Starting phenix.real_space_refine on Tue Jun 24 23:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.map" model { file = "/net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z81_39835/06_2025/8z81_39835.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 72 5.21 5 S 63 5.16 5 C 20916 2.51 5 N 3645 2.21 5 O 4617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29349 Number of models: 1 Model: "" Number of chains: 108 Chain: "A" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "C" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "E" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "F" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "G" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "H" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "I" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "K" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "M" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Q" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "T" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "U" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "W" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "4" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "5" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "6" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "7" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "8" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "9" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "0" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "a" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "c" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "e" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "g" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "i" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "k" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "m" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "o" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "q" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "T" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "X" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "2" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'BCL': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "0" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 225 Unusual residues: {'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 225 Unusual residues: {'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 225 Unusual residues: {'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "j" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "p" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 269 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.71, per 1000 atoms: 0.60 Number of scatterers: 29349 At special positions: 0 Unit cell: (136.94, 137.76, 78.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 36 15.00 Mg 72 11.99 O 4617 8.00 N 3645 7.00 C 20916 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=72, symmetry=0 Number of additional bonds: simple=72, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.520A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 35 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'C' and resid 1 through 7 Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.766A pdb=" N VAL C 15 " --> pdb=" O ARG C 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 44 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.502A pdb=" N LEU E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 35 Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'G' and resid 1 through 7 Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.760A pdb=" N VAL G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 44 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 9 through 35 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 1 through 7 Processing helix chain 'K' and resid 9 through 35 removed outlier: 3.782A pdb=" N VAL K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 44 Processing helix chain 'M' and resid 3 through 8 removed outlier: 3.507A pdb=" N LEU M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 35 Processing helix chain 'N' and resid 11 through 44 Processing helix chain 'O' and resid 1 through 7 Processing helix chain 'O' and resid 9 through 34 removed outlier: 3.761A pdb=" N VAL O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 3 through 8 Processing helix chain 'Q' and resid 9 through 35 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 1 through 7 Processing helix chain 'S' and resid 9 through 35 removed outlier: 3.824A pdb=" N VAL S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'V' and resid 11 through 44 Processing helix chain 'W' and resid 1 through 7 Processing helix chain 'W' and resid 9 through 35 removed outlier: 3.781A pdb=" N VAL W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 44 Processing helix chain 'Y' and resid 3 through 8 Processing helix chain 'Y' and resid 9 through 35 Processing helix chain 'Z' and resid 11 through 44 Processing helix chain '1' and resid 1 through 7 Processing helix chain '1' and resid 9 through 35 removed outlier: 3.814A pdb=" N VAL 1 15 " --> pdb=" O ARG 1 11 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 44 Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 9 through 35 Processing helix chain '4' and resid 11 through 44 Processing helix chain '5' and resid 1 through 7 Processing helix chain '5' and resid 9 through 35 removed outlier: 3.798A pdb=" N VAL 5 15 " --> pdb=" O ARG 5 11 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 3 through 8 Processing helix chain '7' and resid 9 through 35 Processing helix chain '8' and resid 11 through 44 Processing helix chain '9' and resid 1 through 7 Processing helix chain '9' and resid 9 through 34 removed outlier: 3.823A pdb=" N VAL 9 15 " --> pdb=" O ARG 9 11 " (cutoff:3.500A) Processing helix chain '0' and resid 11 through 44 Processing helix chain 'a' and resid 3 through 9 removed outlier: 3.639A pdb=" N TRP a 7 " --> pdb=" O ALA a 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL a 9 " --> pdb=" O ILE a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 36 Proline residue: a 17 - end of helix Processing helix chain 'a' and resid 39 through 47 Processing helix chain 'b' and resid 22 through 55 Processing helix chain 'c' and resid 3 through 9 removed outlier: 3.604A pdb=" N TRP c 7 " --> pdb=" O ALA c 4 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL c 9 " --> pdb=" O ILE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 36 Proline residue: c 17 - end of helix Processing helix