51 Processing helix chain '8' and resid 52 through 67 removed outlier: 3.588A pdb=" N ARG 8 62 " --> pdb=" O GLU 8 58 " (cutoff:3.500A) Processing helix chain '8' and resid 70 through 83 Processing helix chain '8' and resid 86 through 100 Processing helix chain '9' and resid 2 through 17 removed outlier: 4.586A pdb=" N VAL 9 8 " --> pdb=" O ALA 9 4 " (cutoff:3.500A) Processing helix chain '9' and resid 19 through 34 removed outlier: 4.085A pdb=" N GLU 9 25 " --> pdb=" O SER 9 21 " (cutoff:3.500A) Processing helix chain '9' and resid 37 through 51 removed outlier: 3.543A pdb=" N TRP 9 41 " --> pdb=" O ASP 9 37 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 68 removed outlier: 3.656A pdb=" N ALA 9 57 " --> pdb=" O ARG 9 53 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU 9 59 " --> pdb=" O ASP 9 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU 9 67 " --> pdb=" O LYS 9 63 " (cutoff:3.500A) Processing helix chain '9' and resid 71 through 86 removed outlier: 3.586A pdb=" N TRP 9 75 " --> pdb=" O ASP 9 71 " (cutoff:3.500A) Processing helix chain '9' and resid 87 through 102 Processing helix chain '9' and resid 105 through 120 Processing helix chain '9' and resid 121 through 136 Processing helix chain 'A' and resid 2 through 17 removed outlier: 4.316A pdb=" N VAL A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 34 removed outlier: 4.161A pdb=" N GLU A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.520A pdb=" N TRP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 86 removed outlier: 3.713A pdb=" N TRP A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.887A pdb=" N ASP A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.925A pdb=" N TYR B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 33 removed outlier: 3.553A pdb=" N ILE B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'C' and resid 2 through 17 removed outlier: 4.334A pdb=" N VAL C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.593A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.587A pdb=" N TRP C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 4.156A pdb=" N GLU C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 105 through 120 Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.667A pdb=" N ILE D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 67 removed outlier: 4.655A pdb=" N GLU D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'E' and resid 2 through 17 removed outlier: 3.642A pdb=" N TYR E 7 " --> pdb=" O SER E 3 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL E 8 " --> pdb=" O ALA E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 34 removed outlier: 3.602A pdb=" N ALA E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.580A pdb=" N TRP E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 68 removed outlier: 4.169A pdb=" N GLU E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.606A pdb=" N TRP E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 105 through 120 removed outlier: 3.562A pdb=" N ALA E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.558A pdb=" N TYR F 7 " --> pdb=" O ALA F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.853A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'F' and resid 52 through 67 removed outlier: 3.645A pdb=" N ILE F 57 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 Processing helix chain 'F' and resid 86 through 100 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.635A pdb=" N TYR G 7 " --> pdb=" O SER G 3 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 34 removed outlier: 4.176A pdb=" N GLU G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 51 removed outlier: 3.557A pdb=" N TRP G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 68 removed outlier: 3.677A pdb=" N LEU G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.647A pdb=" N TRP G 75 " --> pdb=" O ASP G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 Processing helix chain 'G' and resid 105 through 120 removed outlier: 4.017A pdb=" N LYS G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 136 Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 18 through 33 removed outlier: 3.751A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 51 Processing helix chain 'H' and resid 52 through 67 removed outlier: 4.210A pdb=" N GLU H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 86 through 100 Processing helix chain 'I' and resid 2 through 17 removed outlier: 4.664A pdb=" N VAL I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 34 removed outlier: 3.934A pdb=" N GLU I 25 " --> pdb=" O SER I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 51 removed outlier: 3.675A pdb=" N TRP I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 68 removed outlier: 3.514A pdb=" N LEU I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 86 removed outlier: 3.585A pdb=" N TRP I 75 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 102 Processing helix chain 'I' and resid 105 through 120 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 18 through 31 Processing helix chain 'J' and resid 36 through 51 removed outlier: 3.840A pdb=" N GLN J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 67 removed outlier: 4.630A pdb=" N GLU J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 86 through 100 Processing helix chain 'K' and resid 2 through 17 removed outlier: 3.755A pdb=" N TYR K 7 " --> pdb=" O SER K 3 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET K 9 " --> pdb=" O LEU K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 34 removed outlier: 3.559A pdb=" N ALA K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU K 25 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 51 removed outlier: 3.610A pdb=" N TRP K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 68 removed outlier: 4.238A pdb=" N GLU K 59 " --> pdb=" O ASP K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 86 removed outlier: 3.543A pdb=" N TRP K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 Processing helix chain 'K' and resid 105 through 120 Processing helix chain 'K' and resid 121 through 136 removed outlier: 3.581A pdb=" N ASP K 136 " --> pdb=" O ALA K 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 18 through 33 removed outlier: 4.436A pdb=" N ARG L 24 " --> pdb=" O ARG L 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG L 32 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 51 Processing helix chain 'L' and resid 52 through 67 removed outlier: 4.329A pdb=" N GLU L 58 " --> pdb=" O ASP L 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 86 through 100 Processing helix chain 'M' and resid 2 through 17 removed outlier: 3.681A pdb=" N TYR M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 34 removed outlier: 4.126A pdb=" N GLU M 25 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 51 removed outlier: 3.518A pdb=" N TRP M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 68 Processing helix chain 'M' and resid 73 through 86 Processing helix chain 'M' and resid 87 through 102 Processing helix chain 'M' and resid 105 through 120 Processing helix chain 'M' and resid 121 through 136 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.804A pdb=" N TYR