Starting phenix.real_space_refine on Mon Aug 25 15:11:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z81_39835/08_2025/8z81_39835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z81_39835/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z81_39835/08_2025/8z81_39835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z81_39835/08_2025/8z81_39835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z81_39835/08_2025/8z81_39835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z81_39835/08_2025/8z81_39835.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.85, per 1000 atoms: 0.27 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: 3.51 Conformation dependent library (CDL) restraints added in 930.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.72 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: 5.11 Time building geometry restraints manager: 4.47 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 102) selection = (chain '8' and resid 7 through 102) selection = (chain 'B' and resid 7 through 102) selection = (chain 'F' and resid 7 through 102) selection = (chain 'J' and resid 7 through 102) selection = (chain 'N' and resid 7 through 102) selection = (chain 'R' and resid 7 through 102) selection = (chain 'V' and resid 7 through 102) selection = chain 'Z' } ncs_group { reference = (chain 'a' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'c' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'e' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'g' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'i' and (resid 1 through 49 or resid 102 or (resid 104 and (name C01 or n \ ame C02 or name C03 or name C04 or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or na \ me O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ))) \ ) selection = (chain 'k' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'm' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'o' and (resid 1 through 49 or resid 102 or resid 104)) selection = (chain 'q' and (resid 1 through 49 or resid 102 or resid 104)) } ncs_group { reference = (chain 'b' and resid 10 through 58) selection = (chain 'd' and resid 10 through 58) selection = (chain 'f' and resid 10 through 58) selection = (chain 'h' and resid 10 through 58) selection = (chain 'j' and resid 10 through 58) selection = (chain 'l' and resid 10 through 58) selection = (chain 'n' and resid 10 through 58) selection = (chain 'p' and resid 10 through 58) selection = (chain 'r' and resid 10 through 58) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.300 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 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:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- 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 : 14.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG 5 11 TYR 0.011 0.002 TYR G 46 PHE 0.016 0.002 PHE b 41 TRP 0.017 0.002 TRP 1 5 HIS 0.006 0.002 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.02321 (30636) covalent geometry : angle 2.31862 (42300) hydrogen bonds : bond 0.16074 ( 1494) hydrogen bonds : angle 5.19837 ( 4344) 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 : 1.016 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: 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: 0.6991 (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: 0.7256 (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: 1.0218 time to fit residues: 508.6951 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.145863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125263 restraints weight = 28660.826| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 0.84 r_work: 0.3279 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 30708 Z= 0.189 Angle : 0.981 17.248 42300 Z= 0.336 Chirality : 0.046 0.386 4266 Planarity : 0.005 0.036 4743 Dihedral : 23.969 179.912 8811 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.81 % Allowed : 7.81 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.16), residues: 2421 helix: 3.22 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.79 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 12 TYR 0.012 0.002 TYR n 32 PHE 0.014 0.002 PHE 3 30 TRP 0.016 0.002 TRP k 40 HIS 0.005 0.002 HIS X 37 Details of bonding type rmsd covalent geometry : bond 0.00457 (30636) covalent geometry : angle 0.98063 (42300) hydrogen bonds : bond 0.05166 ( 1494) hydrogen bonds : angle 3.58244 ( 4344) Misc. bond : bond 0.04996 ( 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 : 1.204 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7023 (tpt) cc_final: 0.6442 (tpt) REVERT: F 14 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7418 (mt-10) REVERT: I 12 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7479 (mtp85) REVERT: J 23 MET cc_start: 0.8298 (mmm) cc_final: 0.7692 (mmm) REVERT: K 1 MET cc_start: 0.6912 (tpt) cc_final: 0.6379 (tpt) REVERT: K 8 LEU cc_start: 0.8460 (mt) cc_final: 0.8224 (mp) REVERT: L 29 TYR cc_start: 0.8909 (t80) cc_final: 0.8571 (t80) REVERT: M 11 ARG