chain 'c' and resid 39 through 47 Processing helix chain 'd' and resid 22 through 55 Processing helix chain 'e' and resid 5 through 10 removed outlier: 4.054A pdb=" N VAL e 9 " --> pdb=" O ARG e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 36 Proline residue: e 17 - end of helix Processing helix chain 'e' and resid 39 through 47 Processing helix chain 'f' and resid 22 through 55 Processing helix chain 'g' and resid 5 through 10 removed outlier: 4.035A pdb=" N VAL g 9 " --> pdb=" O ARG g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 36 Proline residue: g 17 - end of helix Processing helix chain 'g' and resid 39 through 47 Processing helix chain 'h' and resid 22 through 55 Processing helix chain 'i' and resid 3 through 9 removed outlier: 3.650A pdb=" N TRP i 7 " --> pdb=" O ALA i 4 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL i 9 " --> pdb=" O ILE i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 36 Proline residue: i 17 - end of helix Processing helix chain 'i' and resid 39 through 47 Processing helix chain 'j' and resid 22 through 55 Processing helix chain 'k' and resid 5 through 10 removed outlier: 4.010A pdb=" N VAL k 9 " --> pdb=" O ARG k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 36 Proline residue: k 17 - end of helix Processing helix chain 'k' and resid 39 through 47 Processing helix chain 'l' and resid 22 through 55 Processing helix chain 'm' and resid 3 through 9 removed outlier: 3.604A pdb=" N TRP m 7 " --> pdb=" O ALA m 4 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL m 9 " --> pdb=" O ILE m 6 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 36 Proline residue: m 17 - end of helix Processing helix chain 'm' and resid 39 through 47 Processing helix chain 'n' and resid 22 through 55 Processing helix chain 'o' and resid 3 through 9 removed outlier: 3.612A pdb=" N TRP o 7 " --> pdb=" O ALA o 4 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL o 9 " --> pdb=" O ILE o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 36 Proline residue: o 17 - end of helix Processing helix chain 'o' and resid 39 through 47 Processing helix chain 'p' and resid 22 through 55 Processing helix chain 'q' and resid 5 through 10 removed outlier: 4.084A pdb=" N VAL q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 36 Proline residue: q 17 - end of helix Processing helix chain 'q' and resid 39 through 47 Processing helix chain 'r' and resid 22 through 55 1494 hydrogen bonds defined for protein. 4344 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: 8.98 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 9178 1.38 - 1.55: 20953 1.55 - 1.71: 91 1.71 - 1.88: 126 1.88 - 2.05: 288 Bond restraints: 30636 Sorted by residual: bond pdb=" NA BCL S 101 " pdb="MG BCL S 101 " ideal model delta sigma weight residual 2.170 1.996 0.174 2.40e-02 1.74e+03 5.28e+01 bond pdb=" NA BCL 5 101 " pdb="MG BCL 5 101 " ideal model delta sigma weight residual 2.170 1.996 0.174 2.40e-02 1.74e+03 5.23e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.22e+01 bond pdb=" NA BCL 1 101 " pdb="MG BCL 1 101 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.21e+01 bond pdb=" NA BCL C 101 " pdb="MG BCL C 101 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.17e+01 ... (remaining 30631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 39166 4.66 - 9.33: 2842 9.33 - 13.99: 237 13.99 - 18.66: 25 18.66 - 23.32: 30 Bond angle restraints: 42300 Sorted by residual: angle pdb=" C2 CRT J 101 " pdb=" C1 CRT J 101 " pdb=" C4 CRT J 101 " ideal model delta sigma weight residual 110.24 86.92 23.32 3.00e+00 1.11e-01 6.04e+01 angle pdb=" C2 CRT V 101 " pdb=" C1 CRT V 101 " pdb=" C4 CRT V 101 " ideal model delta sigma weight residual 110.24 86.92 23.32 3.00e+00 1.11e-01 6.04e+01 angle pdb=" C2 CRT 4 101 " pdb=" C1 CRT 4 101 " pdb=" C4 CRT 4 101 " ideal model delta sigma weight residual 110.24 87.04 23.20 3.00e+00 1.11e-01 5.98e+01 angle pdb=" C2 CRT F 101 " pdb=" C1 CRT F 101 " pdb=" C4 CRT F 101 " ideal model delta sigma weight residual 110.24 87.09 23.15 3.00e+00 1.11e-01 5.95e+01 angle pdb=" C2 CRT N 101 " pdb=" C1 CRT N 101 " pdb=" C4 CRT N 101 " ideal model delta sigma weight residual 110.24 87.13 23.11 3.00e+00 1.11e-01 5.93e+01 ... (remaining 42295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 16345 35.82 - 71.64: 1158 71.64 - 107.46: 329 107.46 - 143.28: 51 143.28 - 179.09: 27 Dihedral angle restraints: 17910 sinusoidal: 10602 harmonic: 7308 Sorted by residual: dihedral pdb=" C1 BCL m 102 " pdb=" C2 BCL m 102 " pdb=" C3 BCL m 102 " pdb=" C5 BCL m 102 " ideal model delta sinusoidal sigma weight residual 180.00 0.91 179.09 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL c 101 " pdb=" C2 BCL c 101 " pdb=" C3 BCL c 101 " pdb=" C5 BCL c 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.98 179.02 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL i 101 " pdb=" C2 BCL i 101 " pdb=" C3 BCL i 101 " pdb=" C5 BCL i 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.99 179.01 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 17907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3003 0.050 - 0.100: 813 0.100 - 0.150: 274 0.150 - 0.200: 150 0.200 - 0.250: 26 Chirality restraints: 4266 Sorted by residual: chirality pdb=" C05 PGV k 105 " pdb=" C04 PGV k 105 " pdb=" C06 PGV k 105 " pdb=" O05 PGV k 105 " both_signs ideal model delta sigma weight residual False 2.29 2.54 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C05 PGV m 105 " pdb=" C04 PGV m 105 " pdb=" C06 PGV m 105 " pdb=" O05 PGV m 105 " both_signs ideal model delta sigma weight residual False 2.29 2.54 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C05 PGV q 105 " pdb=" C04 PGV q 105 " pdb=" C06 PGV q 105 " pdb=" O05 PGV q 105 " both_signs ideal model delta sigma weight residual False 2.29 2.54 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4263 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL k 103 " -0.336 3.00e-02 1.11e+03 2.75e-01 4.20e+02 pdb=" CBA BCL k 103 " -0.182 3.00e-02 1.11e+03 pdb=" CGA BCL k 103 " 0.076 3.00e-02 1.11e+03 pdb=" O1A BCL k 103 " -0.032 3.00e-02 1.11e+03 pdb=" O2A BCL k 103 " 0.474 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL g 102 " -0.335 3.00e-02 1.11e+03 2.73e-01 4.14e+02 pdb=" CBA BCL g 102 " -0.184 3.00e-02 1.11e+03 pdb=" CGA BCL g 102 " 0.076 3.00e-02 1.11e+03 pdb=" O1A BCL g 102 " -0.027 3.00e-02 1.11e+03 pdb=" O2A BCL g 102 " 0.470 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL q 103 " 0.332 3.00e-02 1.11e+03 2.71e-01 4.09e+02 pdb=" CBA BCL q 103 " 0.182 3.00e-02 1.11e+03 pdb=" CGA BCL q 103 " -0.074 3.00e-02 1.11e+03 pdb=" O1A BCL q 103 " 0.028 