N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 removed outlier: 3.972A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 51 Processing helix chain 'N' and resid 52 through 67 removed outlier: 4.134A pdb=" N GLU N 58 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR N 59 " --> pdb=" O GLU N 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG N 62 " --> pdb=" O GLU N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 83 Processing helix chain 'N' and resid 86 through 100 Processing helix chain 'O' and resid 2 through 17 removed outlier: 4.286A pdb=" N VAL O 8 " --> pdb=" O ALA O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 34 removed outlier: 4.087A pdb=" N GLU O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 51 removed outlier: 3.557A pdb=" N TRP O 41 " --> pdb=" O ASP O 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 68 removed outlier: 3.909A pdb=" N GLU O 59 " --> pdb=" O ASP O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 86 removed outlier: 3.654A pdb=" N TRP O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 102 Processing helix chain 'O' and resid 105 through 120 removed outlier: 3.547A pdb=" N ALA O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 136 Processing helix chain 'P' and resid 2 through 16 removed outlier: 3.739A pdb=" N TYR P 7 " --> pdb=" O ALA P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 31 removed outlier: 4.099A pdb=" N ARG P 24 " --> pdb=" O ARG P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 51 Processing helix chain 'P' and resid 52 through 66 removed outlier: 3.976A pdb=" N ARG P 62 " --> pdb=" O GLU P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 86 through 100 Processing helix chain 'Q' and resid 2 through 17 removed outlier: 4.276A pdb=" N VAL Q 8 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 34 removed outlier: 3.542A pdb=" N ALA Q 23 " --> pdb=" O ARG Q 19 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 51 Processing helix chain 'Q' and resid 53 through 68 removed outlier: 4.164A pdb=" N GLU Q 59 " --> pdb=" O ASP Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 86 removed outlier: 3.658A pdb=" N TRP Q 75 " --> pdb=" O ASP Q 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS Q 76 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 102 Processing helix chain 'Q' and resid 105 through 120 removed outlier: 3.726A pdb=" N ALA Q 109 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 136 removed outlier: 3.697A pdb=" N ASP Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 16 Processing helix chain 'R' and resid 18 through 31 Processing helix chain 'R' and resid 36 through 51 Processing helix chain 'R' and resid 52 through 67 removed outlier: 4.318A pdb=" N GLU R 58 " --> pdb=" O ASP R 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 85 Processing helix chain 'R' and resid 86 through 100 Processing helix chain 'S' and resid 2 through 17 removed outlier: 4.150A pdb=" N TYR S 7 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL S 8 " --> pdb=" O ALA S 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET S 9 " --> pdb=" O LEU S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 34 removed outlier: 4.122A pdb=" N GLU S 25 " --> pdb=" O SER S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.621A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 66 removed outlier: 4.266A pdb=" N GLU S 59 " --> pdb=" O ASP S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 86 removed outlier: 3.612A pdb=" N TRP S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 102 Processing helix chain 'S' and resid 105 through 120 Processing helix chain 'S' and resid 121 through 136 Processing helix chain 'T' and resid 2 through 16 Processing helix chain 'T' and resid 18 through 33 removed outlier: 3.761A pdb=" N ILE T 28 " --> pdb=" O ARG T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 50 Processing helix chain 'T' and resid 52 through 66 removed outlier: 4.713A pdb=" N GLU T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR T 59 " --> pdb=" O GLU T 55 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 86 through 100 Processing helix chain 'U' and resid 2 through 17 removed outlier: 4.319A pdb=" N VAL U 8 " --> pdb=" O ALA U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 34 removed outlier: 4.163A pdb=" N GLU U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 51 removed outlier: 3.586A pdb=" N TRP U 41 " --> pdb=" O ASP U 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU U 42 " --> pdb=" O ALA U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 68 removed outlier: 4.045A pdb=" N GLU U 59 " --> pdb=" O ASP U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 86 removed outlier: 3.543A pdb=" N TRP U 75 " --> pdb=" O ASP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 102 Processing helix chain 'U' and resid 105 through 120 Processing helix chain 'U' and resid 121 through 136 Processing helix chain 'V' and resid 2 through 16 removed outlier: 3.535A pdb=" N TYR V 7 " --> pdb=" O ALA V 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 33 removed outlier: 3.880A pdb=" N ARG V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG V 32 " --> pdb=" O ILE V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 36 through 51 Processing helix chain 'V' and resid 52 through 67 removed outlier: 4.660A pdb=" N GLU V 58 " --> pdb=" O ASP V 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 84 Processing helix chain 'V' and resid 86 through 100 Processing helix chain 'W' and resid 2 through 17 removed outlier: 3.856A pdb=" N TYR W 7 " --> pdb=" O SER W 3 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL W 8 " --> pdb=" O ALA W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 34 removed outlier: 4.009A pdb=" N GLU W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 51 removed outlier: 3.697A pdb=" N LYS W 50 " --> pdb=" O SER W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 66 removed outlier: 4.026A pdb=" N GLU W 59 " --> pdb=" O ASP W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 86 Processing helix chain 'W' and resid 87 through 102 Processing helix chain 'W' and resid 105 through 120 removed outlier: 3.575A pdb=" N ALA W 109 " --> pdb=" O ASP W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 136 Processing helix chain 'X' and resid 2 through 16 removed outlier: 3.561A pdb=" N TYR X 7 " --> pdb=" O ALA X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 Processing helix chain 'X' and resid 36 through 51 Processing helix chain 'X' and resid 52 through 67 removed outlier: 3.606A pdb=" N ARG X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 84 Processing helix chain 'X' and resid 86 through 100 Processing helix chain 'Y' and resid 2 through 17 removed outlier: 3.673A pdb=" N TYR Y 7 " --> pdb=" O SER Y 3 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL Y 8 " --> pdb=" O ALA Y 4 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 34 removed outlier: 3.801A pdb=" N GLU Y 25 " --> pdb=" O SER Y 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS Y 29 " --> pdb=" O GLU Y 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 51 removed outlier: 3.529A pdb=" N GLU Y 49 " --> pdb=" O GLY Y 45 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Y 