Starting phenix.real_space_refine on Fri Feb 6 23:59:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1u_51772/02_2026/9h1u_51772.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 20 7.16 5 S 132 5.16 5 C 18411 2.51 5 N 5012 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29095 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1233 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "E" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1233 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "F" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1233 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "G" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "H" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "I" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 155 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 12} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 158 Classifications: {'peptide': 26} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 72 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 176 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 285 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Classifications: {'peptide': 5} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 160 Classifications: {'peptide': 26} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 13} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 158 Classifications: {'peptide': 26} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 72 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 176 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 285 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Classifications: {'peptide': 5} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 141 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 10} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 158 Classifications: {'peptide': 26} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 72 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 176 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 285 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Classifications: {'peptide': 5} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 155 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 12} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 158 Classifications: {'peptide': 26} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 72 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 176 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 285 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Classifications: {'peptide': 5} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "N" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "O" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "P" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "Q" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "R" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "S" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "T" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "U" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "V" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "W" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "X" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.93, per 1000 atoms: 0.20 Number of scatterers: 29095 At special positions: 0 Unit cell: (127.6, 125.4, 126.5, 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) Fe 20 26.01 S 132 16.00 O 5520 8.00 N 5012 7.00 C 18411 6.00 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 - 3.00 Amino acid : True - 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=4, symmetry=0 Links applied TRANS " UNK I 27 " - " PHE I 26 " " UNK I 32 " - " MET I 31 " " UNK I 38 " - " PHE I 37 " " UNK I 64 " - " LEU I 63 " " UNK I 68 " - " GLY I 67 " " UNK I 81 " - " GLY I 80 " " UNK I 110 " - " GLU I 109 " " UNK I 154 " - " SER I 153 " " UNK J 27 " - " PHE J 26 " " UNK J 32 " - " MET J 31 " " UNK J 38 " - " PHE J 37 " " UNK J 64 " - " LEU J 63 " " UNK J 68 " - " GLY J 67 " " UNK J 81 " - " GLY J 80 " " UNK J 110 " - " GLU J 109 " " UNK J 154 " - " SER J 153 " " UNK K 27 " - " PHE K 26 " " UNK K 32 " - " MET K 31 " " UNK K 38 " - " PHE K 37 " " UNK K 64 " - " LEU K 63 " " UNK K 68 " - " GLY K 67 " " UNK K 81 " - " GLY K 80 " " UNK K 110 " - " GLU K 109 " " UNK K 154 " - " SER K 153 " " UNK L 27 " - " PHE L 26 " " UNK L 32 " - " MET L 31 " " UNK L 38 " - " PHE L 37 " " UNK L 64 " - " LEU L 63 " " UNK L 68 " - " GLY L 67 " " UNK L 81 " - " GLY L 80 " " UNK L 110 " - " GLU L 109 " " UNK L 154 " - " SER L 153 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 863.8 milliseconds 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7072 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 0 sheets defined 96.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 114 through 155 removed outlier: 6.202A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 36 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 82 through 111 Processing helix chain 'B' and resid 113 through 145 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'C' and resid 5 through 35 Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 82 through 111 Processing helix chain 'C' and resid 113 through 145 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'D' and resid 5 through 35 Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 82 through 111 Processing helix chain 'D' and resid 113 through 145 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'E' and resid 6 through 36 Processing helix chain 'E' and resid 37 through 65 Processing helix chain 'E' and resid 82 through 111 Processing helix chain 'E' and resid 114 through 145 Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'F' and resid 6 through 35 Processing helix chain 'F' and resid 37 through 65 Processing helix chain 'F' and resid 82 through 111 Processing helix chain 'F' and resid 113 through 145 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 37 through 65 Processing helix chain 'G' and resid 82 through 111 Processing helix chain 'G' and resid 113 through 145 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'H' and resid 5 through 36 Processing helix chain 'H' and resid 37 through 65 Processing helix chain 'H' and resid 82 through 111 removed outlier: 3.885A pdb=" N ASP H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 145 Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'I' and resid 4 through 36 Processing helix chain 'I' and resid 37 through 65 No H-bonds generated for 'chain 'I' and resid 37 through 65' Processing helix chain 'I' and resid 82 through 111 Processing helix chain 'I' and resid 113 through 130 Processing helix chain 'I' and resid 131 through 145 Processing helix chain 'I' and resid 146 through 156 Processing helix chain 'J' and resid 4 through 35 Processing helix chain 'J' and resid 37 through 65 No H-bonds generated for 'chain 'J' and resid 37 through 65' Processing helix chain 'J' and resid 82 through 111 Processing helix chain 'J' and resid 113 through 130 Processing helix chain 'J' and resid 131 through 145 removed outlier: 4.227A pdb=" N ASP J 143 " --> pdb=" O UNK J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 156 Processing helix chain 'K' and resid 6 through 35 Processing helix chain 'K' and resid 37 through 65 No H-bonds generated for 'chain 'K' and resid 37 through 65' Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'K' and resid 113 through 129 Processing helix chain 'K' and resid 131 through 145 removed outlier: 3.814A pdb=" N ASP K 143 " --> pdb=" O UNK K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 156 Processing helix chain 'L' and resid 4 through 36 Processing helix chain 'L' and resid 37 through 65 No H-bonds generated for 'chain 