cc_start: 0.8629 (ttt-90) cc_final: 0.8251 (ttt180) REVERT: N 24 GLN cc_start: 0.7788 (mt0) cc_final: 0.7157 (tt0) REVERT: O 1 MET cc_start: 0.7185 (mmm) cc_final: 0.6327 (tpt) REVERT: Q 12 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7451 (mtp85) REVERT: R 12 ASP cc_start: 0.7355 (m-30) cc_final: 0.6834 (m-30) REVERT: R 14 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7272 (mt-10) REVERT: T 29 TYR cc_start: 0.8868 (t80) cc_final: 0.8388 (t80) REVERT: V 14 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7349 (mt-10) REVERT: V 24 GLN cc_start: 0.7830 (mt0) cc_final: 0.7255 (tt0) REVERT: Z 14 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7175 (mt-10) REVERT: Z 23 MET cc_start: 0.8456 (mmm) cc_final: 0.7972 (mmm) REVERT: Z 24 GLN cc_start: 0.7724 (mt0) cc_final: 0.7377 (mt0) REVERT: 4 12 ASP cc_start: 0.7170 (m-30) cc_final: 0.6728 (m-30) REVERT: 4 24 GLN cc_start: 0.7866 (mt0) cc_final: 0.7243 (tt0) REVERT: 5 1 MET cc_start: 0.7106 (tpt) cc_final: 0.6785 (tpt) REVERT: 5 8 LEU cc_start: 0.8361 (mt) cc_final: 0.7998 (mp) REVERT: 6 16 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8040 (mttt) REVERT: 8 12 ASP cc_start: 0.7166 (m-30) cc_final: 0.6935 (m-30) REVERT: 8 24 GLN cc_start: 0.7735 (mt0) cc_final: 0.7362 (mt0) REVERT: 9 21 MET cc_start: 0.8965 (mmm) cc_final: 0.8758 (mmt) REVERT: h 32 TYR cc_start: 0.8278 (m-80) cc_final: 0.7939 (m-80) outliers start: 17 outliers final: 5 residues processed: 406 average time/residue: 0.9624 time to fit residues: 441.1094 Evaluate side-chains 369 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 363 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 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 150 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3738 r_free = 0.3738 target = 0.145559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124945 restraints weight = 28778.653| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.84 r_work: 0.3274 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 30708 Z= 0.190 Angle : 0.950 17.159 42300 Z= 0.325 Chirality : 0.044 0.348 4266 Planarity : 0.004 0.036 4743 Dihedral : 23.124 179.993 8811 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.05 % Allowed : 8.72 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.59 (0.16), residues: 2421 helix: 3.14 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.75 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 12 TYR 0.008 0.002 TYR A 8 PHE 0.014 0.002 PHE 8 29 TRP 0.015 0.002 TRP k 40 HIS 0.007 0.002 HIS 4 37 Details of bonding type rmsd covalent geometry : bond 0.00459 (30636) covalent geometry : angle 0.94966 (42300) hydrogen bonds : bond 0.05107 ( 1494) hydrogen bonds : angle 3.57224 ( 4344) Misc. bond : bond 0.03699 ( 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 412 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 390 time to evaluate : 1.052 Fit side-chains REVERT: C 1 MET cc_start: 0.7001 (tpt) cc_final: 0.6484 (tpt) REVERT: E 11 ARG cc_start: 0.8593 (ttt-90) cc_final: 0.8284 (ttt-90) REVERT: F 14 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7404 (mt-10) REVERT: I 12 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7471 (mtp85) REVERT: J 23 MET cc_start: 0.8313 (mmm) cc_final: 0.7739 (mmm) REVERT: J 38 PHE cc_start: 0.8575 (m-80) cc_final: 0.8312 (m-80) REVERT: K 1 MET cc_start: 0.6901 (tpt) cc_final: 0.6342 (tpt) REVERT: K 8 LEU cc_start: 0.8448 (mt) cc_final: 0.8208 (mp) REVERT: L 29 TYR cc_start: 0.8907 (t80) cc_final: 0.8635 (t80) REVERT: N 10 LEU cc_start: 0.7778 (tp) cc_final: 0.7512 (tp) REVERT: N 24 GLN cc_start: 0.7790 (mt0) cc_final: 0.7454 (mt0) REVERT: R 11 SER cc_start: 0.8078 (p) cc_final: 0.7409 (t) REVERT: R 12 ASP cc_start: 0.7276 (m-30) cc_final: 0.6736 (m-30) REVERT: T 29 TYR cc_start: 0.8860 (t80) cc_final: 0.8394 (t80) REVERT: V 10 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7389 (tp) REVERT: V 14 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7224 (mt-10) REVERT: V 24 GLN cc_start: 0.7847 (mt0) cc_final: 0.7347 (tt0) REVERT: Z 10 LEU cc_start: 0.7647 (tp) cc_final: 0.7411 (tp) REVERT: Z 14 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7153 (mt-10) REVERT: Z 23 MET cc_start: 0.8443 (mmm) cc_final: 0.7982 (mmm) REVERT: Z 24 GLN cc_start: 0.7736 (mt0) cc_final: 0.7392 (mt0) REVERT: Z 51 GLU cc_start: 0.7277 (pm20) cc_final: 0.7048 (pm20) REVERT: 2 16 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7989 (mttt) REVERT: 4 12 ASP cc_start: 0.7286 (m-30) cc_final: 0.7057 (m-30) REVERT: 4 24 GLN cc_start: 0.7819 (mt0) cc_final: 0.7224 (tt0) REVERT: 5 1 MET cc_start: 0.6940 (tpt) cc_final: 0.6607 (tpt) REVERT: 5 6 LYS cc_start: 0.8026 (mttt) cc_final: 0.7761 (mtmt) REVERT: 5 8 LEU cc_start: 0.8390 (mt) cc_final: 0.8057 (mp) REVERT: 6 16 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: 8 12 ASP cc_start: 0.7162 (m-30) cc_final: 0.6835 (m-30) REVERT: 8 24 GLN cc_start: 0.7737 (mt0) cc_final: 0.7428 (mt0) REVERT: 9 21 MET cc_start: 0.8977 (mmm) cc_final: 0.8764 (mmt) REVERT: h 32 TYR cc_start: 