51 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 68 removed outlier: 3.557A pdb=" N ALA Y 57 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 86 removed outlier: 3.515A pdb=" N TRP Y 75 " --> pdb=" O ASP Y 71 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 102 Processing helix chain 'Y' and resid 105 through 120 Processing helix chain 'Y' and resid 121 through 136 Processing helix chain 'Z' and resid 2 through 16 Processing helix chain 'Z' and resid 18 through 31 Processing helix chain 'Z' and resid 36 through 51 Processing helix chain 'Z' and resid 52 through 67 removed outlier: 3.756A pdb=" N ARG Z 62 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 84 Processing helix chain 'Z' and resid 86 through 100 Processing helix chain 'a' and resid 2 through 17 removed outlier: 3.670A pdb=" N TYR a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL a 8 " --> pdb=" O ALA a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 34 removed outlier: 4.025A pdb=" N GLU a 25 " --> pdb=" O SER a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 51 removed outlier: 3.630A pdb=" N TRP a 41 " --> pdb=" O ASP a 37 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU a 42 " --> pdb=" O ALA a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 3.791A pdb=" N GLU a 59 " --> pdb=" O ASP a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 86 removed outlier: 3.660A pdb=" N TRP a 75 " --> pdb=" O ASP a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 102 Processing helix chain 'a' and resid 105 through 120 Processing helix chain 'a' and resid 121 through 136 Processing helix chain 'b' and resid 2 through 16 removed outlier: 3.549A pdb=" N TYR b 7 " --> pdb=" O ALA b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 33 removed outlier: 3.781A pdb=" N ILE b 28 " --> pdb=" O ARG b 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG b 32 " --> pdb=" O ILE b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 51 Processing helix chain 'b' and resid 52 through 67 removed outlier: 4.178A pdb=" N GLU b 58 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 83 Processing helix chain 'b' and resid 86 through 100 Processing helix chain 'c' and resid 2 through 17 removed outlier: 4.247A pdb=" N VAL c 8 " --> pdb=" O ALA c 4 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 34 removed outlier: 4.040A pdb=" N GLU c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 37 through 51 removed outlier: 3.512A pdb=" N TRP c 41 " --> pdb=" O ASP c 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS c 50 " --> pdb=" O SER c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 removed outlier: 3.700A pdb=" N GLU c 59 " --> pdb=" O ASP c 55 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA c 60 " --> pdb=" O GLU c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 86 removed outlier: 3.654A pdb=" N LYS c 76 " --> pdb=" O ALA c 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL c 81 " --> pdb=" O GLU c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 102 Processing helix chain 'c' and resid 105 through 120 Processing helix chain 'c' and resid 121 through 136 Processing helix chain 'd' and resid 2 through 16 Processing helix chain 'd' and resid 18 through 31 removed outlier: 4.061A pdb=" N ARG d 24 " --> pdb=" O ARG d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 51 Processing helix chain 'd' and resid 52 through 67 Processing helix chain 'd' and resid 70 through 84 Processing helix chain 'd' and resid 86 through 100 Processing helix chain 'e' and resid 2 through 17 removed outlier: 4.521A pdb=" N VAL e 8 " --> pdb=" O ALA e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 34 removed outlier: 4.014A pdb=" N GLU e 25 " --> pdb=" O SER e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 51 removed outlier: 3.732A pdb=" N TRP e 41 " --> pdb=" O ASP e 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 68 Processing helix chain 'e' and resid 71 through 86 removed outlier: 3.889A pdb=" N LYS e 76 " --> pdb=" O ALA e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 102 Processing helix chain 'e' and resid 105 through 120 removed outlier: 3.643A pdb=" N ALA e 109 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 136 Processing helix chain 'f' and resid 2 through 16 removed outlier: 4.072A pdb=" N TYR f 7 " --> pdb=" O ALA f 3 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 33 removed outlier: 3.927A pdb=" N ILE f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG f 32 " --> pdb=" O ILE f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 36 through 51 Processing helix chain 'f' and resid 52 through 67 Processing helix chain 'f' and resid 70 through 84 Processing helix chain 'f' and resid 86 through 100 Processing helix chain 'g' and resid 2 through 17 removed outlier: 4.182A pdb=" N VAL g 8 " --> pdb=" O ALA g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 34 removed outlier: 4.033A pdb=" N GLU g 25 " --> pdb=" O SER g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 51 removed outlier: 3.767A pdb=" N TRP g 41 " --> pdb=" O ASP g 37 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU g 42 " --> pdb=" O ALA g 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER g 46 " --> pdb=" O LEU g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 68 removed outlier: 4.083A pdb=" N GLU g 59 " --> pdb=" O ASP g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 86 removed outlier: 3.847A pdb=" N LYS g 76 " --> pdb=" O ALA g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 102 Processing helix chain 'g' and resid 105 through 120 Processing helix chain 'g' and resid 121 through 136 Processing helix chain 'h' and resid 2 through 16 Processing helix chain 'h' and resid 18 through 31 Processing helix chain 'h' and resid 36 through 51 Processing helix chain 'h' and resid 52 through 67 removed outlier: 4.678A pdb=" N GLU h 58 " --> pdb=" O ASP h 54 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR h 59 " --> pdb=" O GLU h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 85 Processing helix chain 'h' and resid 86 through 100 Processing helix chain 'i' and resid 2 through 17 removed outlier: 3.669A pdb=" N TYR i 7 " --> pdb=" O SER i 3 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL i 8 " --> pdb=" O ALA i 4 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET i 9 " --> pdb=" O LEU i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 34 removed outlier: 3.961A pdb=" N GLU i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 51 removed outlier: 3.551A pdb=" N TRP i 41 " --> pdb=" O ASP i 37 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 68 removed outlier: 3.743A pdb=" N ALA i 57 " --> pdb=" O ARG i 53 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU i 59 " --> pdb=" O ASP i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 86 Processing helix chain 'i' and resid 87 through 102 Processing helix chain 'i' and resid 105 through 120 removed outlier: 3.948A pdb=" N ALA i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 121 through 135 Processing helix chain 'j' and resid 2 through 16 Processing helix chain 'j' and resid 18 through 33 removed outlier: 3.967A pdb=" N ARG j 24 " --> pdb=" O ARG