'L' and resid 37 through 65' Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 130 Processing helix chain 'L' and resid 131 through 145 Processing helix chain 'L' and resid 146 through 156 Processing helix chain 'M' and resid 4 through 36 Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 Processing helix chain 'M' and resid 114 through 130 Processing helix chain 'M' and resid 131 through 146 Processing helix chain 'M' and resid 146 through 156 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 111 Processing helix chain 'N' and resid 113 through 131 removed outlier: 3.502A pdb=" N ARG N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 146 Processing helix chain 'N' and resid 146 through 156 Processing helix chain 'O' and resid 4 through 36 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 Processing helix chain 'O' and resid 113 through 130 removed outlier: 3.584A pdb=" N ARG O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 146 Processing helix chain 'O' and resid 146 through 156 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 Processing helix chain 'P' and resid 82 through 111 Processing helix chain 'P' and resid 113 through 130 Processing helix chain 'P' and resid 131 through 146 Processing helix chain 'P' and resid 146 through 156 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 Processing helix chain 'Q' and resid 82 through 111 Processing helix chain 'Q' and resid 113 through 130 Processing helix chain 'Q' and resid 130 through 146 removed outlier: 3.649A pdb=" N TRP Q 134 " --> pdb=" O ASP Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 156 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 Processing helix chain 'R' and resid 82 through 111 Processing helix chain 'R' and resid 113 through 131 Processing helix chain 'R' and resid 131 through 146 Processing helix chain 'R' and resid 146 through 156 Processing helix chain 'S' and resid 4 through 36 Processing helix chain 'S' and resid 37 through 65 Processing helix chain 'S' and resid 82 through 111 Processing helix chain 'S' and resid 113 through 131 Processing helix chain 'S' and resid 131 through 146 Processing helix chain 'S' and resid 146 through 156 removed outlier: 3.533A pdb=" N GLY S 156 " --> pdb=" O GLN S 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 Processing helix chain 'T' and resid 82 through 111 Processing helix chain 'T' and resid 113 through 131 removed outlier: 3.589A pdb=" N ARG T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 156 removed outlier: 6.332A pdb=" N LEU T 147 " --> pdb=" O ASP T 143 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LYS T 148 " --> pdb=" O LYS T 144 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN T 149 " --> pdb=" O LEU T 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 36 Processing helix chain 'U' and resid 37 through 65 Processing helix chain 'U' and resid 82 through 111 Processing helix chain 'U' and resid 113 through 130 Processing helix chain 'U' and resid 131 through 146 Processing helix chain 'U' and resid 146 through 156 Processing helix chain 'V' and resid 4 through 36 Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 131 Processing helix chain 'V' and resid 131 through 146 Processing helix chain 'V' and resid 146 through 156 Processing helix chain 'W' and resid 4 through 36 Processing helix chain 'W' and resid 37 through 65 Processing helix chain 'W' and resid 82 through 111 Processing helix chain 'W' and resid 113 through 130 Processing helix chain 'W' and resid 130 through 156 removed outlier: 6.211A pdb=" N LEU W 147 " --> pdb=" O ASP W 143 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LYS W 148 " --> pdb=" O LYS W 144 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN W 149 " --> pdb=" O LEU W 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 36 Processing helix chain 'X' and resid 37 through 65 Processing helix chain 'X' and resid 82 through 111 Processing helix chain 'X' and resid 113 through 130 Processing helix chain 'X' and resid 130 through 146 Processing helix chain 'X' and resid 146 through 156 2549 hydrogen bonds defined for protein. 7647 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: 4.99 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 11862 1.39 - 1.57: 17389 1.57 - 1.74: 0 1.74 - 1.91: 232 1.91 - 2.08: 16 Bond restraints: 29499 Sorted by residual: bond pdb=" CB GLN N 138 " pdb=" CG GLN N 138 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CG ASP A 118 " pdb=" OD1 ASP A 118 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.26e+00 bond pdb=" CB MET B 52 " pdb=" CG MET B 52 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CB GLU C 135 " pdb=" CG GLU C 135 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CD GLU A 126 " pdb=" OE1 GLU A 126 " ideal model delta sigma weight residual 1.249 1.231 0.018 1.90e-02 2.77e+03 9.44e-01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 39738 3.14 - 6.28: 151 6.28 - 9.43: 14 9.43 - 12.57: 1 12.57 - 15.71: 3 Bond angle restraints: 39907 Sorted by residual: angle pdb=" C MET A 144 " pdb=" N GLY A 145 " pdb=" CA GLY A 145 " ideal model delta sigma weight residual 121.41 114.75 6.66 1.96e+00 2.60e-01 1.15e+01 angle pdb=" CB MET O 87 " pdb=" CG MET O 87 " pdb=" SD MET O 87 " ideal model delta sigma weight residual 112.70 122.04 -9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" CA GLU A 126 " pdb=" CB GLU A 126 " pdb=" CG GLU A 126 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 angle pdb=" CA GLU G 60 " pdb=" CB GLU G 60 " pdb=" CG GLU G 60 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.06e+00 angle pdb=" CA MET W 87 " pdb=" CB MET W 87 " pdb=" CG MET W 87 " ideal model delta sigma weight residual 114.10 108.17 5.93 2.00e+00 2.50e-01 8.78e+00 ... (remaining 39902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 15188 18.44 - 36.88: 1901 36.88 - 55.31: 601 55.31 - 73.75: 135 73.75 - 92.19: 76 Dihedral angle restraints: 17901 sinusoidal: 6990 harmonic: 10911 Sorted by residual: dihedral pdb=" C1A HEM G 201 " pdb=" C2A HEM G 201 " pdb=" CAA HEM G 201 " pdb=" CBA HEM G 201 " ideal model delta sinusoidal sigma weight residual 180.00 92.21 87.79 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEM B 201 " pdb=" C3D HEM B 201 " pdb=" CAD HEM B 201 " pdb=" CBD HEM B 201 " ideal model delta sinusoidal sigma weight residual -180.00 -94.41 -85.59 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C2D HEM C 201 " pdb=" C3D HEM C 201 " pdb=" CAD HEM C 201 " pdb=" CBD HEM C 201 " ideal model delta sinusoidal sigma weight residual -180.00 -95.28 -84.72 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 17898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2709 0.025 - 0.049: 1216 0.049 - 0.074: 494 0.074 - 0.099: 104 0.099 - 0.123: 41 Chirality restraints: 4564 Sorted by residual: chirality pdb=" CA MET B 31 " pdb=" N MET B 31 " pdb=" C MET B 31 " pdb=" CB MET B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL U 68 " pdb=" N VAL U 68 " pdb=" C VAL U 68 " pdb=" CB VAL U 68 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA PRO T 5 " pdb=" N PRO T 5 " pdb=" C PRO T 5 " pdb=" CB PRO T 5 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 4561 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN U 96 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" CD GLN U 96 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN U 96 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN U 96 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 17 " 0.017 2.00e-02 2.50e+03 1.43e-02 3.07e+00 pdb=" CG HIS A 17 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 17 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 17 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 17 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 17 