Starting phenix.real_space_refine on Tue May 27 01:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z81_39835/05_2025/8z81_39835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z81_39835/05_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_39835/05_2025/8z81_39835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z81_39835/05_2025/8z81_39835.map" model { file = "/net/cci-nas-00/data/ceres_data/8z81_39835/05_2025/8z81_39835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z81_39835/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 19.31, per 1000 atoms: 0.66 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: 9.37 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: 2.00 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: 7.14 Time building geometry restraints manager: 10.50 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: 0.010 Normalize map: mean=0, sd=1: 3.410 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: 0.040 Extract box with map and model: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 61.810 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.250 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:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.290 ------------------------------------------------------------------------------- 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 : 2.511 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: 1.9046 time to fit residues: 955.6988 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 : 2.494 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125355 restraints weight = 28547.590| |-----------------------------------------------------------------------------| 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 : 2.777 Fit side-chains revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7909 (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: 0.7689 (mmm) REVERT: K 1 MET cc_start: 0.6914 (tpt) cc_final: 0.6379 (tpt) REVERT: K 8 LEU cc_start: 0.8467 (mt) cc_final: 0.8232 (mp) REVERT: L 29 TYR cc_start: 0.8894 (t80) cc_final: 0.8561 (t80) REVERT: M 11 ARG cc_start: 0.8630 (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: 0.7825 (mtp85) cc_final: 0.7454 (mtp85) REVERT: R 12 ASP cc_start: 0.7354 (m-30) cc_final: 0.6833 (m-30) REVERT: R 14 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7263 (mt-10) REVERT: T 29 TYR cc_start: 0.8869 (t80) cc_final: 0.8391 (t80) REVERT: V 10 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7479 (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: 0.7976 (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: 0.8366 (mt) cc_final: 0.8002 (mp) REVERT: 6 16 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (mttt) REVERT: 8 12 ASP cc_start: 0.7165 (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: 0.8758 (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: 1.7874 time to fit residues: 823.0697 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 : 2.824 ------------------------------------------------------------------------------- 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: 0.9980 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: 6.9990 chunk 26 optimal weight: 8.9990 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: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125569 restraints weight = 28652.438| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.84 r_work: 0.3284 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 30708 Z= 0.175 Angle : 0.915 16.471 42300 Z= 0.315 Chirality : 0.044 0.353 4266 Planarity : 0.004 0.036 4743 Dihedral : 22.897 179.930 8811 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.96 % Allowed : 8.67 % Favored : 90.37 % 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: 3.69 (0.16), residues: 2421 helix: 3.22 (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 0.006 0.002 HIS 4 37 PHE 0.013 0.002 PHE 8 29 TYR 0.008 0.001 TYR G 10 ARG 0.007 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 1494) hydrogen bonds : angle 3.52019 ( 4344) covalent geometry : bond 0.00420 (30636) covalent geometry : angle 0.91546 (42300) Misc. bond : bond 0.03935 ( 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 410 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 390 time to evaluate : 2.589 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7037 (tpt) cc_final: 0.6559 (tpt) REVERT: E 11 ARG cc_start: 0.8590 (ttt-90) cc_final: 0.8283 (ttt-90) REVERT: F 14 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7395 (mt-10) REVERT: I 12 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7456 (mtp85) REVERT: J 23 MET cc_start: 0.8323 (mmm) cc_final: 0.7771 (mmm) REVERT: J 38 PHE cc_start: 0.8568 (m-80) cc_final: 0.8313 (m-80) REVERT: K 1 MET cc_start: 0.6872 (tpt) cc_final: 0.6384 (tpt) REVERT: K 8 LEU cc_start: 0.8445 (mt) cc_final: 0.8202 (mp) REVERT: L 29 TYR cc_start: 0.8884 (t80) cc_final: 0.8592 (t80) REVERT: N 10 LEU cc_start: 0.7765 (tp) cc_final: 0.7496 (tp) REVERT: N 24 GLN cc_start: 0.7786 (mt0) cc_final: 0.7444 (mt0) REVERT: Q 12 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7466 (mtp85) REVERT: R 12 ASP cc_start: 0.7269 (m-30) cc_final: 0.6780 (m-30) REVERT: T 29 TYR cc_start: 0.8848 (t80) cc_final: 0.8375 (t80) REVERT: V 14 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7208 (mt-10) REVERT: V 24 GLN cc_start: 0.7824 (mt0) cc_final: 0.7316 (tt0) REVERT: Z 10 LEU cc_start: 0.7628 (tp) cc_final: 0.7393 (tp) REVERT: Z 14 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7151 (mt-10) REVERT: Z 23 MET cc_start: 0.8444 (mmm) cc_final: 0.7968 (mmm) REVERT: Z 24 GLN cc_start: 0.7724 (mt0) cc_final: 0.7386 (mt0) REVERT: Z 51 GLU cc_start: 0.7247 (pm20) cc_final: 0.7022 (pm20) REVERT: 2 16 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7994 (mttt) REVERT: 4 24 GLN cc_start: 0.7859 (mt0) cc_final: 0.7219 (tt0) REVERT: 5 1 MET cc_start: 0.6965 (tpt) cc_final: 0.6667 (tpt) REVERT: 5 6 LYS cc_start: 0.8029 (mttt) cc_final: 0.7785 (mtmt) REVERT: 5 8 LEU cc_start: 0.8378 (mt) cc_final: 0.8051 (mp) REVERT: 6 16 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8061 (mttt) REVERT: 8 12 ASP cc_start: 0.7171 (m-30) cc_final: 0.6809 (m-30) REVERT: 8 24 GLN cc_start: 0.7736 (mt0) cc_final: 0.7355 (mt0) REVERT: 9 21 MET cc_start: 0.8970 (mmm) cc_final: 0.8711 (mmm) REVERT: h 32 TYR cc_start: 0.8268 (m-80) cc_final: 0.7907 (m-80) outliers start: 20 outliers final: 9 residues processed: 403 average time/residue: 1.7527 time to fit residues: 802.5679 Evaluate side-chains 377 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 366 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3739 r_free = 0.3739 target = 0.145700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125095 restraints weight = 28772.159| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.84 r_work: 0.3278 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 30708 Z= 0.189 Angle : 0.934 17.248 42300 Z= 0.324 Chirality : 0.044 0.387 4266 Planarity : 0.004 0.037 4743 Dihedral : 22.666 179.897 8811 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.10 % Allowed : 9.43 % Favored : 89.46 % 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: 3.57 (0.16), residues: 2421 helix: 3.13 (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 0.015 0.002 TRP k 40 HIS 0.007 0.002 HIS H 37 PHE 0.014 0.002 PHE l 41 TYR 0.008 0.001 TYR n 32 ARG 0.008 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 1494) hydrogen bonds : angle 3.53979 ( 4344) covalent geometry : bond 0.00456 (30636) covalent geometry : angle 0.93359 (42300) Misc. bond : bond 0.03727 ( 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 : 2.534 Fit side-chains REVERT: B 17 GLU cc_start: 0.7918 (tt0) cc_final: 0.7692 (tt0) REVERT: C 1 MET cc_start: 0.6951 (tpt) cc_final: 0.6455 (tpt) REVERT: E 11 ARG cc_start: 0.8591 (ttt-90) cc_final: 0.8277 (ttt-90) REVERT: F 14 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7339 (mt-10) REVERT: I 12 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7470 (mtp85) REVERT: J 23 MET cc_start: 0.8313 (mmm) cc_final: 0.7749 (mmm) REVERT: J 38 PHE cc_start: 0.8562 (m-80) cc_final: 0.8290 (m-80) REVERT: K 1 MET cc_start: 0.6840 (tpt) cc_final: 0.6321 (tpt) REVERT: K 8 LEU cc_start: 0.8471 (mt) cc_final: 0.8231 (mp) REVERT: L 29 TYR cc_start: 0.8923 (t80) cc_final: 0.8639 (t80) REVERT: N 10 LEU cc_start: 0.7712 (tp) cc_final: 0.7477 (tp) REVERT: N 24 GLN cc_start: 0.7804 (mt0) cc_final: 0.7461 (mt0) REVERT: Q 12 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7438 (mtp85) REVERT: R 11 SER cc_start: 0.8056 (p) cc_final: 0.7423 (t) REVERT: R 12 ASP cc_start: 0.7272 (m-30) cc_final: 0.6786 (m-30) REVERT: T 29 TYR cc_start: 0.8877 (t80) cc_final: 0.8383 (t80) REVERT: V 10 