3.00e-02 1.11e+03 pdb=" O2A BCL q 103 " -0.467 3.00e-02 1.11e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 523 2.65 - 3.21: 24044 3.21 - 3.78: 52337 3.78 - 4.34: 74961 4.34 - 4.90: 116454 Nonbonded interactions: 268319 Sorted by model distance: nonbonded pdb=" O2B LMT G 103 " pdb=" O3' LMT G 105 " model vdw 2.091 3.040 nonbonded pdb=" O2B LMT 1 103 " pdb=" O3' LMT 1 105 " model vdw 2.117 3.040 nonbonded pdb=" O2B LMT W 103 " pdb=" O3' LMT W 105 " model vdw 2.120 3.040 nonbonded pdb=" O2B LMT S 103 " pdb=" O3' LMT S 105 " model vdw 2.124 3.040 nonbonded pdb=" O2B LMT 5 103 " pdb=" O3' LMT 5 105 " model vdw 2.141 3.040 ... (remaining 268314 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 '0' and resid 9 through 53) selection = (chain '2' and resid 9 through 53) selection = (chain '6' and resid 9 through 53) selection = (chain 'D' and resid 9 through 53) selection = (chain 'H' and resid 9 through 53) selection = (chain 'L' and resid 9 through 53) selection = (chain 'P' and resid 9 through 53) selection = (chain 'T' and resid 9 through 53) selection = (chain 'X' and resid 9 through 53) } ncs_group { reference = chain '1' selection = chain '5' selection = chain '9' selection = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain '3' selection = chain '7' selection = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = (chain '4' and (resid 7 through 53 or resid 101 through 102)) selection = (chain '8' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'B' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'F' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'J' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'N' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'R' and (resid 7 through 53 or resid 101 through 102)) selection = (chain 'V' and (resid 7 through 53 or resid 101 through 102)) selection = chain 'Z' } ncs_group { reference = (chain 'a' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'c' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'e' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'g' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'i' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'k' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'm' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'o' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'q' and (resid 1 through 49 or resid 102 or resid 104)) } ncs_group { reference = (chain 'b' and resid 10 through 58) selection = (chain 'd' and resid 10 through 58) selection = (chain 'f' and resid 10 through 58) selection = (chain 'h' and resid 10 through 58) selection = (chain 'j' and resid 10 through 58) selection = (chain 'l' and resid 10 through 58) selection = (chain 'n' and resid 10 through 58) selection = (chain 'p' and resid 10 through 58) selection = (chain 'r' and resid 10 through 58) } 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.500 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 61.860 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.270 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:73.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.026 0.631 30708 Z= 1.426 Angle : 2.319 23.323 42300 Z= 0.977 Chirality : 0.061 0.250 4266 Planarity : 0.026 0.275 4743 Dihedral : 25.812 179.094 13158 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 4.41 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.16), residues: 2421 helix: 3.01 (0.11), residues: 1629 sheet: None (None), residues: 0 loop : 0.78 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 1 5 HIS 0.006 0.002 HIS a 31 PHE 0.016 0.002 PHE b 41 TYR 0.011 0.002 TYR G 46 ARG 0.004 0.001 ARG 5 11 Details of bonding type rmsd hydrogen bonds : bond 0.16074 ( 1494) hydrogen bonds : angle 5.19837 ( 4344) covalent geometry : bond 0.02321 (30636) covalent geometry : angle 2.31862 (42300) Misc. bond : bond 0.24737 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 424 time to evaluate : 2.771 Fit side-chains REVERT: B 12 ASP cc_start: 0.7204 (m-30) cc_final: 0.6945 (m-30) REVERT: B 17 GLU cc_start: 0.7669 (tt0) cc_final: 0.7444 (tt0) REVERT: C 1 MET cc_start: 0.7015 (tpt) cc_final: 0.6373 (tpt) REVERT: F 14 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7415 (mt-10) REVERT: G 1 MET cc_start: 0.6916 (tpt) cc_final: 0.6372 (tpt) REVERT: I 3 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7599 (mtt180) REVERT: I 12 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7319 (mtp85) REVERT: J 23 MET cc_start: 0.8302 (mmm) cc_final: 0.7737 (mmm) REVERT: K 1 MET cc_start: 0.6917 (tpt) cc_final: 0.6343 (tpt) REVERT: K 8 LEU cc_start: 0.8465 (mt) cc_final: 0.8216 (mp) REVERT: L 29 TYR cc_start: 0.8898 (t80) cc_final: 0.8560 (t80) REVERT: N 24 GLN cc_start: 0.7701 (mt0) cc_final: 0.7424 (tt0) REVERT: R 14 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7192 (mt-10) REVERT: R 23 MET cc_start: 0.8540 (mmm) cc_final: 0.8180 (mmm) REVERT: T 29 TYR cc_start: 0.8834 (t80) cc_final: 0.8333 (t80) REVERT: V 14 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7338 (mt-10) REVERT: V 24 GLN cc_start: 0.7611 (mt0) cc_final: 0.7276 (tt0) REVERT: W 6 LYS cc_start: 0.7831 (mtpm) cc_final: 0.7623 (mtmt) REVERT: Y 1 MET cc_start: 0.8103 (tpp) cc_final: 0.7689 (tpp) REVERT: Z 12 ASP cc_start: 0.7280 (m-30) cc_final: 0.6990 (m-30) REVERT: Z 14 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7224 (mt-10) REVERT: Z 17 GLU cc_start: 0.7533 (tt0) cc_final: 0.7283 (tt0) REVERT: Z 23 MET cc_start: 0.8458 (mmm) cc_final: 0.8042 (mmm) REVERT: 4 24 GLN cc_start: 0.7725 (mt0) cc_final: 0.7356 (tt0) REVERT: 5 1 MET cc_start: 0.6930 (tpt) cc_final: 0.6262 (tpt) REVERT: 5 8 LEU cc_start: 0.8449 (mt) cc_final: 0.8220 (mt) REVERT: 8 23 MET cc_start: 0.8380 (mmm) cc_final: 0.7959 (mmm) REVERT: 8 24 GLN cc_start: 0.7593 (mt0) cc_final: 0.7262 (mt0) REVERT: 9 21 MET cc_start: 0.8986 (mmm) cc_final: 0.8774 (mmm) outliers start: 22 outliers final: 0 residues processed: 444 average time/residue: 2.0916 time to fit residues: 1051.5969 Evaluate side-chains 379 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 2 ASN e 2 ASN g 2 ASN i 2 ASN i 37 ASN k 2 ASN m 37 ASN o 37 ASN q 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125355 restraints weight = 28547.591| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.83 r_work: 0.3281 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 30708 Z= 0.188 Angle : 0.981 17.501 42300 Z= 0.335 Chirality : 0.046 0.386 4266 Planarity : 0.005 0.036 4743 Dihedral : 23.954 179.937 8811 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.81 % Allowed : 7.90 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.16), residues: 