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 96 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" CD GLN O 96 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN O 96 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN O 96 " 0.009 2.00e-02 2.50e+03 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 185 2.58 - 3.16: 23647 3.16 - 3.74: 52309 3.74 - 4.32: 67446 4.32 - 4.90: 112855 Nonbonded interactions: 256442 Sorted by model distance: nonbonded pdb=" OD1 ASP A 113 " pdb=" OG SER A 116 " model vdw 2.002 3.040 nonbonded pdb=" OH TYR E 25 " pdb=" OE1 GLU E 94 " model vdw 2.031 3.040 nonbonded pdb=" OE2 GLU B 44 " pdb=" OH TYR B 134 " model vdw 2.058 3.040 nonbonded pdb=" OE1 GLU V 51 " pdb="FE FE V 301 " model vdw 2.063 2.260 nonbonded pdb=" OE1 GLU O 18 " pdb="FE FE O 301 " model vdw 2.069 2.260 ... (remaining 256437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 5 through 157) selection = (chain 'C' and resid 5 through 157) selection = (chain 'D' and resid 5 through 157) selection = (chain 'E' and resid 5 through 157) selection = chain 'F' selection = (chain 'G' and resid 5 through 157) selection = (chain 'H' and resid 5 through 157) } ncs_group { reference = (chain 'I' and resid 5 through 158) selection = (chain 'J' and resid 5 through 158) selection = chain 'K' selection = (chain 'L' and resid 5 through 158) } ncs_group { reference = (chain 'M' and resid 1 through 158) selection = (chain 'N' and resid 1 through 158) selection = (chain 'O' and resid 1 through 158) selection = chain 'P' selection = (chain 'Q' and resid 1 through 158) selection = (chain 'R' and resid 1 through 158) selection = chain 'S' selection = (chain 'T' and resid 1 through 158) selection = (chain 'U' and resid 1 through 158) selection = (chain 'V' and resid 1 through 158) selection = (chain 'W' and resid 1 through 158) selection = (chain 'X' and resid 1 through 158) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.546 29535 Z= 0.154 Angle : 0.561 15.710 40003 Z= 0.271 Chirality : 0.033 0.123 4564 Planarity : 0.003 0.052 5164 Dihedral : 19.279 92.191 10733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.52 % Allowed : 26.68 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.14), residues: 3149 helix: 2.95 (0.09), residues: 2693 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 118 TYR 0.020 0.002 TYR N 25 PHE 0.014 0.002 PHE M 64 TRP 0.017 0.001 TRP F 35 HIS 0.012 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00344 (29499) covalent geometry : angle 0.56094 (39907) hydrogen bonds : bond 0.08202 ( 2549) hydrogen bonds : angle 4.78377 ( 7647) Misc. bond : bond 0.40889 ( 4) link_TRANS : bond 0.00092 ( 32) link_TRANS : angle 0.40195 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 638 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: C 137 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: G 51 GLU cc_start: 0.7712 (tp30) cc_final: 0.7455 (tp30) REVERT: N 66 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: O 48 ARG cc_start: 0.7071 (ttp80) cc_final: 0.6628 (ttp80) outliers start: 73 outliers final: 64 residues processed: 699 average time/residue: 0.8005 time to fit residues: 640.6297 Evaluate side-chains 692 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 625 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 115 ASP Chi-restraints excluded: chain T residue 145 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 132 VAL Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 81 SER Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain X residue 38 LYS Chi-restraints excluded: chain X residue 118 ARG Chi-restraints excluded: chain X residue 123 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN B 70 ASN B 72 GLN C 17 HIS C 111 GLN C 137 GLN D 82 ASN D 89 ASN D 98 HIS E 72 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN L 24 GLN M 60 ASN M 122 HIS N 24 GLN N 129 GLN O 129 GLN Q 60 ASN R 96 GLN R 129 GLN R 131 HIS R 149 ASN S 131 HIS S 138 GLN T 96 GLN ** T 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 96 GLN ** U 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 GLN V 96 GLN W 131 HIS W 138 GLN W 149 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129688 restraints weight = 30156.910| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.20 r_work: 0.3327 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.445 29535 Z= 0.135 Angle : 0.502 11.265 40003 Z= 0.245 Chirality : 0.032 0.125 4564 Planarity : 0.003 0.038 5164 Dihedral : 7.424 87.690 4157 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 5.04 % Allowed : 22.58 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.14), residues: 3149 helix: 3.17 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.45 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 118 TYR 0.017 0.002 TYR N 25 PHE 0.011 0.001 PHE N 26 TRP 0.012 0.001 TRP F 35 HIS 0.011 0.001 HIS M 122 Details of bonding type rmsd covalent geometry : bond 0.00293 (29499) covalent geometry : angle 0.50214 (39907) hydrogen bonds : bond 0.04345 ( 2549) hydrogen bonds : angle 3.83585 ( 7647) Misc. bond : bond 0.36121 ( 4) link_TRANS : bond 0.00077 ( 32) link_TRANS : angle 0.27618 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 671 time to evaluate : 1.066 Fit side-chains REVERT: B 122 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 126 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: B 139 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: C 46 LYS cc_start: 0.8443 (mttt) cc_final: 0.8202 (mttt) REVERT: C 47 GLU cc_start: 0.7829 (tt0) cc_final: 0.7390 (tp30) REVERT: C 137 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7639 (mp-120) REVERT: D 60 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: D 61 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7904 (tpm-80) REVERT: D 125 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: G 51 GLU cc_start: 0.7871 (tp30) cc_final: 0.7601 (tp30) REVERT: H 44 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: K 117 ARG cc_start: 0.8652 (ttt-90) cc_final: 0.8411 (ttt90) REVERT: O 48 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6756 (ttp-170) REVERT: R 126 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7858 (mt-10) REVERT: S 157 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: T 12 ASN cc_start: 0.8814 (m-40) cc_final: 0.8413 (m-40) REVERT: T 70 ASP cc_start: 0.7526 (t0) cc_final: 0.7303 (t0) REVERT: T 148 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8381 (mtpp) REVERT: U 147 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7779 (tp) REVERT: W 23 ASP cc_start: 0.7731 (m-30) cc_final: 0.7339 (m-30) REVERT: W 96 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: W 143 ASP cc_start: 0.7501 (t70) cc_final: 0.7043 (m-30) REVERT: X 125 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7733 (tt0) outliers start: 146 outliers final: 51 residues processed: 764 average time/residue: 0.8048 time to fit residues: 703.4810 Evaluate side-chains 697 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 633 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN C 17 HIS C 111 GLN D 82 ASN D 111 GLN E 72 GLN G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 60 ASN M 122 HIS N 24 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN U 149 ASN X 96 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126333 restraints weight = 30378.133| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.20 r_work: 0.3283 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.487 29535 Z= 0.226 Angle : 0.611 14.524 40003 Z= 0.291 Chirality : 0.036 0.124 4564 Planarity : 0.004 0.056 5164 Dihedral : 6.543 89.028 4075 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.97 % Allowed : 22.26 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.14), residues: 3149 helix: 2.87 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 