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7415 (tp) REVERT: V 14 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7189 (mt-10) REVERT: V 24 GLN cc_start: 0.7928 (mt0) cc_final: 0.7381 (tt0) REVERT: Z 14 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7166 (mt-10) REVERT: Z 23 MET cc_start: 0.8444 (mmm) cc_final: 0.7987 (mmm) REVERT: Z 24 GLN cc_start: 0.7793 (mt0) cc_final: 0.7506 (mt0) REVERT: Z 51 GLU cc_start: 0.7236 (pm20) cc_final: 0.6998 (pm20) REVERT: 2 16 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: 4 24 GLN cc_start: 0.7837 (mt0) cc_final: 0.7230 (tt0) REVERT: 5 1 MET cc_start: 0.6944 (tpt) cc_final: 0.6612 (tpt) REVERT: 5 8 LEU cc_start: 0.8402 (mt) cc_final: 0.8089 (mp) REVERT: 6 16 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8043 (mttt) REVERT: 8 12 ASP cc_start: 0.7115 (m-30) cc_final: 0.6768 (m-30) REVERT: 8 24 GLN cc_start: 0.7735 (mt0) cc_final: 0.7418 (mt0) REVERT: 9 21 MET cc_start: 0.8978 (mmm) cc_final: 0.8689 (mmt) REVERT: f 28 GLU cc_start: 0.7625 (tp30) cc_final: 0.7306 (tp30) REVERT: h 32 TYR cc_start: 0.8256 (m-80) cc_final: 0.7983 (m-80) outliers start: 23 outliers final: 9 residues processed: 400 average time/residue: 1.7955 time to fit residues: 813.7045 Evaluate side-chains 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 364 time to evaluate : 2.842 ------------------------------------------------------------------------------- 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 V residue 10 LEU 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 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: 5.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 200 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 e 37 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 = 0.3756 r_free = 0.3756 target = 0.147038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126526 restraints weight = 28572.345| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 0.84 r_work: 0.3299 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 30708 Z= 0.155 Angle : 0.855 16.774 42300 Z= 0.299 Chirality : 0.043 0.397 4266 Planarity : 0.004 0.038 4743 Dihedral : 21.857 179.937 8811 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.01 % Allowed : 9.87 % 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: 3.74 (0.16), residues: 2421 helix: 3.28 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.74 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 40 HIS 0.006 0.002 HIS 4 37 PHE 0.012 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 0.04694 ( 1494) hydrogen bonds : angle 3.41633 ( 4344) covalent geometry : bond 0.00368 (30636) covalent geometry : angle 0.85534 (42300) Misc. bond : bond 0.04297 ( 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 405 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 384 time to evaluate : 3.013 Fit side-chains revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8690 (m-80) cc_final: 0.8457 (m-80) REVERT: C 1 MET cc_start: 0.6932 (tpt) cc_final: 0.6509 (tpt) REVERT: E 11 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8287 (ttt-90) REVERT: F 14 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7320 (mt-10) REVERT: I 12 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7444 (mtp85) REVERT: J 23 MET cc_start: 0.8332 (mmm) cc_final: 0.7911 (mmm) REVERT: J 38 PHE cc_start: 0.8568 (m-80) cc_final: 0.8299 (m-80) REVERT: K 1 MET cc_start: 0.6785 (tpt) cc_final: 0.6296 (tpt) REVERT: K 8 LEU cc_start: 0.8454 (mt) cc_final: 0.8219 (mp) REVERT: K 11 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7477 (mtp85) REVERT: L 29 TYR cc_start: 0.8896 (t80) cc_final: 0.8651 (t80) REVERT: M 12 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7824 (mtp85) REVERT: N 10 LEU cc_start: 0.7757 (tp) cc_final: 0.7490 (tp) REVERT: N 24 GLN cc_start: 0.7791 (mt0) cc_final: 0.7422 (mt0) REVERT: O 11 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7507 (ttm-80) REVERT: O 12 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6950 (mtp-110) REVERT: O 16 LEU cc_start: 0.8768 (tp) cc_final: 0.8549 (tt) REVERT: Q 12 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7416 (mtp85) REVERT: R 12 ASP cc_start: 0.7248 (m-30) cc_final: 0.6837 (m-30) REVERT: R 23 MET cc_start: 0.8495 (mmm) cc_final: 0.8119 (mmm) REVERT: T 14 GLU cc_start: 0.7203 (tt0) cc_final: 0.6937 (tt0) REVERT: T 29 TYR cc_start: 0.8851 (t80) cc_final: 0.8385 (t80) REVERT: V 10 LEU cc_start: 0.7622 (tp) cc_final: 0.7317 (tp) REVERT: V 14 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7225 (mt-10) REVERT: V 24 GLN cc_start: 0.7939 (mt0) cc_final: 0.7387 (tt0) REVERT: Z 14 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7170 (mt-10) REVERT: Z 23 MET cc_start: 0.8471 (mmm) cc_final: 0.7973 (mmm) REVERT: Z 24 GLN cc_start: 0.7793 (mt0) cc_final: 0.7509 (mt0) REVERT: Z 51 GLU cc_start: 0.7253 (pm20) cc_final: 0.7014 (pm20) REVERT: 2 16 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8028 (mttt) REVERT: 4 24 GLN cc_start: 0.7843 (mt0) cc_final: 0.7210 (tt0) REVERT: 5 1 MET cc_start: 0.6911 (tpt) cc_final: 0.6650 (tpt) REVERT: 5 8 LEU cc_start: 0.8401 (mt) cc_final: 0.8064 (mp) REVERT: 6 16 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8041 (mttt) REVERT: 8 12 ASP cc_start: 0.7106 (m-30) cc_final: 0.6722 (m-30) REVERT: 8 24 GLN cc_start: 0.7740 (mt0) cc_final: 0.7418 (mt0) REVERT: 9 21 MET cc_start: 0.8945 (mmm) cc_final: 0.8716 (mmt) REVERT: f 28 GLU cc_start: 0.7628 (tp30) cc_final: 0.7340 (tp30) REVERT: h 32 TYR cc_start: 0.8236 (m-80) cc_final: 0.7939 (m-80) outliers start: 21 outliers final: 12 residues processed: 399 average time/residue: 1.7611 time to fit residues: 797.2721 Evaluate side-chains 379 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 364 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain P residue 16 LYS 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 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: 0.6980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124705 restraints weight = 28651.531| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.84 r_work: 0.3271 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 30708 Z= 0.207 Angle : 0.943 18.654 42300 Z= 0.334 Chirality : 0.046 0.402 4266 Planarity : 0.004 0.040 4743 Dihedral : 22.349 179.958 8811 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.15 % Allowed : 9.96 % 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: 3.46 (0.16), residues: 2421 helix: 3.07 (0.10), residues: 1629 sheet: None (None), residues: 0 loop : 0.65 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 5 5 HIS 0.008 0.002 HIS H 37 PHE 0.017 0.002 PHE l 41 TYR 0.009 0.002 TYR G 46 ARG 0.009 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 1494) hydrogen bonds : angle 3.55034 ( 4344) covalent geometry : bond 0.00499 (30636) covalent geometry : angle 0.94261 (42300) Misc. bond : bond 0.03567 ( 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 397 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 373 time to evaluate : 2.681 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7022 (tpt) cc_final: 0.6537 (tpt) REVERT: E 11 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8306 (ttt-90) REVERT: F 14 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7330 (mt-10) REVERT: I 12 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7507 (mtp85) REVERT: J 23 MET cc_start: 0.8308 (mmm) cc_final: 0.7752 (mmm) REVERT: J 38 PHE cc_start: 0.8564 (m-80) cc_final: 0.8300 (m-80) REVERT: K 1 MET cc_start: 0.6850 (tpt) cc_final: 0.6314 (tpt) REVERT: K 8 LEU cc_start: 0.8464 (mt) cc_final: 0.8229 (mp) REVERT: K 11 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7525 (mtp85) REVERT: L 29 TYR cc_start: 0.8952 (t80) cc_final: 0.8689 (t80) REVERT: N 10 LEU cc_start: 0.7771 (tp) cc_final: 0.7570 (tp) REVERT: N 24 GLN cc_start: 0.7785 (mt0) cc_final: 0.7518 (mt0) REVERT: O 11 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7604 (ttm-80) REVERT: O 12 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7001 (mtp-110) REVERT: O 16 LEU cc_start: 0.8761 (tp) cc_final: 0.8530 (tt) REVERT: Q 12 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7451 (mtp85) REVERT: R 12 ASP cc_start: 0.7240 (m-30) cc_final: 0.6880 (m-30) REVERT: R 23 MET cc_start: 0.8518 (mmm) cc_final: 0.8223 (mmm) REVERT: T 29 TYR cc_start: 0.8911 (t80) cc_final: 0.8394 (t80) REVERT: V 10 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7503 (tp) REVERT: V 14 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7246 (mt-10) REVERT: V 24 GLN cc_start: 0.7906 (mt0) cc_final: 0.7390 (tt0) REVERT: Z 14 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7162 (mt-10) REVERT: Z 24 GLN cc_start: 0.7825 (mt0) cc_final: 0.7535 (mt0) REVERT: Z 51 GLU cc_start: 0.7287 (pm20) cc_final: 