2421 helix: 3.23 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP k 40 HIS 0.006 0.002 HIS X 37 PHE 0.013 0.002 PHE 3 30 TYR 0.011 0.002 TYR n 32 ARG 0.006 0.001 ARG S 12 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 1494) hydrogen bonds : angle 3.57652 ( 4344) covalent geometry : bond 0.00452 (30636) covalent geometry : angle 0.98069 (42300) Misc. bond : bond 0.05126 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 396 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7910 (tt0) cc_final: 0.7576 (tt0) REVERT: C 1 MET cc_start: 0.7021 (tpt) cc_final: 0.6528 (tpt) REVERT: F 14 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7420 (mt-10) REVERT: I 12 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7469 (mtp85) REVERT: J 23 MET cc_start: 0.8297 (mmm) cc_final: 0.7688 (mmm) REVERT: K 1 MET cc_start: 0.6914 (tpt) cc_final: 0.6378 (tpt) REVERT: K 8 LEU cc_start: 0.8466 (mt) cc_final: 0.8232 (mp) REVERT: L 29 TYR cc_start: 0.8894 (t80) cc_final: 0.8560 (t80) REVERT: M 11 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.8253 (ttt180) REVERT: N 24 GLN cc_start: 0.7784 (mt0) cc_final: 0.7156 (tt0) REVERT: O 1 MET cc_start: 0.7188 (mmm) cc_final: 0.6328 (tpt) REVERT: Q 12 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7454 (mtp85) REVERT: R 12 ASP cc_start: 0.7355 (m-30) cc_final: 0.6833 (m-30) REVERT: R 14 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7264 (mt-10) REVERT: T 29 TYR cc_start: 0.8868 (t80) cc_final: 0.8390 (t80) REVERT: V 10 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7478 (tp) REVERT: V 14 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7328 (mt-10) REVERT: V 24 GLN cc_start: 0.7828 (mt0) cc_final: 0.7256 (tt0) REVERT: Z 14 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7176 (mt-10) REVERT: Z 23 MET cc_start: 0.8459 (mmm) cc_final: 0.7975 (mmm) REVERT: Z 24 GLN cc_start: 0.7723 (mt0) cc_final: 0.7430 (mt0) REVERT: 4 12 ASP cc_start: 0.7174 (m-30) cc_final: 0.6738 (m-30) REVERT: 4 24 GLN cc_start: 0.7862 (mt0) cc_final: 0.7244 (tt0) REVERT: 5 1 MET cc_start: 0.7107 (tpt) cc_final: 0.6783 (tpt) REVERT: 5 8 LEU cc_start: 0.8365 (mt) cc_final: 0.8001 (mp) REVERT: 6 16 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: 8 12 ASP cc_start: 0.7164 (m-30) cc_final: 0.6925 (m-30) REVERT: 8 24 GLN cc_start: 0.7733 (mt0) cc_final: 0.7360 (mt0) REVERT: 9 21 MET cc_start: 0.8962 (mmm) cc_final: 0.8757 (mmt) REVERT: h 32 TYR cc_start: 0.8274 (m-80) cc_final: 0.7948 (m-80) outliers start: 17 outliers final: 5 residues processed: 406 average time/residue: 1.8361 time to fit residues: 844.6478 Evaluate side-chains 373 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain k residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN a 2 ASN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 2 ASN m 2 ASN o 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125554 restraints weight = 28637.629| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.85 r_work: 0.3284 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 30708 Z= 0.174 Angle : 0.911 16.450 42300 Z= 0.313 Chirality : 0.043 0.349 4266 Planarity : 0.004 0.036 4743 Dihedral : 22.873 179.914 8811 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.05 % Allowed : 8.67 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.16), residues: 2421 helix: 3.23 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.78 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP k 40 HIS 0.006 0.002 HIS 0 37 PHE 0.013 0.002 PHE 8 29 TYR 0.008 0.001 TYR A 8 ARG 0.008 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1494) hydrogen bonds : angle 3.51437 ( 4344) covalent geometry : bond 0.00416 (30636) covalent geometry : angle 0.91092 (42300) Misc. bond : bond 0.03871 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 394 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7020 (tpt) cc_final: 0.6551 (tpt) REVERT: E 11 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.8281 (ttt-90) REVERT: F 14 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7399 (mt-10) REVERT: I 12 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7458 (mtp85) REVERT: J 23 MET cc_start: 0.8306 (mmm) cc_final: 0.7745 (mmm) REVERT: J 38 PHE cc_start: 0.8569 (m-80) cc_final: 0.8303 (m-80) REVERT: K 1 MET cc_start: 0.6862 (tpt) cc_final: 0.6376 (tpt) REVERT: K 8 LEU cc_start: 0.8453 (mt) cc_final: 0.8211 (mp) REVERT: L 29 TYR cc_start: 0.8885 (t80) cc_final: 0.8592 (t80) REVERT: N 10 LEU cc_start: 0.7757 (tp) cc_final: 0.7500 (tp) REVERT: N 24 GLN cc_start: 0.7779 (mt0) cc_final: 0.7435 (mt0) REVERT: Q 12 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7460 (mtp85) REVERT: R 12 ASP cc_start: 0.7268 (m-30) cc_final: 0.6783 (m-30) REVERT: T 14 GLU cc_start: 0.7266 (tt0) cc_final: 0.6976 (tt0) REVERT: T 29 TYR cc_start: 0.8851 (t80) cc_final: 0.8376 (t80) REVERT: U 1 MET cc_start: 0.8151 (tpp) cc_final: 0.7420 (tpp) REVERT: V 14 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7302 (mt-10) REVERT: V 24 GLN cc_start: 0.7817 (mt0) cc_final: 0.7316 (tt0) REVERT: Z 10 LEU cc_start: 0.7635 (tp) cc_final: 0.7397 (tp) REVERT: Z 14 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7151 (mt-10) REVERT: Z 23 MET cc_start: 0.8449 (mmm) cc_final: 0.7972 (mmm) REVERT: Z 24 GLN cc_start: 0.7718 (mt0) cc_final: 0.7382 (mt0) REVERT: Z 51 GLU cc_start: 0.7241 (pm20) cc_final: 0.7014 (pm20) REVERT: 2 16 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7997 (mttt) REVERT: 4 24 GLN cc_start: 0.7871 (mt0) cc_final: 0.7216 (tt0) REVERT: 5 1 MET cc_start: 0.6937 (tpt) cc_final: 0.6645 (tpt) REVERT: 5 6 LYS cc_start: 0.8030 (mttt) cc_final: 0.7787 (mtmt) REVERT: 5 8 LEU cc_start: 0.8387 (mt) cc_final: 0.8059 (mp) REVERT: 6 16 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8063 (mttt) REVERT: 8 12 ASP cc_start: 0.7181 (m-30) cc_final: 0.6824 (m-30) REVERT: 8 24 GLN cc_start: 0.7738 (mt0) cc_final: 0.7424 (mt0) REVERT: 9 21 MET cc_start: 0.8971 (mmm) cc_final: 0.8710 (mmm) REVERT: h 32 TYR cc_start: 0.8266 (m-80) cc_final: 0.7903 (m-80) outliers start: 22 outliers final: 10 residues processed: 408 average time/residue: 2.2116 time to fit residues: 1020.4501 Evaluate side-chains 378 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain q residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN S 42 GLN a 2 ASN e 2 ASN e 37 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN o 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125334 restraints weight = 28766.036| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 0.85 r_work: 0.3281 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 30708 Z= 0.184 