74 TYR 0.020 0.002 TYR N 93 PHE 0.016 0.002 PHE B 26 TRP 0.015 0.001 TRP F 35 HIS 0.011 0.001 HIS M 122 Details of bonding type rmsd covalent geometry : bond 0.00530 (29499) covalent geometry : angle 0.61089 (39907) hydrogen bonds : bond 0.05087 ( 2549) hydrogen bonds : angle 3.96097 ( 7647) Misc. bond : bond 0.40093 ( 4) link_TRANS : bond 0.00232 ( 32) link_TRANS : angle 0.45724 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 680 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 ASP cc_start: 0.8519 (t70) cc_final: 0.8314 (t70) REVERT: B 116 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8511 (p) REVERT: C 47 GLU cc_start: 0.7765 (tt0) cc_final: 0.7531 (tp30) REVERT: C 66 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: C 81 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6631 (pp20) REVERT: C 103 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7470 (ttpp) REVERT: C 137 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7735 (mp-120) REVERT: D 56 ASP cc_start: 0.8344 (t70) cc_final: 0.7837 (t70) REVERT: D 60 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 61 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7907 (tpm-80) REVERT: D 125 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: E 77 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7544 (mp) REVERT: E 113 ASP cc_start: 0.8797 (t0) cc_final: 0.8507 (t0) REVERT: G 30 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7519 (mmp-170) REVERT: G 33 LYS cc_start: 0.8290 (mttp) cc_final: 0.7931 (mttp) REVERT: H 44 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: J 128 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: K 117 ARG cc_start: 0.8717 (ttt-90) cc_final: 0.8471 (ttt90) REVERT: M 87 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: N 112 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7816 (mmt90) REVERT: N 127 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7323 (t) REVERT: O 42 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7478 (mm-30) REVERT: O 48 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6667 (ttp-170) REVERT: O 50 ASP cc_start: 0.7034 (m-30) cc_final: 0.6705 (m-30) REVERT: O 136 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7411 (tp30) REVERT: R 126 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7785 (mt-10) REVERT: S 85 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: S 157 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: T 70 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7316 (t0) REVERT: U 147 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7895 (tp) REVERT: V 107 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8503 (tt) REVERT: V 148 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8278 (mmtm) REVERT: W 96 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: W 152 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: X 125 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7687 (tt0) outliers start: 173 outliers final: 69 residues processed: 780 average time/residue: 0.8097 time to fit residues: 721.9233 Evaluate side-chains 740 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 647 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain J residue 31 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain S residue 85 LYS Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 148 LYS Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 125 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 190 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 270 optimal weight: 0.0050 chunk 119 optimal weight: 3.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN C 17 HIS C 111 GLN D 82 ASN D 89 ASN D 111 GLN E 72 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 60 ASN M 122 HIS N 24 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN U 129 GLN V 96 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127707 restraints weight = 30190.400| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.17 r_work: 0.3302 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.459 29535 Z= 0.184 Angle : 0.561 14.304 40003 Z= 0.269 Chirality : 0.034 0.120 4564 Planarity : 0.003 0.038 5164 Dihedral : 6.463 88.404 4074 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.90 % Allowed : 22.75 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.14), residues: 3149 helix: 2.94 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.56 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 48 TYR 0.019 0.002 TYR N 150 PHE 0.013 0.002 PHE G 26 TRP 0.009 0.001 TRP F 35 HIS 0.012 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00424 (29499) covalent geometry : angle 0.56153 (39907) hydrogen bonds : bond 0.04795 ( 2549) hydrogen bonds : angle 3.86995 ( 7647) Misc. bond : bond 0.38240 ( 4) link_TRANS : bond 0.00157 ( 32) link_TRANS : angle 0.37163 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 672 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7228 (p) REVERT: B 113 ASP cc_start: 0.8475 (t70) cc_final: 0.8240 (t70) REVERT: B 126 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: C 47 GLU cc_start: 0.7777 (tt0) cc_final: 0.7462 (mm-30) REVERT: C 66 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: C 81 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6612 (pp20) REVERT: C 103 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7437 (ttpp) REVERT: C 137 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7785 (mp-120) REVERT: D 60 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: D 61 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7851 (tpm-80) REVERT: D 125 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: E 77 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7577 (mp) REVERT: E 94 GLU cc_start: 0.8023 (tp30) cc_final: 0.7453 (tp30) REVERT: E 113 ASP cc_start: 0.8827 (t0) cc_final: 0.8562 (t0) REVERT: G 30 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7492 (mmp-170) REVERT: G 51 GLU cc_start: 0.7823 (tp30) cc_final: 0.7589 (tp30) REVERT: H 44 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: J 128 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: K 94 GLU cc_start: 0.8416 (tp30) cc_final: 0.8203 (tp30) REVERT: K 117 ARG cc_start: 0.8719 (ttt-90) cc_final: 0.8450 (ttt90) REVERT: M 60 ASN cc_start: 0.8247 (m-40) cc_final: 0.7813 (m110) REVERT: M 100 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: M 102 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.8014 (mmmt) REVERT: N 30 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7809 (mmt90) REVERT: N 112 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7729 (mmt90) REVERT: N 127 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7313 (t) REVERT: O 42 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7446 (mm-30) REVERT: O 48 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6739 (ttp80) REVERT: O 50 ASP cc_start: 0.6800 (m-30) cc_final: 0.6393 (m-30) REVERT: O 136 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7350 (tp30) REVERT: R 126 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7805 (mt-10) REVERT: S 157 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: T 53 ASP cc_start: 0.7420 (m-30) cc_final: 0.7037 (m-30) REVERT: U 147 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7860 (tp) REVERT: W 96 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: W 152 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: X 125 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7706 (tt0) outliers start: 171 outliers final: 72 residues processed: 773 average time/residue: 0.8061 time to fit residues: 712.9376 Evaluate side-chains 751 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 656 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 145 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 