j 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE j 28 " --> pdb=" O ARG j 24 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG j 32 " --> pdb=" O ILE j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 51 Processing helix chain 'j' and resid 52 through 67 removed outlier: 4.185A pdb=" N GLU j 58 " --> pdb=" O ASP j 54 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR j 59 " --> pdb=" O GLU j 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG j 62 " --> pdb=" O GLU j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 84 Processing helix chain 'j' and resid 86 through 100 Processing helix chain 'k' and resid 2 through 17 removed outlier: 4.254A pdb=" N VAL k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 34 removed outlier: 4.115A pdb=" N GLU k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 51 removed outlier: 3.666A pdb=" N TRP k 41 " --> pdb=" O ASP k 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU k 42 " --> pdb=" O ALA k 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 68 removed outlier: 4.224A pdb=" N GLU k 59 " --> pdb=" O ASP k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 71 through 86 removed outlier: 3.504A pdb=" N TRP k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 102 Processing helix chain 'k' and resid 105 through 120 Processing helix chain 'k' and resid 121 through 136 Processing helix chain 'l' and resid 2 through 16 removed outlier: 3.589A pdb=" N TYR l 7 " --> pdb=" O ALA l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 18 through 33 removed outlier: 4.096A pdb=" N ARG l 24 " --> pdb=" O ARG l 20 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE l 28 " --> pdb=" O ARG l 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA l 29 " --> pdb=" O ALA l 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG l 32 " --> pdb=" O ILE l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 50 Processing helix chain 'l' and resid 52 through 67 removed outlier: 4.188A pdb=" N GLU l 58 " --> pdb=" O ASP l 54 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR l 59 " --> pdb=" O GLU l 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 84 Processing helix chain 'l' and resid 86 through 100 3624 hydrogen bonds defined for protein. 10872 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: 32.85 Time building geometry restraints manager: 54.90 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: 40200 1.03 - 1.22: 0 1.22 - 1.42: 17544 1.42 - 1.61: 25896 1.61 - 1.81: 192 Bond restraints: 83832 Sorted by residual: bond pdb=" C ASP T 67 " pdb=" N PRO T 68 " ideal model delta sigma weight residual 1.337 1.350 -0.014 1.11e-02 8.12e+03 1.53e+00 bond pdb=" CA PRO T 68 " pdb=" HA PRO T 68 " ideal model delta sigma weight residual 0.970 0.992 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" N LEU U 51 " pdb=" CA LEU U 51 " ideal model delta sigma weight residual 1.457 1.468 -0.012 1.40e-02 5.10e+03 6.97e-01 bond pdb=" C LEU G 135 " pdb=" N ASP G 136 " ideal model delta sigma weight residual 1.332 1.325 0.007 8.60e-03 1.35e+04 6.39e-01 bond pdb=" N GLY 7 45 " pdb=" CA GLY 7 45 " ideal model delta sigma weight residual 1.454 1.445 0.010 1.24e-02 6.50e+03 6.05e-01 ... (remaining 83827 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 725 106.47 - 113.36: 100351 113.36 - 120.24: 26273 120.24 - 127.13: 23278 127.13 - 134.01: 261 Bond angle restraints: 150888 Sorted by residual: angle pdb=" N PRO I 69 " pdb=" CA PRO I 69 " pdb=" C PRO I 69 " ideal model delta sigma weight residual 111.22 114.70 -3.48 1.40e+00 5.10e-01 6.18e+00 angle pdb=" N PRO i 69 " pdb=" CA PRO i 69 " pdb=" C PRO i 69 " ideal model delta sigma weight residual 111.22 114.62 -3.40 1.40e+00 5.10e-01 5.90e+00 angle pdb=" N PRO E 69 " pdb=" CA PRO E 69 " pdb=" C PRO E 69 " ideal model delta sigma weight residual 111.22 114.54 -3.32 1.40e+00 5.10e-01 5.63e+00 angle pdb=" C ARG W 53 " pdb=" CA ARG W 53 " pdb=" CB ARG W 53 " ideal model delta sigma weight residual 111.88 108.56 3.32 1.41e+00 5.03e-01 5.54e+00 angle pdb=" N PRO Y 69 " pdb=" CA PRO Y 69 " pdb=" C PRO Y 69 " ideal model delta sigma weight residual 110.40 114.00 -3.60 1.61e+00 3.86e-01 5.00e+00 ... (remaining 150883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 36288 17.97 - 35.93: 1853 35.93 - 53.90: 585 53.90 - 71.87: 168 71.87 - 89.83: 34 Dihedral angle restraints: 38928 sinusoidal: 20232 harmonic: 18696 Sorted by residual: dihedral pdb=" CA ARG Y 53 " pdb=" C ARG Y 53 " pdb=" N LEU Y 54 " pdb=" CA LEU Y 54 " ideal model delta harmonic sigma weight residual -180.00 -148.78 -31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA LEU G 16 " pdb=" C LEU G 16 " pdb=" N LEU G 17 " pdb=" CA LEU G 17 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU S 16 " pdb=" C LEU S 16 " pdb=" N LEU S 17 " pdb=" CA LEU S 17 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 38925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4882 0.027 - 0.053: 1345 0.053 - 0.080: 390 0.080 - 0.107: 178 0.107 - 0.133: 45 Chirality restraints: 6840 Sorted by residual: chirality pdb=" CA PRO k 69 " pdb=" N PRO k 69 " pdb=" C PRO k 69 " pdb=" CB PRO k 69 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA PRO 5 69 " pdb=" N PRO 5 69 " pdb=" C PRO 5 69 " pdb=" CB PRO 5 69 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO a 69 " pdb=" N PRO a 69 " pdb=" C PRO a 69 " pdb=" CB PRO a 69 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 6837 not shown) Planarity restraints: 12360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Y 68 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO Y 69 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO Y 69 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO Y 69 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 68 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO O 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO O 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO O 69 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP i 102 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO i 103 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO i 103 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO i 103 " 0.019 5.00e-02 4.00e+02 ... (remaining 12357 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 2040 2.17 - 2.77: 157541 2.77 - 3.38: 235628 3.38 - 3.99: 284423 3.99 - 4.60: 464105 Nonbonded interactions: 1143737 Sorted by model distance: nonbonded pdb=" HH TYR Q 61 " pdb=" OE1 GLU Q 77 " model vdw 1.557 1.850 nonbonded pdb=" HZ1 LYS 1 76 " pdb=" OD2 ASP 1 105 " model vdw 1.596 1.850 nonbonded pdb=" HZ3 LYS 9 76 " pdb=" OD2 ASP 9 105 " model vdw 1.606 1.850 nonbonded pdb=" OD1 ASP 5 71 " pdb=" HG SER 5 73 " model vdw 1.660 1.850 nonbonded pdb=" HZ3 LYS 7 76 " pdb=" OD2 ASP 7 105 " model vdw 1.664 1.850 ... (remaining 1143732 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 '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.030 Extract box with map and model: 13.990 Check model and map are aligned: 0.940 Set scattering table: 0.590 Process input model: 207.300 Find NCS groups from input model: 3.450 Set up NCS constraints: 0.890 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: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.003 