Angle : 0.921 17.079 42300 Z= 0.320 Chirality : 0.044 0.390 4266 Planarity : 0.004 0.036 4743 Dihedral : 22.537 179.869 8811 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.10 % Allowed : 9.67 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.16), residues: 2421 helix: 3.16 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.72 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP k 40 HIS 0.006 0.002 HIS H 37 PHE 0.014 0.002 PHE 8 29 TYR 0.008 0.001 TYR n 32 ARG 0.008 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 1494) hydrogen bonds : angle 3.51901 ( 4344) covalent geometry : bond 0.00445 (30636) covalent geometry : angle 0.92051 (42300) Misc. bond : bond 0.03750 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 384 time to evaluate : 2.444 Fit side-chains REVERT: B 17 GLU cc_start: 0.7911 (tt0) cc_final: 0.7682 (tt0) REVERT: C 1 MET cc_start: 0.6946 (tpt) cc_final: 0.6523 (tpt) REVERT: E 11 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8358 (ttt-90) REVERT: F 14 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7404 (mt-10) REVERT: I 12 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7461 (mtp85) REVERT: J 23 MET cc_start: 0.8327 (mmm) cc_final: 0.7759 (mmm) REVERT: J 38 PHE cc_start: 0.8564 (m-80) cc_final: 0.8290 (m-80) REVERT: K 1 MET cc_start: 0.6815 (tpt) cc_final: 0.6302 (tpt) REVERT: K 8 LEU cc_start: 0.8465 (mt) cc_final: 0.8224 (mp) REVERT: L 29 TYR cc_start: 0.8919 (t80) cc_final: 0.8629 (t80) REVERT: N 10 LEU cc_start: 0.7732 (tp) cc_final: 0.7495 (tp) REVERT: N 24 GLN cc_start: 0.7802 (mt0) cc_final: 0.7444 (mt0) REVERT: Q 12 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7436 (mtp85) REVERT: R 11 SER cc_start: 0.8026 (p) cc_final: 0.7399 (t) REVERT: R 12 ASP cc_start: 0.7261 (m-30) cc_final: 0.6763 (m-30) REVERT: T 14 GLU cc_start: 0.7276 (tt0) cc_final: 0.6974 (tt0) REVERT: T 29 TYR cc_start: 0.8874 (t80) cc_final: 0.8374 (t80) REVERT: V 14 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7243 (mt-10) REVERT: V 24 GLN cc_start: 0.7942 (mt0) cc_final: 0.7391 (tt0) REVERT: Z 14 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7183 (mt-10) REVERT: Z 23 MET cc_start: 0.8451 (mmm) cc_final: 0.7996 (mmm) REVERT: Z 24 GLN cc_start: 0.7787 (mt0) cc_final: 0.7441 (mt0) REVERT: Z 51 GLU cc_start: 0.7254 (pm20) cc_final: 0.7023 (pm20) REVERT: 2 16 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8021 (mttt) REVERT: 4 24 GLN cc_start: 0.7812 (mt0) cc_final: 0.7209 (tt0) REVERT: 5 1 MET cc_start: 0.6927 (tpt) cc_final: 0.6606 (tpt) REVERT: 5 8 LEU cc_start: 0.8389 (mt) cc_final: 0.8070 (mp) REVERT: 6 16 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (mttt) REVERT: 8 12 ASP cc_start: 0.7109 (m-30) cc_final: 0.6778 (m-30) REVERT: 8 24 GLN cc_start: 0.7736 (mt0) cc_final: 0.7415 (mt0) REVERT: 9 21 MET cc_start: 0.8978 (mmm) cc_final: 0.8695 (mmt) REVERT: f 28 GLU cc_start: 0.7628 (tp30) cc_final: 0.7311 (tp30) REVERT: h 32 TYR cc_start: 0.8267 (m-80) cc_final: 0.7919 (m-80) outliers start: 23 outliers final: 10 residues processed: 401 average time/residue: 1.8687 time to fit residues: 848.0573 Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 371 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain q residue 22 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 80 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 143 optimal weight: 0.1980 chunk 200 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** a 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 ASN e 2 ASN g 2 ASN g 37 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN o 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127039 restraints weight = 28564.330| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 0.84 r_work: 0.3307 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 30708 Z= 0.146 Angle : 0.840 16.251 42300 Z= 0.293 Chirality : 0.042 0.394 4266 Planarity : 0.004 0.038 4743 Dihedral : 21.712 179.936 8811 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.10 % Allowed : 9.77 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.16), residues: 2421 helix: 3.35 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP k 40 HIS 0.005 0.001 HIS 4 37 PHE 0.012 0.002 PHE 8 29 TYR 0.008 0.001 TYR A 8 ARG 0.009 0.001 ARG K 11 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1494) hydrogen bonds : angle 3.37998 ( 4344) covalent geometry : bond 0.00344 (30636) covalent geometry : angle 0.83975 (42300) Misc. bond : bond 0.04405 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 386 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8687 (m-80) cc_final: 0.8454 (m-80) REVERT: C 1 MET cc_start: 0.6976 (tpt) cc_final: 0.6566 (tpt) REVERT: E 11 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8285 (ttt-90) REVERT: F 14 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7326 (mt-10) REVERT: I 12 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7453 (mtp85) REVERT: J 23 MET cc_start: 0.8374 (mmm) cc_final: 0.7957 (mmm) REVERT: J 38 PHE cc_start: 0.8573 (m-80) cc_final: 0.8290 (m-80) REVERT: K 1 MET cc_start: 0.6802 (tpt) cc_final: 0.6342 (tpt) REVERT: K 8 LEU cc_start: 0.8469 (mt) cc_final: 0.8234 (mp) REVERT: K 11 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7485 (mtp85) REVERT: L 29 TYR cc_start: 0.8871 (t80) cc_final: 0.8620 (t80) REVERT: M 12 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7822 (mtp85) REVERT: N 10 LEU cc_start: 0.7746 (tp) cc_final: 0.7486 (tp) REVERT: N 24 GLN cc_start: 0.7790 (mt0) cc_final: 0.7408 (mt0) REVERT: O 12 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6944 (mtp-110) REVERT: O 16 LEU cc_start: 0.8752 (tp) cc_final: 0.8538 (tt) REVERT: Q 12 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7413 (mtp85) REVERT: R 12 ASP cc_start: 0.7217 (m-30) cc_final: 0.6793 (m-30) REVERT: T 14 GLU cc_start: 0.7268 (tt0) cc_final: 0.6987 (tt0) REVERT: T 29 TYR cc_start: 0.8842 (t80) cc_final: 0.8370 (t80) REVERT: V 14 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7246 (mt-10) REVERT: V 24 GLN cc_start: 0.7929 (mt0) cc_final: 0.7379 (tt0) REVERT: Z 14 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7122 (mt-10) REVERT: Z 23 MET cc_start: 0.8480 (mmm) cc_final: 0.7971 (mmm) REVERT: Z 24 GLN cc_start: 0.7799 (mt0) cc_final: 0.7517 (mt0) REVERT: Z 51 GLU cc_start: 0.7267 (pm20) cc_final: 0.7025 (pm20) REVERT: 2 16 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8014 (mttt) REVERT: 4 24 GLN cc_start: 0.7845 (mt0) cc_final: 0.7214 (tt0) REVERT: 5 1 MET cc_start: 0.6979 (tpt) cc_final: 0.6725 (tpt) REVERT: 5 6 LYS cc_start: 0.8043 (mttt) cc_final: 0.7822 (mtpm) REVERT: 5 8 LEU cc_start: 0.8386 (mt) cc_final: 0.8044 (mp) REVERT: 6 16 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8044 (mttt) REVERT: 8 12 ASP cc_start: 0.7120 (m-30) cc_final: 0.6701 (m-30) REVERT: 8 24 GLN cc_start: 0.7739 (mt0) cc_final: 0.7414 (mt0) REVERT: 9 21 MET cc_start: 0.8938 (mmm) cc_final: 0.8722 (mmt) REVERT: f 28 GLU cc_start: 0.7625 (tp30) cc_final: 0.7316 (tp30) REVERT: h 32 TYR cc_start: 0.8225 (m-80) cc_final: 0.7880 (m-80) outliers start: 23 outliers final: 10 residues processed: 403 average time/residue: 1.8242 time to fit residues: 834.3584 Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 370 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN o 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125905 restraints weight = 28611.975| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.84 r_work: 0.3290 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 30708 Z= 0.170 Angle : 0.873 17.316 42300 Z= 0.309 Chirality : 0.044 0.400 4266 Planarity : 0.004 0.038 4743 Dihedral : 21.718 179.939 8811 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.20 % Allowed : 9.91 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.16), residues: 2421 helix: 3.21 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.72 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 40 HIS 0.006 0.002 HIS 4 37 PHE 0.013 0.002 PHE 8 29 TYR 0.007 0.001 TYR G 10 ARG 0.009 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 1494) hydrogen bonds : angle 3.42303 ( 4344) covalent geometry : bond 0.00404 (30636) covalent geometry : angle 0.87344 (42300) Misc. bond : bond 0.03932 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 380 time to evaluate : 2.681 Fit side-chains revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8684 (m-80) cc_final: 0.8453 (m-80) REVERT: C 1 MET cc_start: 0.7001 (tpt) cc_final: 0.6558 (tpt) REVERT: E 11 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.8240 (ttt-90) REVERT: F 14 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7288 (mt-10) REVERT: I 12 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7473 (mtp85) REVERT: J 23 MET cc_start: 0.8327 (mmm) cc_final: 0.7786 (mmm) REVERT: J 38 PHE cc_start: 0.8568 (m-80) cc_final: 0.8294 (m-80) REVERT: K 1 MET cc_start: 0.6765 (tpt) cc_final: 0.6258 (tpt) REVERT: K 8 LEU cc_start: 0.8456 (mt) cc_final: 0.8223 (mp) REVERT: K 11 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7498 (mtp85) REVERT: L 29 TYR cc_start: 0.8910 (t80) cc_final: 0.8613 (t80) REVERT: N 10 LEU cc_start: 0.7809 (tp) cc_final: 0.7567 (tp) REVERT: N 24 GLN cc_start: 0.7800 (mt0) cc_final: 0.7427 (mt0) REVERT: O 12 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6907 (mtp-110) REVERT: O 16 LEU cc_start: 0.8758 (tp) cc_final: 0.8537 (tt) REVERT: Q 12 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7434 (mtp85) REVERT: R 12 ASP cc_start: 0.7212 (m-30) cc_final: 0.6819 (m-30) REVERT: T 14 GLU cc_start: 0.7258 (tt0) cc_final: 0.6963 (tt0) REVERT: T 29 TYR cc_start: 0.8876 (t80) cc_final: 0.8393 (t80) REVERT: V 14 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7206 (mt-10) REVERT: V 24 GLN cc_start: 0.7939 (mt0) cc_final: 0.7392 (tt0) REVERT: V 27 LEU cc_start: 0.8258 (mt) cc_final: 0.8042 (tp) REVERT: Z 14 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7090 (mt-10) REVERT: Z 23 MET cc_start: 0.8469 (mmm) cc_final: 0.7955 (mmm) REVERT: Z 24 GLN cc_start: 0.7797 (mt0) cc_final: 0.7510 (mt0) REVERT: Z 51 GLU cc_start: 0.7278 (pm20) cc_final: 0.7030 (pm20) REVERT: 2 16 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (mttt) REVERT: 4 24 GLN cc_start: 0.7852 (mt0) cc_final: 0.7231 (tt0) REVERT: 5 1 MET cc_start: 0.6931 (tpt) cc_final: 0.6626 (tpt) REVERT: 5 6 LYS cc_start: 0.8033 (mttt) cc_final: 0.7761 (mtmt) REVERT: 5 8 LEU cc_start: 0.8391 (mt) cc_final: 0.8074 (mp) REVERT: 6 16 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8065 (mttt) REVERT: 8 12 ASP cc_start: 0.7155 (m-30) cc_final: 0.6799 (m-30) REVERT: 8 24 GLN cc_start: 0.7750 (mt0) cc_final: 0.7420 (mt0) REVERT: 9 21 MET cc_start: 0.8976 (mmm) cc_final: 0.8773 (mmt) REVERT: f 28 GLU cc_start: 0.7565 (tp30) cc_final: 0.7233 (tp30) REVERT: h 32 TYR cc_start: 0.8219 (m-80) cc_final: 0.7935 (m-80) outliers start: 25 outliers final: 13 residues processed: 398 average time/residue: 1.8784 time to fit residues: 851.4662 Evaluate side-chains 382 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 366 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain r residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 119 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 142 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN c 37 ASN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN o 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129055 restraints weight = 28676.167| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 0.84 r_work: 0.3338 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 30708 Z= 0.126 Angle : 0.789 14.814 42300 Z= 0.278 Chirality : 0.041 0.398 4266 Planarity : 0.004 0.039 4743 Dihedral : 20.690 179.969 8811 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.86 % Allowed : 10.54 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.16), residues: 2421 helix: 3.53 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.78 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 40 HIS 0.004 0.001 HIS l 30 PHE 0.010 0.001 PHE B 29 TYR 0.008 0.001 TYR A 8 ARG 0.008 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 1494) hydrogen bonds : angle 3.21409 ( 4344) covalent geometry : bond 0.00290 (30636) covalent geometry : angle 0.78906 (42300) Misc. bond : bond 0.04691 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 387 time to evaluate : 3.015 Fit side-chains revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8672 (m-80) cc_final: 0.8447 (m-80) REVERT: C 1 MET cc_start: 0.6840 (tpt) cc_final: 0.6564 (tpt) REVERT: E 11 ARG cc_start: 0.8545 (ttt-90) cc_final: 0.8249 (ttt-90) REVERT: F 14 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7324 (mt-10) REVERT: I 12 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7474 (mtp85) REVERT: J 23 MET cc_start: 0.8366 (mmm) cc_final: 0.7952 (mmm) REVERT: J 38 PHE cc_start: 0.8581 (m-80) cc_final: 0.8306 (m-80) REVERT: K 1 MET cc_start: 0.6728 (tpt) cc_final: 0.6141 (tpt) REVERT: K 8 LEU cc_start: 0.8438 (mt) cc_final: 0.8196 (mp) REVERT: K 11 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7473 (mtp85) REVERT: M 11 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.8245 (ttt180) REVERT: M 12 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7807 (mtp85) REVERT: N 10 LEU cc_start: 0.7751 (tp) cc_final: 