111 GLN D 82 ASN D 89 ASN D 98 HIS D 111 GLN E 72 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS M 131 HIS N 24 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126301 restraints weight = 30288.886| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.19 r_work: 0.3283 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.497 29535 Z= 0.218 Angle : 0.604 15.419 40003 Z= 0.289 Chirality : 0.036 0.123 4564 Planarity : 0.004 0.038 5164 Dihedral : 6.498 87.221 4070 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 6.18 % Allowed : 23.13 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.14), residues: 3149 helix: 2.79 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 48 TYR 0.021 0.002 TYR N 150 PHE 0.016 0.002 PHE N 26 TRP 0.009 0.001 TRP F 35 HIS 0.013 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00509 (29499) covalent geometry : angle 0.60465 (39907) hydrogen bonds : bond 0.05060 ( 2549) hydrogen bonds : angle 3.93718 ( 7647) Misc. bond : bond 0.39890 ( 4) link_TRANS : bond 0.00210 ( 32) link_TRANS : angle 0.44349 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 687 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7203 (p) REVERT: B 126 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: B 157 LEU cc_start: 0.7623 (tp) cc_final: 0.7280 (mt) REVERT: C 47 GLU cc_start: 0.7796 (tt0) cc_final: 0.7555 (tp30) REVERT: C 52 MET cc_start: 0.7829 (mtt) cc_final: 0.7568 (mtt) REVERT: C 66 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: C 81 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6624 (pp20) REVERT: C 103 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7433 (ttpp) REVERT: C 137 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7787 (mp-120) REVERT: D 60 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: D 61 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7843 (tpm-80) REVERT: D 125 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: E 77 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7576 (mp) REVERT: E 94 GLU cc_start: 0.8059 (tp30) cc_final: 0.7559 (tp30) REVERT: E 113 ASP cc_start: 0.8950 (t0) cc_final: 0.8724 (t0) REVERT: G 30 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7610 (mmp-170) REVERT: G 51 GLU cc_start: 0.7924 (tp30) cc_final: 0.7715 (tp30) REVERT: G 131 MET cc_start: 0.8074 (ttp) cc_final: 0.7866 (ttm) REVERT: H 44 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: J 128 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: K 117 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.8468 (ttt90) REVERT: M 100 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: M 102 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (mmmt) REVERT: N 30 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7792 (mmt90) REVERT: N 112 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7840 (mmt90) REVERT: N 127 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7284 (t) REVERT: O 42 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7333 (mt-10) REVERT: O 48 ARG cc_start: 0.7220 (ttp80) cc_final: 0.6778 (ttp80) REVERT: O 50 ASP cc_start: 0.6788 (m-30) cc_final: 0.6355 (m-30) REVERT: O 136 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7338 (tp30) REVERT: R 123 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8054 (mp) REVERT: R 126 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7687 (mt-10) REVERT: S 157 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: T 53 ASP cc_start: 0.7401 (m-30) cc_final: 0.7008 (m-30) REVERT: T 70 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7314 (t0) REVERT: U 128 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: U 147 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7817 (tp) REVERT: V 18 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: V 107 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8496 (tt) REVERT: V 148 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8227 (mmtm) REVERT: W 96 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: W 152 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: X 125 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: X 130 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) outliers start: 179 outliers final: 76 residues processed: 791 average time/residue: 0.7997 time to fit residues: 724.2852 Evaluate side-chains 770 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 665 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain J residue 31 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 70 ASP Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 148 LYS Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 125 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 104 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 111 GLN D 82 ASN D 89 ASN D 111 GLN E 72 GLN G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS N 24 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127759 restraints weight = 30087.271| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.19 r_work: 0.3301 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.483 29535 Z= 0.166 Angle : 0.553 15.155 40003 Z= 0.265 Chirality : 0.033 0.121 4564 Planarity : 0.003 0.035 5164 Dihedral : 6.361 88.569 4070 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.25 % Allowed : 24.23 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.14), residues: 3149 helix: 2.96 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.56 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 48 TYR 0.023 0.002 TYR N 150 PHE 0.013 0.002 PHE H 26 TRP 0.007 0.001 TRP W 134 HIS 0.012 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00377 (29499) covalent geometry : angle 0.55382 (39907) hydrogen bonds : bond 0.04665 ( 2549) hydrogen bonds : angle 3.82969 ( 7647) Misc. bond : bond 0.39454 ( 4) link_TRANS : bond 0.00124 ( 32) link_TRANS : angle 0.34103 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 681 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: B 122 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: B 126 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: B 157 LEU cc_start: 0.7519 (tp) cc_final: 0.7203 (mt) REVERT: C 47 GLU cc_start: 0.7696 (tt0) cc_final: 0.7373 (mm-30) REVERT: C 66 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: C 81 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: C 103 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7410 (ttpp) REVERT: C 137 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7758 (mp-120) REVERT: D 56 ASP cc_start: 0.8333 (t70) cc_final: 0.7705 (t70) REVERT: D 60 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: D 61 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7850 (tpm-80) REVERT: D 125 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: E 77 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7589 (mp) REVERT: E 94 GLU cc_start: 0.8072 (tp30) cc_final: 0.7532 (tp30) REVERT: E 113 ASP cc_start: 0.8985 (t0) cc_final: 0.8757 (t0) REVERT: G 30 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7580 (mmp-170) REVERT: G 51 GLU cc_start: 0.7903 (tp30) cc_final: 0.7654 (tp30) REVERT: H 44 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: H 90 ASP cc_start: 0.8661 (m-30) cc_final: 0.8432 (m-30) REVERT: H 125 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: J 128 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: K 117 ARG cc_start: 0.8701 (ttt-90) cc_final: 0.8444 (ttt90) REVERT: M 60 ASN cc_start: 0.8201 (m-40) cc_final: 0.7783 (m110) REVERT: M 100 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: M 102 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8008 (mmmt) REVERT: N 30 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (mmt90) REVERT: N 112 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7816 (mmt90) REVERT: N 127 