0.7040 (pm20) REVERT: 2 16 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (mttt) REVERT: 4 24 GLN cc_start: 0.7817 (mt0) cc_final: 0.7235 (tt0) REVERT: 5 1 MET cc_start: 0.6810 (tpt) cc_final: 0.6536 (tpt) REVERT: 5 8 LEU cc_start: 0.8409 (mt) cc_final: 0.8100 (mp) REVERT: 6 16 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.8016 (mttt) REVERT: 8 12 ASP cc_start: 0.7087 (m-30) cc_final: 0.6763 (m-30) REVERT: 9 21 MET cc_start: 0.8985 (mmm) cc_final: 0.8723 (mmt) REVERT: h 32 TYR cc_start: 0.8237 (m-80) cc_final: 0.7986 (m-80) outliers start: 24 outliers final: 11 residues processed: 389 average time/residue: 1.8313 time to fit residues: 813.1367 Evaluate side-chains 378 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 363 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU 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 k residue 22 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 119 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.146217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125570 restraints weight = 28622.309| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.84 r_work: 0.3285 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 30708 Z= 0.178 Angle : 0.890 17.014 42300 Z= 0.316 Chirality : 0.044 0.400 4266 Planarity : 0.004 0.041 4743 Dihedral : 21.849 179.941 8811 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.05 % Allowed : 10.30 % Favored : 88.65 % 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: 3.15 (0.10), residues: 1629 sheet: None (None), residues: 0 loop : 0.65 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP k 40 HIS 0.006 0.002 HIS H 37 PHE 0.014 0.002 PHE 3 30 TYR 0.007 0.001 TYR n 32 ARG 0.009 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 1494) hydrogen bonds : angle 3.46513 ( 4344) covalent geometry : bond 0.00425 (30636) covalent geometry : angle 0.89012 (42300) Misc. bond : bond 0.03980 ( 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 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 372 time to evaluate : 2.668 Fit side-chains REVERT: C 1 MET cc_start: 0.7018 (tpt) cc_final: 0.6561 (tpt) REVERT: E 11 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8278 (ttt-90) REVERT: F 14 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7287 (mt-10) REVERT: I 12 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7477 (mtp85) REVERT: J 23 MET cc_start: 0.8314 (mmm) cc_final: 0.7768 (mmm) REVERT: J 38 PHE cc_start: 0.8564 (m-80) cc_final: 0.8301 (m-80) REVERT: K 1 MET cc_start: 0.6797 (tpt) cc_final: 0.6349 (tpt) REVERT: K 8 LEU cc_start: 0.8440 (mt) cc_final: 0.8202 (mp) REVERT: K 11 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7511 (mtp85) REVERT: L 29 TYR cc_start: 0.8903 (t80) cc_final: 0.8624 (t80) REVERT: N 10 LEU cc_start: 0.7835 (tp) cc_final: 0.7595 (tp) REVERT: N 24 GLN cc_start: 0.7778 (mt0) cc_final: 0.7408 (mt0) REVERT: O 11 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7595 (ttm-80) REVERT: O 12 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6992 (mtp-110) REVERT: O 16 LEU cc_start: 0.8750 (tp) cc_final: 0.8522 (tt) REVERT: Q 12 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7442 (mtp85) REVERT: R 12 ASP cc_start: 0.7218 (m-30) cc_final: 0.6860 (m-30) REVERT: T 29 TYR cc_start: 0.8888 (t80) cc_final: 0.8382 (t80) REVERT: U 1 MET cc_start: 0.8136 (tpp) cc_final: 0.7420 (tpp) REVERT: V 10 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7384 (tp) REVERT: V 14 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7199 (mt-10) REVERT: V 24 GLN cc_start: 0.7916 (mt0) cc_final: 0.7384 (tt0) REVERT: Z 14 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7128 (mt-10) REVERT: Z 24 GLN cc_start: 0.7793 (mt0) cc_final: 0.7501 (mt0) REVERT: Z 51 GLU cc_start: 0.7275 (pm20) cc_final: 0.7024 (pm20) REVERT: 2 16 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8028 (mttt) REVERT: 4 24 GLN cc_start: 0.7889 (mt0) cc_final: 0.7241 (tt0) REVERT: 5 1 MET cc_start: 0.6911 (tpt) cc_final: 0.6613 (tpt) REVERT: 5 6 LYS cc_start: 0.7996 (mttt) cc_final: 0.7715 (mtmt) REVERT: 5 8 LEU cc_start: 0.8395 (mt) cc_final: 0.8074 (mp) REVERT: 6 16 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: 8 12 ASP cc_start: 0.7108 (m-30) cc_final: 0.6785 (m-30) REVERT: 9 21 MET cc_start: 0.8984 (mmm) cc_final: 0.8745 (mmt) REVERT: f 28 GLU cc_start: 0.7621 (tp30) cc_final: 