0.7462 (tp) REVERT: N 24 GLN cc_start: 0.7786 (mt0) cc_final: 0.7123 (tt0) REVERT: N 27 LEU cc_start: 0.8206 (mp) cc_final: 0.7798 (tp) REVERT: O 1 MET cc_start: 0.7137 (mmm) cc_final: 0.6334 (tpt) REVERT: O 12 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6914 (mtp-110) REVERT: O 16 LEU cc_start: 0.8707 (tp) cc_final: 0.8505 (tt) REVERT: Q 12 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7409 (mtp85) REVERT: R 12 ASP cc_start: 0.7151 (m-30) cc_final: 0.6813 (m-30) REVERT: T 14 GLU cc_start: 0.7236 (tt0) cc_final: 0.6961 (tt0) REVERT: V 14 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7307 (mt-10) REVERT: V 24 GLN cc_start: 0.7922 (mt0) cc_final: 0.7374 (tt0) REVERT: V 27 LEU cc_start: 0.8305 (mt) cc_final: 0.8062 (tp) REVERT: W 11 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7644 (ttm-80) REVERT: Z 14 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7136 (mt-10) REVERT: Z 23 MET cc_start: 0.8502 (mmm) cc_final: 0.7991 (mmm) REVERT: Z 24 GLN cc_start: 0.7739 (mt0) cc_final: 0.7461 (mt0) REVERT: Z 51 GLU cc_start: 0.7247 (pm20) cc_final: 0.7000 (pm20) REVERT: 4 24 GLN cc_start: 0.7802 (mt0) cc_final: 0.7200 (tt0) REVERT: 5 6 LYS cc_start: 0.8052 (mttt) cc_final: 0.7767 (mtmt) REVERT: 5 8 LEU cc_start: 0.8399 (mt) cc_final: 0.8046 (mp) REVERT: 6 16 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8077 (mttt) REVERT: 8 12 ASP cc_start: 0.7163 (m-30) cc_final: 0.6771 (m-30) REVERT: 8 24 GLN cc_start: 0.7768 (mt0) cc_final: 0.7435 (mt0) REVERT: 9 1 MET cc_start: 0.7127 (mmm) cc_final: 0.6887 (tpt) REVERT: f 28 GLU cc_start: 0.7606 (tp30) cc_final: 0.7257 (tp30) REVERT: h 32 TYR cc_start: 0.8180 (m-80) cc_final: 0.7908 (m-80) REVERT: j 28 GLU cc_start: 0.7340 (tp30) cc_final: 0.7124 (tp30) outliers start: 18 outliers final: 7 residues processed: 398 average time/residue: 1.8498 time to fit residues: 834.6436 Evaluate side-chains 374 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 365 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 51 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124899 restraints weight = 28660.446| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.84 r_work: 0.3274 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 30708 Z= 0.220 Angle : 0.942 18.596 42300 Z= 0.338 Chirality : 0.047 0.410 4266 Planarity : 0.005 0.042 4743 Dihedral : 21.912 179.931 8811 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.62 % Allowed : 11.06 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.16), residues: 2421 helix: 3.11 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.71 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 5 5 HIS 0.009 0.002 HIS 0 37 PHE 0.019 0.002 PHE p 41 TYR 0.010 0.002 TYR n 32 ARG 0.008 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 1494) hydrogen bonds : angle 3.51790 ( 4344) covalent geometry : bond 0.00531 (30636) covalent geometry : angle 0.94248 (42300) Misc. bond : bond 0.03588 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 370 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6973 (tpt) cc_final: 0.6525 (tpt) REVERT: F 14 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7356 (mt-10) REVERT: I 12 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7520 (mtp85) REVERT: J 23 MET cc_start: 0.8309 (mmm) cc_final: 0.7753 (mmm) REVERT: J 38 PHE cc_start: 0.8560 (m-80) cc_final: 0.8288 (m-80) REVERT: K 1 MET cc_start: 0.6817 (tpt) cc_final: 0.6327 (tpt) REVERT: K 8 LEU cc_start: 0.8440 (mt) cc_final: 0.8224 (mp) REVERT: K 11 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7522 (mtp85) REVERT: M 12 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7798 (mtp85) REVERT: N 10 LEU cc_start: 0.7813 (tp) cc_final: 0.7572 (tp) REVERT: N 24 GLN cc_start: 0.7794 (mt0) cc_final: 0.7442 (mt0) REVERT: O 12 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6943 (mtp-110) REVERT: O 16 LEU cc_start: 0.8740 (tp) cc_final: 0.8514 (tt) REVERT: Q 12 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7450 (mtp85) REVERT: R 12 ASP cc_start: 0.7235 (m-30) cc_final: 0.6898 (m-30) REVERT: V 14 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7232 (mt-10) REVERT: V 24 GLN cc_start: 0.7956 (mt0) cc_final: 0.7408 (tt0) REVERT: V 27 LEU cc_start: 0.8279 (mt) cc_final: 0.8051 (tp) REVERT: Z 14 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7155 (mt-10) REVERT: Z 23 MET cc_start: 0.8443 (mmm) cc_final: 0.8027 (mmm) REVERT: Z 24 GLN cc_start: 0.7821 (mt0) cc_final: 0.7533 (mt0) REVERT: Z 51 GLU cc_start: 0.7252 (pm20) cc_final: 0.7004 (pm20) REVERT: 2 16 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7995 (mttm) REVERT: 5 6 LYS cc_start: 0.8033 (mttt) cc_final: 0.7780 (mtmt) REVERT: 5 8 LEU cc_start: 0.8401 (mt) cc_final: 0.8085 (mp) REVERT: 8 12 ASP cc_start: 0.7081 (m-30) cc_final: 0.6776 (m-30) REVERT: 8 24 GLN cc_start: 0.7758 (mt0) cc_final: 0.7503 (mt0) REVERT: h 32 TYR cc_start: 0.8246 (m-80) cc_final: 0.7973 (m-80) outliers start: 13 outliers final: 6 residues processed: 376 average time/residue: 2.0903 time to fit residues: 902.8691 Evaluate side-chains 372 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 364 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain r residue 23 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126799 restraints weight = 28595.548| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.84 r_work: 0.3305 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 30708 Z= 0.151 Angle : 0.841 16.594 42300 Z= 0.300 Chirality : 0.043 0.409 4266 Planarity : 0.004 0.044 4743 Dihedral : 21.192 179.950 8811 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.38 % Allowed : 11.93 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.16), residues: 2421 helix: 3.27 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.72 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 40 HIS 0.005 0.001 HIS 4 37 PHE 0.012 0.002 PHE 8 29 TYR 0.009 0.001 TYR n 32 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 1494) hydrogen bonds : angle 3.35404 ( 4344) covalent geometry : bond 0.00353 (30636) covalent geometry : angle 0.84100 (42300) Misc. bond : bond 0.04283 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 368 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6956 (tpt) cc_final: 0.6535 (tpt) REVERT: F 14 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7269 (mt-10) REVERT: I 12 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7462 (mtp85) REVERT: J 23 MET cc_start: 0.8325 (mmm) cc_final: 0.7897 (mmm) REVERT: J 38 PHE cc_start: 0.8571 (m-80) cc_final: 0.8299 (m-80) REVERT: K 1 MET cc_start: 0.6749 (tpt) cc_final: 0.6217 (tpt) REVERT: K 8 LEU cc_start: 0.8446 (mt) cc_final: 0.8205 (mp) REVERT: K 11 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7520 (mtp85) REVERT: M 12 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7800 (mtp85) REVERT: N 10 LEU cc_start: 0.7715 (tp) cc_final: 0.7442 (tp) REVERT: N 24 GLN cc_start: 0.7794 (mt0) cc_final: 0.7413 (mt0) REVERT: O 11 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7651 (ttm-80) REVERT: O 12 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6927 (mtp-110) REVERT: O 16 LEU cc_start: 0.8734 (tp) cc_final: 0.8518 (tt) REVERT: Q 12 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7424 (mtp85) REVERT: R 12 ASP cc_start: 0.7157 (m-30) cc_final: 0.6834 (m-30) REVERT: T 14 GLU cc_start: 0.7230 (tt0) cc_final: 0.6967 (tt0) REVERT: V 14 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7205 (mt-10) REVERT: V 24 GLN cc_start: 0.7942 (mt0) cc_final: 0.7389 (tt0) REVERT: V 27 LEU cc_start: 0.8286 (mt) cc_final: 0.8056 (tp) REVERT: Z 14 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7103 (mt-10) REVERT: Z 23 MET cc_start: 0.8473 (mmm) cc_final: 0.7970 (mmm) REVERT: Z 24 GLN cc_start: 0.7787 (mt0) cc_final: 0.7500 (mt0) REVERT: Z 51 GLU cc_start: 0.7235 (pm20) cc_final: 0.6986 (pm20) REVERT: 2 16 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8007 (mttt) REVERT: 4 11 SER cc_start: 0.8032 (p) cc_final: 0.7534 (t) REVERT: 5 6 LYS cc_start: 0.8045 (mttt) cc_final: 0.7768 (mtmt) REVERT: 5 8 LEU cc_start: 0.8392 (mt) cc_final: 0.8056 (mp) REVERT: 8 12 ASP cc_start: 0.7119 (m-30) cc_final: 0.6787 (m-30) REVERT: 8 24 GLN cc_start: 0.7783 (mt0) cc_final: 0.7544 (mt0) REVERT: a 2 ASN cc_start: 0.6931 (p0) cc_final: 0.6517 (p0) REVERT: f 28 GLU cc_start: 0.7570 (tp30) cc_final: 0.7325 (tp30) REVERT: h 32 TYR cc_start: 0.8219 (m-80) cc_final: 0.7968 (m-80) outliers start: 8 outliers final: 3 residues processed: 372 average time/residue: 1.9266 time to fit residues: 814.5922 Evaluate side-chains 366 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 361 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 206 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126218 restraints weight = 28680.952| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 0.84 r_work: 0.3295 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 30708 Z= 0.163 Angle : 0.858 16.558 42300 Z= 0.308 Chirality : 0.044 0.414 4266 Planarity : 0.004 0.044 4743 Dihedral : 21.159 179.933 8811 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.48 % Allowed : 11.73 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.16), residues: 2421 helix: 3.23 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.71 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP q 40 HIS 0.006 0.002 HIS 4 37 PHE 0.013 0.002 PHE 8 29 TYR 0.012 0.001 TYR d 32 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1494) hydrogen bonds : angle 3.38119 ( 4344) covalent geometry : bond 0.00386 (30636) covalent geometry : angle 0.85779 (42300) Misc. bond : bond 0.03928 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 365 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8709 (m-80) cc_final: 0.8479 (m-80) REVERT: C 1 MET cc_start: 0.6987 (tpt) cc_final: 0.6587 (tpt) REVERT: E 11 ARG cc_start: 0.8587 (ttt-90) cc_final: 0.8344 (ttt-90) REVERT: F 11 SER cc_start: 0.7965 (p) cc_final: 0.7527 (t) REVERT: F 14 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7352 (mt-10) REVERT: I 12 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7476 (mtp85) REVERT: J 23 MET cc_start: 0.8313 (mmm) cc_final: 0.7768 (mmm) REVERT: J 38 PHE cc_start: 0.8568 (m-80) cc_final: 0.8297 (m-80) REVERT: K 1 MET cc_start: 0.6748 (tpt) cc_final: 0.6225 (tpt) REVERT: K 8 LEU cc_start: 0.8449 (mt) cc_final: 0.8209 (mp) REVERT: K 11 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7509 (mtp85) REVERT: M 12 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7809 (mtp85) REVERT: N 10 LEU cc_start: 0.7771 (tp) cc_final: 0.7508 (tp) REVERT: N 24 GLN cc_start: 0.7800 (mt0) cc_final: 0.7510 (mt0) REVERT: O 12 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6929 (mtp-110) REVERT: O 16 LEU cc_start: 0.8740 (tp) cc_final: 0.8526 (tt) REVERT: Q 12 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7441 (mtp85) REVERT: R 12 ASP cc_start: 0.7170 (m-30) cc_final: 0.6854 (m-30) REVERT: V 14 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7281 (mt-10) REVERT: V 24 GLN cc_start: 0.7949 (mt0) cc_final: 0.7410 (tt0) REVERT: V 27 LEU cc_start: 0.8275 (mt) cc_final: 0.8061 (tp) REVERT: Z 14 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7101 (mt-10) REVERT: Z 23 MET cc_start: 0.8471 (mmm) cc_final: 0.7955 (mmm) REVERT: Z 24 GLN cc_start: 0.7787 (mt0) cc_final: 0.7448 (mt0) REVERT: Z 51 GLU cc_start: 0.7266 (pm20) cc_final: 0.7012 (pm20) REVERT: 2 16 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7994 (mttt) REVERT: 4 11 SER cc_start: 0.8037 (p) cc_final: 0.7556 (t) REVERT: 5 6 LYS cc_start: 0.8042 (mttt) cc_final: 0.7773 (mtmt) REVERT: 5 8 LEU cc_start: 0.8390 (mt) cc_final: 0.8056 (mp) REVERT: 8 12 ASP cc_start: 0.7113 (m-30) cc_final: 0.6783 (m-30) REVERT: f 28 GLU cc_start: 0.7564 (tp30) cc_final: 0.7328 (tp30) REVERT: h 32 TYR cc_start: 0.8225 (m-80) cc_final: 0.7973 (m-80) outliers start: 10 outliers final: 8 residues processed: 371 average time/residue: 1.8514 time to fit residues: 778.1540 Evaluate side-chains 371 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 361 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain r residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN 8 24 GLN e 2 ASN g 2 ASN ** i 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124277 restraints weight = 28648.073| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.84 r_work: 0.3268 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.156 30708 Z= 0.232 Angle : 0.973 18.380 42300 Z= 0.351 Chirality : 0.048 0.408 4266 Planarity : 0.005 0.048 4743 Dihedral : 22.001 179.981 8811 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.43 % Allowed : 11.88 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.16), residues: 2421 helix: 2.99 (0.11), residues: 1629 sheet: None (None), residues: 0 loop : 0.65 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 5 5 HIS 0.009 0.002 HIS X 37 PHE 0.019 0.003 PHE l 41 TYR 0.013 0.002 TYR P 29 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05205 ( 1494) hydrogen bonds : angle 3.57796 ( 4344) covalent geometry : bond 0.00563 (30636) covalent geometry : angle 0.97288 (42300) Misc. bond : bond 0.03578 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24713.26 seconds wall clock time: 428 minutes 8.17 seconds (25688.17 seconds total)