0.023 43632 Z= 0.172 Angle : 0.522 6.576 59112 Z= 0.290 Chirality : 0.031 0.133 6840 Planarity : 0.003 0.046 7608 Dihedral : 12.693 89.833 15864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.11), residues: 5640 helix: 1.01 (0.07), residues: 5088 sheet: None (None), residues: 0 loop : 0.94 (0.32), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 4 40 TYR 0.009 0.001 TYR l 41 ARG 0.005 0.001 ARG 5 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 859 time to evaluate : 5.063 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: 3 18 ASN cc_start: 0.8055 (t0) cc_final: 0.7724 (t0) REVERT: 4 11 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: 8 36 ASN cc_start: 0.7902 (m-40) cc_final: 0.7640 (m-40) REVERT: 8 49 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7888 (mmtt) REVERT: D 2 GLU cc_start: 0.6506 (tt0) cc_final: 0.6228 (tt0) REVERT: V 2 GLU cc_start: 0.6706 (tt0) cc_final: 0.6468 (tt0) REVERT: X 2 GLU cc_start: 0.6387 (tt0) cc_final: 0.6180 (tt0) REVERT: Y 27 TYR cc_start: 0.8414 (m-80) cc_final: 0.7742 (m-10) REVERT: Z 57 ILE cc_start: 0.7932 (mm) cc_final: 0.7598 (mm) REVERT: f 36 ASN cc_start: 0.8215 (t0) cc_final: 0.8013 (t0) REVERT: j 67 ASP cc_start: 0.8249 (t0) cc_final: 0.8044 (t0) REVERT: l 36 ASN cc_start: 0.8277 (t0) cc_final: 0.7973 (t0) outliers start: 2 outliers final: 0 residues processed: 860 average time/residue: 1.3093 time to fit residues: 1725.4885 Evaluate side-chains 510 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 509 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 11 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 0.7980 chunk 418 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 432 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 501 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 69 ASN B 36 ASN D 69 ASN J 69 ASN J 76 ASN L 84 GLN M 70 ASN P 76 ASN Z 69 ASN d 69 ASN h 45 ASN j 69 ASN l 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43632 Z= 0.255 Angle : 0.522 4.892 59112 Z= 0.284 Chirality : 0.031 0.135 6840 Planarity : 0.003 0.035 7608 Dihedral : 4.331 56.590 6243 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 7.06 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.11), residues: 5640 helix: 1.58 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : 0.70 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 40 TYR 0.012 0.001 TYR P 19 ARG 0.004 0.000 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 504 time to evaluate : 5.158 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: 8 36 ASN cc_start: 0.7899 (m-40) cc_final: 0.7556 (m-40) REVERT: 8 57 ILE cc_start: 0.7789 (mm) cc_final: 0.7392 (mm) REVERT: A 67 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 83 ASN cc_start: 0.8373 (m110) cc_final: 0.8168 (m110) REVERT: F 15 LYS cc_start: 0.8426 (tttp) cc_final: 0.8095 (tttp) REVERT: F 36 ASN cc_start: 0.7795 (t0) cc_final: 0.7426 (m-40) REVERT: H 15 LYS cc_start: 0.8400 (tttp) cc_final: 0.8140 (tttp) REVERT: T 67 ASP cc_start: 0.7899 (t70) cc_final: 0.7424 (t70) REVERT: X 36 ASN cc_start: 0.7885 (t0) cc_final: 0.7685 (t0) REVERT: Y 27 TYR cc_start: 0.8539 (m-80) cc_final: 0.7809 (m-10) REVERT: Z 57 ILE cc_start: 0.7933 (mm) cc_final: 0.7582 (mm) REVERT: b 2 GLU cc_start: 0.6705 (tt0) cc_final: 0.6291 (tt0) REVERT: l 2 GLU cc_start: 0.6940 (tt0) cc_final: 0.6588 (tt0) REVERT: l 36 ASN cc_start: 0.7872 (t0) cc_final: 0.7476 (m-40) outliers start: 42 outliers final: 22 residues processed: 526 average time/residue: 1.1215 time to fit residues: 934.7531 Evaluate side-chains 483 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 460 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 36 ASN Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 9 MET Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 36 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 417 optimal weight: 0.0010 chunk 341 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 502 optimal weight: 1.9990 chunk 542 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 chunk 497 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 402 optimal weight: 9.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 70 ASN L 69 ASN f 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43632 Z= 0.236 Angle : 0.497 5.142 59112 Z= 0.268 Chirality : 0.030 0.130 6840 Planarity : 0.003 0.045 7608 Dihedral : 4.011 29.694 6240 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.40 % Allowed : 8.71 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.11), residues: 5640 helix: 1.83 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : 0.48 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 40 TYR 0.018 0.001 TYR B 19 ARG 0.004 0.000 ARG h 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 489 time to evaluate : 5.135 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: 1 118 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7891 (ttmt) REVERT: 3 73 SER cc_start: 0.7411 (m) cc_final: 0.6979 (p) REVERT: 6 19 TYR cc_start: 0.8394 (m-80) cc_final: 0.8187 (m-80) REVERT: 7 67 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8738 (mm) REVERT: 8 36 ASN cc_start: 0.7941 (m-40) cc_final: 0.7613 (m-40) REVERT: 8 57 ILE cc_start: 0.7785 (mm) cc_final: 0.7417 (mm) REVERT: A 67 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8924 (mm) REVERT: E 67 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8882 (mm) REVERT: F 36 ASN cc_start: 0.7882 (t0) cc_final: 0.7494 (m-40) REVERT: H 15 LYS cc_start: 0.8372 (tttp) cc_final: 0.8104 (tttp) REVERT: J 36 ASN cc_start: 0.7855 (t0) cc_final: 0.7390 (m-40) REVERT: M 100 MET cc_start: 0.7939 (mtm) cc_final: 0.7733 (mtp) REVERT: T 67 ASP cc_start: 0.7920 (t70) cc_final: 0.7493 (t70) REVERT: W 100 MET cc_start: 0.7898 (mtt) cc_final: 0.7689 (mtm) REVERT: d 20 ARG cc_start: 0.7867 (tmt-80) cc_final: 0.7481 (tmt-80) REVERT: f 35 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8250 (p0) REVERT: j 15 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8492 (tttp) REVERT: k 100 MET cc_start: 0.8000 (mtt) cc_final: 0.7795 (mmt) REVERT: l 2 GLU cc_start: 0.6920 (tt0) cc_final: 0.6601 (tt0) outliers start: 55 outliers final: 33 residues processed: 516 average time/residue: 1.1159 time to fit residues: 934.2685 Evaluate side-chains 491 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 454 time to evaluate : 5.