0.7344 (tp30) REVERT: h 32 TYR cc_start: 0.8237 (m-80) cc_final: 0.7942 (m-80) outliers start: 22 outliers final: 13 residues processed: 385 average time/residue: 1.7696 time to fit residues: 773.6759 Evaluate side-chains 381 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 364 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU 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 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: 5.9990 chunk 204 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 o 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124376 restraints weight = 28664.946| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.84 r_work: 0.3269 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 30708 Z= 0.218 Angle : 0.960 16.988 42300 Z= 0.342 Chirality : 0.047 0.394 4266 Planarity : 0.005 0.042 4743 Dihedral : 22.265 179.976 8811 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.86 % Allowed : 10.58 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.16), residues: 2421 helix: 2.97 (0.11), residues: 1629 sheet: None (None), residues: 0 loop : 0.62 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 5 5 HIS 0.008 0.002 HIS X 37 PHE 0.017 0.002 PHE l 41 TYR 0.010 0.002 TYR A 8 ARG 0.009 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 1494) hydrogen bonds : angle 3.57272 ( 4344) covalent geometry : bond 0.00526 (30636) covalent geometry : angle 0.95953 (42300) Misc. bond : bond 0.03615 ( 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 387 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 369 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7019 (tpt) cc_final: 0.6576 (tpt) REVERT: E 11 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.8264 (ttt-90) REVERT: F 14 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7326 (mt-10) REVERT: I 12 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7511 (mtp85) REVERT: J 23 MET cc_start: 0.8283 (mmm) cc_final: 0.7735 (mmm) REVERT: K 1 MET cc_start: 0.6783 (tpt) cc_final: 0.6242 (tpt) REVERT: K 8 LEU cc_start: 0.8461 (mt) cc_final: 0.8236 (mp) REVERT: K 11 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7522 (mtp85) REVERT: L 29 TYR cc_start: 0.8944 (t80) cc_final: 0.8625 (t80) REVERT: N 10 LEU cc_start: 0.7804 (tp) cc_final: 0.7587 (tp) REVERT: N 24 GLN cc_start: 0.7782 (mt0) cc_final: 0.7499 (mt0) REVERT: O 11 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7629 (ttm-80) REVERT: O 12 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7015 (mtp-110) REVERT: O 16 LEU cc_start: 0.8759 (tp) cc_final: 0.8528 (tt) REVERT: Q 12 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7453 (mtp85) REVERT: R 12 ASP cc_start: 0.7263 (m-30) cc_final: 0.6915 (m-30) REVERT: T 29 TYR cc_start: 0.8923 (t80) cc_final: 0.8451 (t80) REVERT: V 10 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7427 (tp) REVERT: V 14 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7217 (mt-10) REVERT: V 24 GLN cc_start: 0.7926 (mt0) cc_final: 0.7399 (tt0) REVERT: Z 14 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7157 (mt-10) REVERT: Z 24 GLN cc_start: 0.7843 (mt0) cc_final: 0.7558 (mt0) REVERT: Z 51 GLU cc_start: 0.7248 (pm20) cc_final: 0.7001 (pm20) REVERT: 2 16 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8035 (mttt) REVERT: 5 1 MET cc_start: 0.6843 (tpt) cc_final: 0.6490 (tpt) REVERT: 5 8 LEU cc_start: 0.8416 (mt) cc_final: 0.8102 (mp) REVERT: 6 16 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: 8 12 ASP cc_start: 0.7061 (m-30) cc_final: 0.6750 (m-30) REVERT: 9 21 MET cc_start: 0.8997 (mmm) cc_final: 0.8751 (mmt) REVERT: f 28 GLU cc_start: 0.7537 (tp30) cc_final: 0.7299 (tp30) REVERT: h 32 TYR cc_start: 0.8264 (m-80) cc_final: 0.7994 (m-80) outliers start: 18 outliers final: 10 residues processed: 378 average time/residue: 1.8686 time to fit residues: 804.0807 Evaluate side-chains 380 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU 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 6 residue 16 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 o 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126070 restraints weight = 28578.689| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.84 r_work: 0.3294 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: 0.8409 moved from start: 0.2122 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= 0.161 Angle : 0.866 15.249 42300 