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7188 (t) REVERT: O 42 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7453 (mm-30) REVERT: O 48 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6812 (ttp80) REVERT: O 50 ASP cc_start: 0.6662 (m-30) cc_final: 0.6185 (m-30) REVERT: O 136 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7311 (tp30) REVERT: P 74 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6701 (tpp80) REVERT: R 23 ASP cc_start: 0.7265 (m-30) cc_final: 0.6855 (m-30) REVERT: R 123 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8042 (mp) REVERT: R 126 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7723 (mt-10) REVERT: S 157 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: T 53 ASP cc_start: 0.7399 (m-30) cc_final: 0.6999 (m-30) REVERT: U 147 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7847 (tp) REVERT: V 18 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7317 (mt-10) REVERT: V 148 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8222 (mmtm) REVERT: W 31 MET cc_start: 0.8252 (mtp) cc_final: 0.8002 (mtp) REVERT: W 96 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: W 152 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: X 125 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: X 128 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7647 (mt-10) outliers start: 152 outliers final: 68 residues processed: 779 average time/residue: 0.7885 time to fit residues: 703.8179 Evaluate side-chains 756 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 660 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ARG Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 148 LYS Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 125 GLU Chi-restraints excluded: chain X residue 128 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 53 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 111 GLN D 38 ASN D 82 ASN D 111 GLN E 72 GLN G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS N 24 GLN O 96 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN V 96 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127384 restraints weight = 30239.146| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.17 r_work: 0.3308 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.534 29535 Z= 0.192 Angle : 0.586 15.563 40003 Z= 0.279 Chirality : 0.035 0.125 4564 Planarity : 0.003 0.036 5164 Dihedral : 6.288 89.803 4065 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 5.59 % Allowed : 24.40 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.14), residues: 3149 helix: 2.87 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 48 TYR 0.026 0.002 TYR N 150 PHE 0.015 0.002 PHE N 26 TRP 0.007 0.001 TRP W 134 HIS 0.013 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00444 (29499) covalent geometry : angle 0.58595 (39907) hydrogen bonds : bond 0.04840 ( 2549) hydrogen bonds : angle 3.87701 ( 7647) Misc. bond : bond 0.39924 ( 4) link_TRANS : bond 0.00163 ( 32) link_TRANS : angle 0.39113 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 672 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 122 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: B 126 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: B 157 LEU cc_start: 0.7597 (tp) cc_final: 0.7293 (mt) REVERT: C 47 GLU cc_start: 0.7741 (tt0) cc_final: 0.7442 (mm-30) REVERT: C 52 MET cc_start: 0.7909 (mtt) cc_final: 0.7592 (mtt) REVERT: C 66 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: C 81 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: C 103 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7458 (ttpp) REVERT: C 137 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7769 (mp-120) REVERT: D 32 MET cc_start: 0.8051 (mtt) cc_final: 0.7831 (mtm) REVERT: D 60 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: D 61 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7830 (tpm-80) REVERT: D 125 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: E 77 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7559 (mp) REVERT: E 113 ASP cc_start: 0.8975 (t0) cc_final: 0.8748 (t0) REVERT: G 27 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8205 (tp) REVERT: G 30 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7628 (mmp-170) REVERT: G 51 GLU cc_start: 0.7921 (tp30) cc_final: 0.7673 (tp30) REVERT: H 44 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: J 128 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: K 117 ARG cc_start: 0.8723 (ttt-90) cc_final: 0.8452 (ttt90) REVERT: M 60 ASN cc_start: 0.8238 (m-40) cc_final: 0.7806 (m110) REVERT: M 87 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: M 100 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: N 30 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7753 (mmt90) REVERT: N 112 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7810 (mmt90) REVERT: N 127 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7241 (t) REVERT: O 42 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7432 (mm-30) REVERT: O 50 ASP cc_start: 0.6759 (m-30) cc_final: 0.6281 (m-30) REVERT: P 74 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6737 (tpp80) REVERT: P 117 ARG cc_start: 0.8450 (tmt170) cc_final: 0.8215 (tmt170) REVERT: R 23 ASP cc_start: 0.7267 (m-30) cc_final: 0.6849 (m-30) REVERT: R 123 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8098 (mp) REVERT: R 126 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7734 (mt-10) REVERT: S 157 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: T 53 ASP cc_start: 0.7417 (m-30) cc_final: 0.7016 (m-30) REVERT: U 128 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: U 147 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7861 (tp) REVERT: V 18 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: V 148 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8237 (mmtm) REVERT: W 96 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: W 152 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: X 125 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: X 128 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7654 (mt-10) outliers start: 162 outliers final: 84 residues processed: 769 average time/residue: 0.7715 time to fit residues: 679.4577 Evaluate side-chains 766 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 652 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 31 MET Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ARG Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 148 LYS Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 125 GLU Chi-restraints excluded: chain X residue 128 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 12 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 111 GLN D 38 ASN D 89 ASN D 111 GLN E 72 GLN G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS O 96 GLN Q 60 ASN R 96 GLN R 129 GLN T 96 GLN U 96 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128486 restraints weight = 30145.177| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.19 r_work: 0.3317 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.537 29535 Z= 0.149 Angle : 0.549 15.095 40003 Z= 0.263 Chirality : 0.033 0.123 4564 Planarity : 0.003 0.033 5164 Dihedral : 6.118 88.889 4062 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.63 % Allowed : 25.65 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.73 (0.14), residues: 3149 helix: 3.03 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.53 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 48 TYR 0.030 0.002 TYR N 150 PHE 0.015 0.002 PHE O 64 TRP 0.007 0.001 TRP T 134 HIS 0.012 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00334 (29499) covalent geometry : angle 0.54931 (39907) hydrogen bonds : bond 0.04497 ( 2549) hydrogen bonds : angle 3.78660 ( 7647) Misc. bond : bond 0.39968 ( 4) link_TRANS : bond 0.00098 ( 32) link_TRANS : angle 0.29001 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 665 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7187 (mp0) REVERT: A 144 MET cc_start: 0.8728 (ptp) cc_final: 0.8489 (ptp) REVERT: B 122 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: B 126 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: C 47 GLU cc_start: 0.7652 (tt0) cc_final: 0.7431 (tp30) REVERT: C 52 MET cc_start: 0.7878 (mtt) cc_final: 0.7615 (mtt) REVERT: C 66 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: C 68 LEU cc_start: 0.8464 (mp) cc_final: 0.8256 (mm) REVERT: C 81 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: C 103 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7399 (ttpp) REVERT: C 137 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7766 (mp-120) REVERT: D 56 ASP cc_start: 0.8346 (t70) cc_final: 0.7755 (t70) REVERT: D 60 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 125 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: D 129 GLU cc_start: 0.5960 (pp20) cc_final: 0.5744 (pp20) REVERT: E 77 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7577 (mp) REVERT: E 113 ASP cc_start: 0.8984 (t0) cc_final: 0.8746 (t0) REVERT: G 27 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8164 (tp) REVERT: G 30 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7563 (mmp-170) REVERT: H 44 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: J 128 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: K 94 GLU cc_start: 0.8313 (tp30) cc_final: 0.7598 (mm-30) REVERT: K 117 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8428 (ttt90) REVERT: M 60 ASN cc_start: 0.8205 (m-40) cc_final: 0.7782 (m110) REVERT: M 100 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: N 30 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7727 (mmt90) REVERT: N 112 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7844 (mmt90) REVERT: N 127 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7247 (t) REVERT: O 42 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7409 (mm-30) REVERT: O 45 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: O 50 ASP cc_start: 0.6774 (m-30) cc_final: 0.6296 (m-30) REVERT: P 117 ARG cc_start: 0.8433 (tmt170) cc_final: 0.8172 (tmt170) REVERT: R 23 ASP cc_start: 0.7257 (m-30) cc_final: 0.6865 (m-30) REVERT: R 123 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8083 (mp) REVERT: R 126 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7629 (mt-10) REVERT: S 157 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: T 53 ASP cc_start: 0.7395 (m-30) cc_final: 0.6991 (m-30) REVERT: T 109 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: U 128 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: U 147 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7873 (tp) REVERT: V 18 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: V 148 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: W 96 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: W 152 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: X 125 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: X 128 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7659 (mt-10) outliers start: 134 outliers final: 67 residues processed: 751 average time/residue: 0.7522 time to fit residues: 648.6115 Evaluate side-chains 743 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 647 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 112 ARG Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 148 LYS Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 148 LYS Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 125 GLU Chi-restraints excluded: chain X residue 128 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 3 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 156 optimal weight: 0.0170 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 111 GLN C 17 HIS C 111 GLN D 38 ASN D 82 ASN D 89 ASN D 98 HIS D 111 GLN E 72 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS O 96 GLN Q 60 ASN R 96 GLN R 129 GLN S 96 GLN U 96 GLN V 96 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130571 restraints weight = 30072.947| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.20 r_work: 0.3338 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.525 29535 Z= 0.124 Angle : 0.520 14.083 40003 Z= 0.251 Chirality : 0.032 0.133 4564 Planarity : 0.003 0.031 5164 Dihedral : 5.898 88.181 4058 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.56 % Allowed : 26.75 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.14), residues: 3149 helix: 3.19 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.49 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 118 TYR 0.025 0.002 TYR N 150 PHE 0.017 0.002 PHE N 26 TRP 0.009 0.001 TRP H 35 HIS 0.012 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00268 (29499) covalent geometry : angle 0.52095 (39907) hydrogen bonds : bond 0.04161 ( 2549) hydrogen bonds : angle 3.69604 ( 7647) Misc. bond : bond 0.39364 ( 4) link_TRANS : bond 0.00053 ( 32) link_TRANS : angle 0.21888 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 674 time to evaluate : 1.356 Fit side-chains REVERT: A 110 LYS cc_start: 0.7314 (mptt) cc_final: 0.6712 (ptmt) REVERT: A 126 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7179 (mp0) REVERT: A 142 LYS cc_start: 0.8201 (tppt) cc_final: 0.7955 (ttmt) REVERT: A 144 MET cc_start: 0.8640 (ptp) cc_final: 0.8404 (ptp) REVERT: B 85 GLU cc_start: 0.7206 (tp30) cc_final: 0.6846 (mt-10) REVERT: B 122 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: B 126 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: B 136 THR cc_start: 0.7507 (m) cc_final: 0.7229 (m) REVERT: B 139 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 47 GLU cc_start: 0.7651 (tt0) cc_final: 0.7410 (tp30) REVERT: C 51 GLU cc_start: 0.7531 (tp30) cc_final: 0.7314 (mm-30) REVERT: C 52 MET cc_start: 0.7825 (mtt) cc_final: 0.7615 (mtt) REVERT: C 66 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: C 68 LEU cc_start: 0.8442 (mp) cc_final: 0.8230 (mm) REVERT: C 103 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7330 (ttpp) REVERT: C 137 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7735 (mp-120) REVERT: D 46 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7222 (mtmp) REVERT: D 56 ASP cc_start: 0.8303 (t70) cc_final: 0.7654 (t70) REVERT: D 60 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: D 110 LYS cc_start: 0.7326 (mmtm) cc_final: 0.6967 (mmtp) REVERT: D 125 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: D 128 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: D 129 GLU cc_start: 0.5691 (pp20) cc_final: 0.5454 (pp20) REVERT: E 113 ASP cc_start: 0.8989 (t0) cc_final: 0.8745 (t0) REVERT: F 88 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7726 (pttp) REVERT: G 33 LYS cc_start: 0.8206 (mttp) cc_final: 0.7987 (mttp) REVERT: G 72 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7437 (tp-100) REVERT: G 131 MET cc_start: 0.8050 (ttp) cc_final: 0.7817 (ttm) REVERT: H 44 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: J 128 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: K 94 GLU cc_start: 0.8282 (tp30) cc_final: 0.7619 (mm-30) REVERT: K 117 ARG cc_start: 0.8635 (ttt-90) cc_final: 0.8339 (ttt90) REVERT: M 60 ASN cc_start: 0.8169 (m-40) cc_final: 0.7727 (m110) REVERT: M 100 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: M 138 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8033 (mm-40) REVERT: N 30 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7680 (mmt90) REVERT: N 102 LYS cc_start: 0.8448 (mttt) cc_final: 0.8205 (mttt) REVERT: O 42 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7555 (mm-30) REVERT: P 117 ARG cc_start: 0.8286 (tmt170) cc_final: 0.7987 (tmt170) REVERT: R 