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 23 ILE Chi-restraints excluded: chain 7 residue 9 MET Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 9 MET Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain i residue 71 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 503 optimal weight: 10.0000 chunk 533 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 70 ASN ** P 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 43632 Z= 0.420 Angle : 0.625 7.244 59112 Z= 0.342 Chirality : 0.034 0.153 6840 Planarity : 0.003 0.046 7608 Dihedral : 4.341 30.834 6240 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.06 % Allowed : 10.54 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.11), residues: 5640 helix: 1.37 (0.07), residues: 5088 sheet: None (None), residues: 0 loop : 0.06 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 41 TYR 0.018 0.002 TYR O 61 ARG 0.004 0.000 ARG b 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 492 time to evaluate : 5.132 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: 0 83 ASN cc_start: 0.8471 (m110) cc_final: 0.8234 (m110) REVERT: 1 118 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7946 (ttmt) REVERT: 3 73 SER cc_start: 0.7659 (m) cc_final: 0.7225 (p) REVERT: 4 36 ASN cc_start: 0.7959 (m-40) cc_final: 0.7723 (m-40) REVERT: 6 36 ASN cc_start: 0.7797 (t0) cc_final: 0.7281 (m-40) REVERT: 7 67 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8888 (mm) REVERT: 8 36 ASN cc_start: 0.7992 (m-40) cc_final: 0.7632 (m-40) REVERT: 8 57 ILE cc_start: 0.7896 (mm) cc_final: 0.7519 (mm) REVERT: C 100 MET cc_start: 0.8386 (mpp) cc_final: 0.8064 (mmt) REVERT: D 36 ASN cc_start: 0.8036 (m-40) cc_final: 0.7769 (m-40) REVERT: H 15 LYS cc_start: 0.8426 (tttp) cc_final: 0.8085 (tttp) REVERT: I 67 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9115 (mm) REVERT: J 36 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7318 (m110) REVERT: M 100 MET cc_start: 0.7906 (mtm) cc_final: 0.7579 (mtp) REVERT: N 36 ASN cc_start: 0.7922 (m-40) cc_final: 0.7712 (m-40) REVERT: N 67 ASP cc_start: 0.8103 (t0) cc_final: 0.7759 (t0) REVERT: T 67 ASP cc_start: 0.7968 (t70) cc_final: 0.7513 (t70) REVERT: W 100 MET cc_start: 0.7921 (mtt) cc_final: 0.7705 (mmt) REVERT: Y 27 TYR cc_start: 0.8767 (m-80) cc_final: 0.7872 (m-10) REVERT: Z 36 ASN cc_start: 0.7890 (t0) cc_final: 0.7631 (m-40) REVERT: d 57 ILE cc_start: 0.7830 (mt) cc_final: 0.7625 (mm) REVERT: j 67 ASP cc_start: 0.8327 (t0) cc_final: 0.8033 (t0) REVERT: k 100 MET cc_start: 0.8024 (mtt) cc_final: 0.7801 (mmt) REVERT: l 2 GLU cc_start: 0.6980 (tt0) cc_final: 0.6700 (tt0) outliers start: 81 outliers final: 57 residues processed: 544 average time/residue: 1.0961 time to fit residues: 976.1860 Evaluate side-chains 527 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 467 time to evaluate : 5.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 71 ASP Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 36 ASN Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 9 residue 9 MET Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 36 ASN Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 36 ASN Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 36 ASN Chi-restraints excluded: chain k residue 71 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 397 optimal weight: 0.4980 chunk 220 optimal weight: 2.9990 chunk 455 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 478 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 36 ASN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43632 Z= 0.203 Angle : 0.481 5.154 59112 Z= 0.256 Chirality : 0.029 0.137 6840 Planarity : 0.003 0.035 7608 Dihedral : 3.964 27.955 6240 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.63 % Allowed : 12.25 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.11), residues: 5640 helix: 1.94 (0.07), residues: 5064 sheet: None (None), residues: 0 loop : 0.24 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 40 TYR 0.018 0.001 TYR H 19 ARG 0.006 0.000 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 477 time to evaluate : 5.111 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: 0 83 ASN cc_start: 0.8448 (m110) cc_final: 0.8220 (m110) REVERT: 1 118 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7977 (ttmt) REVERT: 2 15 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8080 (tttt) REVERT: 3 73 SER cc_start: 0.7431 (m) cc_final: 0.7144 (p) REVERT: 4 36 ASN cc_start: 0.7914 (m-40) cc_final: 0.7655 (m-40) REVERT: 6 36 ASN cc_start: 0.7585 (t0) cc_final: 0.7139 (m110) REVERT: 7 67 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (mm) REVERT: 8 36 ASN cc_start: 0.7990 (m-40) cc_final: 0.7624 (m-40) REVERT: C 100 MET cc_start: 0.8336 (mpp) cc_final: 0.8028 (mmt) REVERT: D 36 ASN cc_start: 0.7898 (m-40) cc_final: 0.7659 (m-40) REVERT: H 15 LYS cc_start: 0.8438 (tttp) cc_final: 0.8062 (tttp) REVERT: J 36 ASN cc_start: 0.7824 (t0) cc_final: 0.7136 (m110) REVERT: N 36 ASN cc_start: 0.7890 (m-40) cc_final: 0.7667 (m-40) REVERT: O 73 SER cc_start: 0.7494 (m) cc_final: 0.7164 (p) REVERT: Y 27 TYR cc_start: 0.8587 (m-80) cc_final: 0.8220 (m-10) REVERT: Z 36 ASN cc_start: 0.7715 (t0) cc_final: 0.7475 (m-40) REVERT: d 36 ASN cc_start: 0.7917 (t0) cc_final: 0.7319 (m-40) REVERT: l 2 GLU cc_start: 0.7018 (tt0) cc_final: 0.6676 (tt0) outliers start: 64 outliers final: 42 residues processed: 518 average time/residue: 1.0477 time to fit residues: 875.3680 Evaluate side-chains 512 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 468 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 ASN Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 2 residue 15 LYS Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 36 ASN Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 71 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 7.9990 chunk 480 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 534 optimal weight: 5.9990 chunk 443 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43632 Z= 0.221 Angle : 0.485 5.570 59112 Z= 0.258 Chirality : 0.030 0.136 6840 Planarity : 0.003 0.034 7608 Dihedral : 3.868 28.099 6240 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.85 % Allowed : 12.63 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.11), residues: 5640 helix: 2.00 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : 0.47 (0.31), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 40 TYR 0.021 0.001 TYR f 19 ARG 0.003 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 481 time to evaluate : 5.173 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: 0 83 ASN cc_start: 0.8449 (m110) cc_final: 0.8228 (m110) REVERT: 1 118 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7978 (ttmt) REVERT: 3 67 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8811 (mm) REVERT: 3 73 SER cc_start: 0.7539 (m) cc_final: 0.7327 (p) REVERT: 4 36 ASN cc_start: 0.7835 (m-40) cc_final: 0.7594 (m-40) REVERT: 6 36 ASN cc_start: 0.7626 (t0) cc_final: 0.7210 (m110) REVERT: 7 67 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8807 (mm) REVERT: 8 36 ASN cc_start: 0.8010 (m-40) cc_final: 0.7622 (m-40) REVERT: C 100 MET cc_start: 0.8353 (mpp) cc_final: 0.8049 (mmt) REVERT: D 36 ASN cc_start: 0.7931 (m-40) cc_final: 0.7684 (m-40) REVERT: I 100 MET cc_start: 0.8035 (mtm) cc_final: 0.7802 (mmt) REVERT: J 36 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7149 (m110) REVERT: N 36 ASN cc_start: 0.7887 (m-40) cc_final: 0.7656 (m-40) REVERT: O 73 SER cc_start: 0.7452 (m) cc_final: 0.7212 (p) REVERT: T 67 ASP cc_start: 0.7867 (t70) cc_final: 0.7625 (t70) REVERT: Y 27 TYR cc_start: 0.8608 (m-10) cc_final: 0.8283 (m-10) REVERT: Z 36 ASN cc_start: 0.7808 (t0) cc_final: 0.7567 (m-40) REVERT: c 71 ASP cc_start: 0.7108 (m-30) cc_final: 0.6644 (m-30) REVERT: d 36 ASN cc_start: 0.7919 (t0) cc_final: 0.7319 (m-40) REVERT: l 2 GLU cc_start: 0.7043 (tt0) cc_final: 0.6677 (tt0) outliers start: 73 outliers final: 53 residues processed: 529 average time/residue: 1.0894 time to fit residues: 936.4331 Evaluate side-chains 523 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 