Z= 0.308 Chirality : 0.044 0.401 4266 Planarity : 0.004 0.044 4743 Dihedral : 21.464 179.944 8811 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.81 % Allowed : 11.06 % Favored : 88.12 % 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: 3.60 (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 0.017 0.001 TRP k 40 HIS 0.006 0.002 HIS H 37 PHE 0.012 0.002 PHE N 29 TYR 0.009 0.001 TYR d 32 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 1494) hydrogen bonds : angle 3.42271 ( 4344) covalent geometry : bond 0.00380 (30636) covalent geometry : angle 0.86610 (42300) Misc. bond : bond 0.04310 ( 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 384 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 367 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6945 (tpt) cc_final: 0.6575 (tpt) REVERT: E 11 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8288 (ttt-90) REVERT: F 14 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7263 (mt-10) REVERT: I 12 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7468 (mtp85) REVERT: J 23 MET cc_start: 0.8321 (mmm) cc_final: 0.7913 (mmm) REVERT: J 38 PHE cc_start: 0.8548 (m-80) cc_final: 0.8269 (m-80) REVERT: K 1 MET cc_start: 0.6782 (tpt) cc_final: 0.6225 (tpt) REVERT: K 8 LEU cc_start: 0.8439 (mt) cc_final: 0.8197 (mp) REVERT: K 11 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7544 (mtp85) REVERT: L 29 TYR cc_start: 0.8902 (t80) cc_final: 0.8631 (t80) REVERT: N 10 LEU cc_start: 0.7818 (tp) cc_final: 0.7582 (tp) REVERT: N 24 GLN cc_start: 0.7773 (mt0) cc_final: 0.7469 (mt0) REVERT: O 12 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6930 (mtp-110) REVERT: O 16 LEU cc_start: 0.8752 (tp) cc_final: 0.8533 (tt) REVERT: Q 12 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7428 (mtp85) REVERT: R 12 ASP cc_start: 0.7185 (m-30) cc_final: 0.6865 (m-30) REVERT: R 23 MET cc_start: 0.8535 (mmm) cc_final: 0.8298 (mmm) REVERT: T 29 TYR cc_start: 0.8877 (t80) cc_final: 0.8368 (t80) REVERT: V 10 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (tp) REVERT: V 14 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7184 (mt-10) REVERT: V 24 GLN cc_start: 0.7911 (mt0) cc_final: 0.7375 (tt0) REVERT: Z 14 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7116 (mt-10) REVERT: Z 24 GLN cc_start: 0.7756 (mt0) cc_final: 0.7475 (mt0) REVERT: Z 51 GLU cc_start: 0.7250 (pm20) cc_final: 0.7001 (pm20) REVERT: 2 16 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8044 (mttt) REVERT: 5 1 MET cc_start: 0.6891 (tpt) cc_final: 0.6643 (tpt) REVERT: 5 6 LYS cc_start: 0.7994 (mttt) cc_final: 0.7712 (mtmt) REVERT: 5 8 LEU cc_start: 0.8406 (mt) cc_final: 0.8072 (mp) REVERT: 6 16 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8054 (mttt) REVERT: 8 12 ASP cc_start: 0.7131 (m-30) cc_final: 0.6783 (m-30) REVERT: 9 21 MET cc_start: 0.8958 (mmm) cc_final: 0.8726 (mmt) REVERT: f 28 GLU cc_start: 0.7593 (tp30) cc_final: 0.7325 (tp30) REVERT: h 32 TYR cc_start: 0.8232 (m-80) cc_final: 0.7937 (m-80) outliers start: 17 outliers final: 11 residues processed: 375 average time/residue: 1.7718 time to fit residues: 754.1183 Evaluate side-chains 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 361 time to evaluate : 2.641 ------------------------------------------------------------------------------- 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 P residue 16 LYS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU 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 6 residue 16 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain m residue 9 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 206 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.147666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127146 restraints weight = 28694.350| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.84 r_work: 0.3312 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 30708 Z= 0.144 Angle : 0.826 14.865 42300 Z= 0.295 Chirality : 0.042 0.391 4266 Planarity : 0.004 0.044 4743 Dihedral : 20.814 179.999 8811 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.86 % Allowed : 10.97 % Favored : 88.17 % 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: 3.80 (0.16), residues: 2421 helix: 3.33 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.76 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP k 40 HIS 0.005 0.001 HIS 4 37 PHE 