23 ASP cc_start: 0.7222 (m-30) cc_final: 0.6921 (m-30) REVERT: R 123 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8045 (mp) REVERT: R 126 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7604 (mt-10) REVERT: S 31 MET cc_start: 0.8917 (mtp) cc_final: 0.8684 (mtp) REVERT: S 157 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: T 118 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7187 (ttp-110) REVERT: U 128 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: U 147 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7847 (tp) REVERT: V 18 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7323 (mt-10) REVERT: W 96 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: W 109 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5849 (mm-30) REVERT: W 152 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: X 125 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: X 128 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7694 (mt-10) outliers start: 103 outliers final: 53 residues processed: 740 average time/residue: 0.7811 time to fit residues: 663.2529 Evaluate side-chains 722 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 649 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain W residue 152 GLN Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 125 GLU Chi-restraints excluded: chain X residue 128 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.0670 chunk 116 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS D 82 ASN D 89 ASN D 111 GLN E 72 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 18 GLN H 38 ASN M 122 HIS O 96 GLN Q 60 ASN R 96 GLN R 129 GLN S 96 GLN T 96 GLN U 96 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129565 restraints weight = 29960.604| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.19 r_work: 0.3331 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.545 29535 Z= 0.152 Angle : 0.557 14.926 40003 Z= 0.268 Chirality : 0.033 0.135 4564 Planarity : 0.003 0.053 5164 Dihedral : 5.818 88.141 4050 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.11 % Allowed : 27.86 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.86 (0.14), residues: 3149 helix: 3.12 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 118 TYR 0.039 0.002 TYR N 150 PHE 0.015 0.002 PHE U 64 TRP 0.006 0.001 TRP W 134 HIS 0.019 0.001 HIS H 17 Details of bonding type rmsd covalent geometry : bond 0.00343 (29499) covalent geometry : angle 0.55702 (39907) hydrogen bonds : bond 0.04378 ( 2549) hydrogen bonds : angle 3.75771 ( 7647) Misc. bond : bond 0.40811 ( 4) link_TRANS : bond 0.00103 ( 32) link_TRANS : angle 0.28573 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6298 Ramachandran restraints generated. 3149 Oldfield, 0 Emsley, 3149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 655 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7174 (mptt) cc_final: 0.6580 (ptmt) REVERT: A 126 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7186 (mp0) REVERT: B 122 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: B 126 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 136 THR cc_start: 0.7516 (m) cc_final: 0.7237 (m) REVERT: B 139 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7484 (mm-30) REVERT: C 47 GLU cc_start: 0.7632 (tt0) cc_final: 0.7414 (tp30) REVERT: C 51 GLU cc_start: 0.7498 (tp30) cc_final: 0.7262 (mm-30) REVERT: C 66 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: C 68 LEU cc_start: 0.8442 (mp) cc_final: 0.8229 (mm) REVERT: C 103 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7406 (ttpp) REVERT: C 137 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7757 (mp-120) REVERT: D 46 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7174 (mtmp) REVERT: D 60 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 110 LYS cc_start: 0.7355 (mmtm) cc_final: 0.6963 (mmtp) REVERT: D 125 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: D 128 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: D 129 GLU cc_start: 0.5968 (pp20) cc_final: 0.5737 (pp20) REVERT: E 113 ASP cc_start: 0.8985 (t0) cc_final: 0.8761 (t0) REVERT: F 88 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7762 (pttp) REVERT: G 33 LYS cc_start: 0.8226 (mttp) cc_final: 0.8019 (mttp) REVERT: G 72 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7414 (tp-100) REVERT: G 131 MET cc_start: 0.8041 (ttp) cc_final: 0.7812 (ttm) REVERT: H 44 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: J 128 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: K 94 GLU cc_start: 0.8261 (tp30) cc_final: 0.7946 (mm-30) REVERT: K 117 ARG cc_start: 0.8630 (ttt-90) cc_final: 0.8323 (ttt90) REVERT: M 60 ASN cc_start: 0.8177 (m-40) cc_final: 0.7708 (m110) REVERT: M 100 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: N 30 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7678 (mmt90) REVERT: N 102 LYS cc_start: 0.8444 (mttt) cc_final: 0.8205 (mttt) REVERT: O 42 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7558 (mm-30) REVERT: O 50 ASP cc_start: 0.6851 (m-30) cc_final: 0.6443 (m-30) REVERT: P 117 ARG cc_start: 0.8348 (tmt170) cc_final: 0.8043 (tmt170) REVERT: R 23 ASP cc_start: 0.7301 (m-30) cc_final: 0.6963 (m-30) REVERT: R 123 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8073 (mp) REVERT: R 126 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7677 (mt-10) REVERT: S 157 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: T 125 GLU cc_start: 0.7485 (tt0) cc_final: 0.7108 (tt0) REVERT: U 128 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: U 147 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7884 (tp) REVERT: V 18 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: W 96 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: W 109 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5876 (mm-30) REVERT: X 125 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: X 128 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7757 (tt0) outliers start: 90 outliers final: 57 residues processed: 708 average time/residue: 0.8066 time to fit residues: 653.0556 Evaluate side-chains 719 residues out of total 2897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 642 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 ARG Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 96 GLN Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 125 GLU Chi-restraints excluded: chain X residue 128 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 0.0770 chunk 236 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS D 111 GLN G 18 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 70 ASN H 38 ASN M 122 HIS O 96 GLN Q 60 ASN R 96 GLN R 129 GLN S 96 GLN T 96 GLN U 96 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129666 restraints weight = 30247.668| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.20 r_work: 0.3328 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.542 29535 Z= 0.145 Angle : 0.554 17.480 40003 Z= 0.266 Chirality : 0.033 0.145 4564 Planarity : 0.003 0.048 5164 Dihedral : 5.805 87.937 4050 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.62 % Allowed : 27.58 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.14), residues: 3149 helix: 3.12 (0.09), residues: 2705 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 118 TYR 0.036 0.002 TYR N 150 PHE 0.014 0.002 PHE G 26 TRP 0.006 0.001 TRP T 134 HIS 0.016 0.001 HIS H 17 Details of bonding type rmsd covalent geometry : bond 0.00325 (29499) covalent geometry : angle 0.55476 (39907) hydrogen bonds : bond 0.04355 ( 2549) hydrogen bonds : angle 3.74389 ( 7647) Misc. bond : bond 0.40192 ( 4) link_TRANS : bond 0.00093 ( 32) link_TRANS : angle 0.28258 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12083.56 seconds wall clock time: 206 minutes 14.43 seconds (12374.43 seconds total)