467 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 LYS Chi-restraints excluded: chain 0 residue 36 ASN Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 71 ASP Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 4 residue 2 GLU Chi-restraints excluded: chain 5 residue 33 LEU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain f residue 52 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 36 ASN Chi-restraints excluded: chain h residue 50 GLN Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 390 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 449 optimal weight: 50.0000 chunk 298 optimal weight: 10.0000 chunk 532 optimal weight: 0.5980 chunk 332 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 43632 Z= 0.230 Angle : 0.489 5.331 59112 Z= 0.260 Chirality : 0.030 0.134 6840 Planarity : 0.003 0.034 7608 Dihedral : 3.833 27.693 6240 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.18 % Allowed : 12.65 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.12), residues: 5640 helix: 2.00 (0.07), residues: 5160 sheet: None (None), residues: 0 loop : -0.28 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 40 TYR 0.017 0.001 TYR P 19 ARG 0.003 0.000 ARG j 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 480 time to evaluate : 5.107 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: 0 36 ASN cc_start: 0.7902 (t0) cc_final: 0.7581 (m-40) REVERT: 1 118 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7984 (ttmt) REVERT: 3 67 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8817 (mm) REVERT: 4 36 ASN cc_start: 0.7880 (m-40) cc_final: 0.7587 (m-40) REVERT: 6 36 ASN cc_start: 0.7670 (t0) cc_final: 0.7292 (m110) REVERT: 7 67 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8832 (mm) REVERT: 8 36 ASN cc_start: 0.8030 (m-40) cc_final: 0.7634 (m-40) REVERT: C 100 MET cc_start: 0.8354 (mpp) cc_final: 0.8048 (mmt) REVERT: D 36 ASN cc_start: 0.7926 (m-40) cc_final: 0.7664 (m-40) REVERT: I 71 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7073 (p0) REVERT: J 36 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7146 (m110) REVERT: K 102 ASP cc_start: 0.7559 (t0) cc_final: 0.7211 (t0) REVERT: N 36 ASN cc_start: 0.7931 (m-40) cc_final: 0.7699 (m-40) REVERT: S 73 SER cc_start: 0.7571 (m) cc_final: 0.7187 (p) REVERT: T 67 ASP cc_start: 0.7980 (t70) cc_final: 0.7710 (t70) REVERT: Y 27 TYR cc_start: 0.8590 (m-10) cc_final: 0.8222 (m-10) REVERT: Z 36 ASN cc_start: 0.7876 (t0) cc_final: 0.7669 (m-40) REVERT: c 71 ASP cc_start: 0.7236 (m-30) cc_final: 0.6847 (m-30) REVERT: d 36 ASN cc_start: 0.7929 (t0) cc_final: 0.7353 (m-40) REVERT: l 2 GLU cc_start: 0.7080 (tt0) cc_final: 0.6732 (tt0) outliers start: 86 outliers final: 61 residues processed: 535 average time/residue: 1.0655 time to fit residues: 935.0874 Evaluate side-chains 525 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 460 time to evaluate : 5.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 LYS Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 71 ASP Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 33 LEU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain P residue 36 ASN Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 36 ASN Chi-restraints excluded: chain h residue 50 GLN Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 1 ASP Chi-restraints excluded: chain k residue 12 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 418 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43632 Z= 0.289 Angle : 0.531 6.619 59112 Z= 0.284 Chirality : 0.031 0.180 6840 Planarity : 0.003 0.036 7608 Dihedral : 3.919 28.382 6240 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.13 % Allowed : 12.98 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.11), residues: 5640 helix: 1.93 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 40 TYR 0.016 0.001 TYR B 19 ARG 0.003 0.000 ARG b 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 479 time to evaluate : 5.174 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: 0 2 GLU cc_start: 0.7390 (tt0) cc_final: 0.7083 (tt0) REVERT: 0 36 ASN cc_start: 0.7935 (t0) cc_final: 0.7534 (m-40) REVERT: 1 118 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8025 (ttmt) REVERT: 3 67 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8812 (mm) REVERT: 4 36 ASN cc_start: 0.7865 (m-40) cc_final: 0.7637 (m-40) REVERT: 6 36 ASN cc_start: 0.7684 (t0) cc_final: 0.7326 (m110) REVERT: 7 67 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (mm) REVERT: 8 36 ASN cc_start: 0.7962 (m-40) cc_final: 0.7598 (m-40) REVERT: C 100 MET cc_start: 0.8366 (mpp) cc_final: 0.8062 (mmt) REVERT: D 36 ASN cc_start: 0.7912 (m-40) cc_final: 0.7658 (m-40) REVERT: F 15 LYS cc_start: 0.8503 (tttp) cc_final: 0.8253 (tttp) REVERT: G 73 SER cc_start: 0.7794 (m) cc_final: 0.7365 (p) REVERT: J 36 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7266 (m110) REVERT: K 102 ASP cc_start: 0.7626 (t0) cc_final: 0.7289 (t0) REVERT: N 36 ASN cc_start: 0.7977 (m-40) cc_final: 0.7721 (m-40) REVERT: S 73 SER cc_start: 0.7643 (m) cc_final: 0.7248 (p) REVERT: T 67 ASP cc_start: 0.8044 (t70) cc_final: 0.7750 (t70) REVERT: Y 27 TYR cc_start: 0.8643 (m-10) cc_final: 0.8263 (m-10) REVERT: Z 36 ASN cc_start: 0.7928 (t0) cc_final: 0.7720 (m-40) REVERT: d 36 ASN cc_start: 0.8025 (t0) cc_final: 0.7434 (m-40) REVERT: k 36 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7881 (m-40) REVERT: l 2 GLU cc_start: 0.7114 (tt0) cc_final: 0.6759 (tt0) outliers start: 84 outliers final: 67 residues processed: 539 average time/residue: 1.0136 time to fit residues: 887.3258 Evaluate side-chains 543 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 472 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 LYS Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 71 ASP Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 33 LEU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain f residue 52 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain h residue 36 ASN Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 50 GLN Chi-restraints excluded: chain i residue 33 LEU Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 1 ASP Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 36 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 2.9990 chunk 509 optimal weight: 0.9980 chunk 465 optimal weight: 3.9990 chunk 495 optimal weight: 50.0000 chunk 298 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 448 optimal weight: 7.9990 chunk 468 optimal weight: 4.9990 chunk 494 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 43632 Z= 0.359 Angle : 0.589 7.050 59112 Z= 0.316 Chirality : 0.033 0.147 6840 Planarity : 0.003 0.038 7608 Dihedral : 4.141 29.478 6240 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.41 % Allowed : 13.03 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.11), residues: 5640 helix: 1.67 (0.07), residues: 5088 sheet: None (None), residues: 0 loop : -0.85 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP a 41 TYR 0.016 0.002 TYR b 19 ARG 0.003 0.000 ARG b 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 482 time to evaluate : 5.162 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: 0 2 GLU cc_start: 0.7332 (tt0) cc_final: 0.7020 (tt0) REVERT: 0 36 ASN cc_start: 0.8036 (t0) cc_final: 0.7493 (m-40) REVERT: 1 118 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8053 (ttmt) REVERT: 3 67 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8843 (mm) REVERT: 4 36 ASN cc_start: 0.7932 (m-40) cc_final: 0.7692 (m-40) REVERT: 6 36 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7459 (m-40) REVERT: 7 67 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8860 (mm) REVERT: 8 36 ASN cc_start: 0.8052 (m-40) cc_final: 0.7670 (m-40) REVERT: C 100 MET cc_start: 0.8388 (mpp) cc_final: 0.8034 (mmt) REVERT: D 36 ASN cc_start: 0.7986 (m-40) cc_final: 0.7722 (m-40) REVERT: F 15 LYS cc_start: 0.8507 (tttp) cc_final: 0.8220 (tttp) REVERT: J 36 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7302 (m110) REVERT: K 102 ASP cc_start: 0.7672 (t0) cc_final: 0.7353 (t0) REVERT: N 36 ASN cc_start: 0.7964 (m-40) cc_final: 0.7696 (m-40) REVERT: Q 27 TYR cc_start: 0.8522 (m-10) cc_final: 0.7723 (m-10) REVERT: T 67 ASP cc_start: 0.8113 (t70) cc_final: 0.7867 (t70) REVERT: W 100 MET cc_start: 0.7593 (mmm) cc_final: 0.7314 (mmt) REVERT: Y 27 TYR cc_start: 0.8658 (m-10) cc_final: 0.8364 (m-10) REVERT: d 36 ASN cc_start: 0.8171 (t0) cc_final: 0.7559 (m-40) REVERT: i 27 TYR cc_start: 0.8501 (m-10) cc_final: 0.8208 (m-10) REVERT: j 67 ASP cc_start: 0.8327 (t0) cc_final: 0.7997 (t0) REVERT: k 36 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7903 (m-40) REVERT: l 2 GLU cc_start: 0.7153 (tt0) cc_final: 0.6826 (tt0) outliers start: 95 outliers final: 74 residues processed: 542 average time/residue: 1.0057 time to fit residues: 887.6227 Evaluate side-chains 548 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 469 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 LYS Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 71 ASP Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 33 LEU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 36 ASN Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 8 residue 15 LYS Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain d residue 52 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain f residue 52 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 50 GLN Chi-restraints excluded: chain i residue 33 LEU Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain k residue 1 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 36 ASN Chi-restraints excluded: chain k residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 0.7980 chunk 524 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 364 optimal weight: 4.9990 chunk 549 optimal weight: 6.9990 chunk 506 optimal weight: 1.9990 chunk 437 optimal weight: 0.9980 chunk 45 optimal weight: 50.0000 chunk 338 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43632 Z= 0.145 Angle : 0.454 6.601 59112 Z= 0.236 Chirality : 0.029 0.128 6840 Planarity : 0.002 0.032 7608 Dihedral : 3.702 26.403 6240 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 13.90 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.12), residues: 5640 helix: 2.24 (0.07), residues: 5136 sheet: None (None), residues: 0 loop : -0.85 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 40 TYR 0.019 0.001 TYR P 19 ARG 0.002 0.000 ARG L 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11280 Ramachandran restraints generated. 5640 Oldfield, 0 Emsley, 5640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 489 time to evaluate : 5.150 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: 0 2 GLU cc_start: 0.7284 (tt0) cc_final: 0.6999 (tt0) REVERT: 0 36 ASN cc_start: 0.7837 (t0) cc_final: 0.7321 (m-40) REVERT: 1 118 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8107 (ttmt) REVERT: 3 67 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8771 (mm) REVERT: 6 36 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7312 (m-40) REVERT: 7 67 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8801 (mm) REVERT: 8 36 ASN cc_start: 0.7998 (m-40) cc_final: 0.7581 (m-40) REVERT: C 100 MET cc_start: 0.8313 (mpp) cc_final: 0.8016 (mmt) REVERT: D 32 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7381 (tpp80) REVERT: D 36 ASN cc_start: 0.7840 (m-40) cc_final: 0.7606 (m-40) REVERT: G 73 SER cc_start: 0.7629 (m) cc_final: 0.7275 (p) REVERT: I 71 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6971 (p0) REVERT: J 36 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7114 (m110) REVERT: K 102 ASP cc_start: 0.7517 (t0) cc_final: 0.7147 (t0) REVERT: W 100 MET cc_start: 0.7541 (mmm) cc_final: 0.7274 (mmt) REVERT: Y 27 TYR cc_start: 0.8414 (m-10) cc_final: 0.8016 (m-10) REVERT: Z 36 ASN cc_start: 0.7623 (m-40) cc_final: 0.7348 (m-40) REVERT: c 71 ASP cc_start: 0.7206 (m-30) cc_final: 0.6813 (m-30) REVERT: d 36 ASN cc_start: 0.7882 (t0) cc_final: 0.7285 (m-40) REVERT: h 36 ASN cc_start: 0.7889 (t0) cc_final: 0.7177 (m-40) REVERT: l 2 GLU cc_start: 0.7111 (tt0) cc_final: 0.6788 (tt0) outliers start: 66 outliers final: 43 residues processed: 535 average time/residue: 1.1041 time to fit residues: 961.0660 Evaluate side-chains 515 residues out of total 4464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 467 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 100 MET Chi-restraints excluded: chain 3 residue 12 LEU Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 71 ASP Chi-restraints excluded: chain 3 residue 100 MET Chi-restraints excluded: chain 5 residue 33 LEU Chi-restraints excluded: chain 5 residue 100 MET Chi-restraints excluded: chain 6 residue 36 ASN Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 71 ASP Chi-restraints excluded: chain 9 residue 12 LEU Chi-restraints excluded: chain 9 residue 100 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 9 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 71 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain f residue 15 LYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain h residue 50 GLN Chi-restraints excluded: chain i residue 33 LEU Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 3.9990 chunk 466 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 403 optimal weight: 50.0000 chunk 64 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 438 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 450 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 80 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.188044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.150301 restraints weight = 204909.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.157558 restraints weight = 105253.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.157575 restraints weight = 54514.456| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43632 Z= 0.131 Angle : 0.439 6.701 59112 Z= 0.226 Chirality : 0.028 0.123 6840 Planarity : 0.002 0.063 7608 Dihedral : 3.469 25.031 6240 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.35 % Allowed : 14.35 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.12), residues: 5640 helix: 2.59 (0.07), residues: 5184 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP T 40 TYR 0.020 0.001 TYR N 19 ARG 0.009 0.000 ARG j 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15616.67 seconds wall clock time: 271 minutes 9.02 seconds (16269.02 seconds total)