0.012 0.002 PHE N 29 TYR 0.011 0.001 TYR d 32 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 1494) hydrogen bonds : angle 3.31873 ( 4344) covalent geometry : bond 0.00336 (30636) covalent geometry : angle 0.82576 (42300) Misc. bond : bond 0.04394 ( 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 397 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 379 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8691 (m-80) cc_final: 0.8450 (m-80) REVERT: C 1 MET cc_start: 0.6918 (tpt) cc_final: 0.6477 (tpt) REVERT: E 11 ARG cc_start: 0.8555 (ttt-90) cc_final: 0.8272 (ttt-90) REVERT: F 11 SER cc_start: 0.7989 (p) cc_final: 0.7486 (t) REVERT: F 14 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7308 (mt-10) REVERT: I 12 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7451 (mtp85) REVERT: J 23 MET cc_start: 0.8326 (mmm) cc_final: 0.7920 (mmm) REVERT: J 24 GLN cc_start: 0.7874 (mt0) cc_final: 0.7189 (tt0) REVERT: J 38 PHE cc_start: 0.8556 (m-80) cc_final: 0.8289 (m-80) REVERT: K 1 MET cc_start: 0.6734 (tpt) cc_final: 0.6261 (tpt) REVERT: K 8 LEU cc_start: 0.8427 (mt) cc_final: 0.8177 (mp) REVERT: K 11 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7538 (mtp85) REVERT: M 12 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7820 (mtp85) REVERT: N 10 LEU cc_start: 0.7792 (tp) cc_final: 0.7550 (tp) REVERT: N 24 GLN cc_start: 0.7787 (mt0) cc_final: 0.7467 (mt0) REVERT: O 1 MET cc_start: 0.7176 (mmm) cc_final: 0.6475 (tpt) REVERT: O 12 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6956 (mtp-110) REVERT: O 16 LEU cc_start: 0.8772 (tp) cc_final: 0.8564 (tt) REVERT: Q 12 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7417 (mtp85) REVERT: R 12 ASP cc_start: 0.7198 (m-30) cc_final: 0.6891 (m-30) REVERT: R 14 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7115 (mt-10) REVERT: R 23 MET cc_start: 0.8565 (mmm) cc_final: 0.8185 (mmm) REVERT: T 14 GLU cc_start: 0.7207 (tt0) cc_final: 0.6951 (tt0) REVERT: T 29 TYR cc_start: 0.8864 (t80) cc_final: 0.8335 (t80) REVERT: V 10 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7351 (tp) REVERT: V 14 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7253 (mt-10) REVERT: V 24 GLN cc_start: 0.7912 (mt0) cc_final: 0.7378 (tt0) REVERT: Z 14 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7189 (mt-10) REVERT: Z 24 GLN cc_start: 0.7760 (mt0) cc_final: 0.7512 (mt0) REVERT: Z 51 GLU cc_start: 0.7254 (pm20) cc_final: 0.6999 (pm20) REVERT: 2 16 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8047 (mttt) REVERT: 5 1 MET cc_start: 0.6889 (tpt) cc_final: 0.6664 (tpt) REVERT: 5 6 LYS cc_start: 0.8034 (mttt) cc_final: 0.7814 (mtpm) REVERT: 5 8 LEU cc_start: 0.8402 (mt) cc_final: 0.8073 (mp) REVERT: 6 16 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8039 (mttt) REVERT: 8 12 ASP cc_start: 0.7132 (m-30) cc_final: 0.6778 (m-30) REVERT: f 28 GLU cc_start: 0.7548 (tp30) cc_final: 0.7258 (tp30) REVERT: h 32 TYR cc_start: 0.8220 (m-80) cc_final: 0.7892 (m-80) outliers start: 18 outliers final: 10 residues processed: 388 average time/residue: 1.8175 time to fit residues: 799.5391 Evaluate side-chains 377 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 363 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain V residue 10 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123547 restraints weight = 28675.452| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 0.83 r_work: 0.3257 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 30708 Z= 0.282 Angle : 1.048 16.151 42300 Z= 0.378 Chirality : 0.051 0.412 4266 Planarity : 0.005 0.053 4743 Dihedral : 22.321 179.995 8811 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.43 % Allowed : 11.59 % Favored : 87.98 % 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: 3.21 (0.16), residues: 2421 helix: 2.86 (0.11), residues: 1629 sheet: None (None), residues: 0 loop : 0.60 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 5 5 HIS 0.010 0.003 HIS L 37 PHE 0.025 0.003 PHE l 41 TYR 0.015 0.003 TYR d 32 ARG 0.010 0.001 ARG 7 12 Details of bonding type rmsd hydrogen bonds : bond 0.05457 ( 1494) hydrogen bonds : angle 3.68087 ( 4344) covalent geometry : bond 0.00690 (30636) covalent geometry : angle 1.04798 (42300) Misc. bond : bond 0.03412 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22745.64 seconds wall clock time: 392 minutes 12.57 seconds (23532.57 seconds total)