0.8277 (m-80) cc_final: 0.7884 (m-80) outliers start: 22 outliers final: 10 residues processed: 404 average time/residue: 0.9684 time to fit residues: 441.4469 Evaluate side-chains 377 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 364 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 188 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** a 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 ASN g 2 ASN i 2 ASN ** 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 = 0.3722 r_free = 0.3722 target = 0.144366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123807 restraints weight = 28621.841| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.84 r_work: 0.3260 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1733 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= 0.245 Angle : 1.039 18.291 42300 Z= 0.360 Chirality : 0.047 0.349 4266 Planarity : 0.005 0.037 4743 Dihedral : 23.601 179.965 8811 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.25 % Allowed : 9.48 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.16), residues: 2421 helix: 2.89 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.65 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 12 TYR 0.010 0.002 TYR 9 46 PHE 0.018 0.003 PHE b 41 TRP 0.017 0.002 TRP k 40 HIS 0.008 0.002 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00598 (30636) covalent geometry : angle 1.03882 (42300) hydrogen bonds : bond 0.05369 ( 1494) hydrogen bonds : angle 3.69153 ( 4344) Misc. bond : bond 0.03568 ( 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 401 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 375 time to evaluate : 1.020 Fit side-chains REVERT: A 1 MET cc_start: 0.8122 (tpp) cc_final: 0.7541 (tpp) REVERT: C 1 MET cc_start: 0.6943 (tpt) cc_final: 0.6459 (tpt) REVERT: E 11 ARG cc_start: 0.8595 (ttt-90) cc_final: 0.8261 (ttt-90) REVERT: F 14 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7395 (mt-10) REVERT: I 12 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7504 (mtp85) REVERT: J 23 MET cc_start: 0.8278 (mmm) cc_final: 0.7743 (mmm) REVERT: K 1 MET cc_start: 0.6939 (tpt) cc_final: 0.6346 (tpt) REVERT: K 8 LEU cc_start: 0.8468 (mt) cc_final: 0.8261 (mp) REVERT: L 29 TYR cc_start: 0.8957 (t80) cc_final: 0.8675 (t80) REVERT: N 10 LEU cc_start: 0.7764 (tp) cc_final: 0.7552 (tp) REVERT: N 24 GLN cc_start: 0.7795 (mt0) cc_final: 0.7445 (mt0) REVERT: R 12 ASP cc_start: 0.7364 (m-30) cc_final: 0.6957 (m-30) REVERT: T 29 TYR cc_start: 0.8911 (t80) cc_final: 0.8424 (t80) REVERT: U 1 MET cc_start: 0.8042 (tpp) cc_final: 0.7426 (tpp) REVERT: V 10 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7517 (tp) REVERT: V 14 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7262 (mt-10) REVERT: V 24 GLN cc_start: 0.7930 (mt0) cc_final: 0.7378 (tt0) REVERT: Z 14 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7061 (mt-10) REVERT: Z 24 GLN cc_start: 0.7804 (mt0) cc_final: 0.7514 (mt0) REVERT: Z 51 GLU cc_start: 0.7281 (pm20) cc_final: 0.7041 (pm20) REVERT: 2 16 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8073 (mttm) REVERT: 4 24 GLN cc_start: 0.7839 (mt0) cc_final: 0.7238 (tt0) REVERT: 5 1 MET cc_start: 0.6888 (tpt) cc_final: 0.6569 (tpt) REVERT: 5 8 LEU cc_start: 0.8404 (mt) cc_final: 0.8091 (mp) REVERT: 6 16 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8012 (mttt) REVERT: 8 12 ASP cc_start: 0.7098 (m-30) cc_final: 0.6768 (m-30) REVERT: 8 24 GLN cc_start: 0.7758 (mt0) cc_final: 0.7460 (mt0) REVERT: 9 21 MET cc_start: 0.9007 (mmm) cc_final: 0.8760 (mmt) REVERT: h 32 TYR cc_start: 0.8288 (m-80) cc_final: 0.7963 (m-80) outliers start: 26 outliers final: 9 residues processed: 394 average time/residue: 0.9919 time to fit residues: 439.8125 Evaluate side-chains 373 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 361 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 Z residue 13 GLU 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 q residue 22 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 95 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 188 optimal weight: 0.0000 chunk 157 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 a 37 ASN c 37 ASN e 2 ASN e 37 ASN g 2 ASN g 37 ASN i 2 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN o 2 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128202 restraints weight = 28777.456| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.84 r_work: 0.3329 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 30708 Z= 0.128 Angle : 0.814 15.809 42300 Z= 0.282 Chirality : 0.042 0.385 4266 Planarity : 0.004 0.039 4743 Dihedral : 21.538 179.958 8811 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.96 % Allowed : 10.06 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.93 (0.16), residues: 2421 helix: 3.42 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 12 TYR 0.007 0.001 TYR G 10 PHE 0.010 0.001 PHE 8 29 TRP 0.016 0.001 TRP k 40 HIS 0.004 0.001 HIS n 30 Details of bonding type rmsd covalent geometry : bond 0.00296 (30636) covalent geometry : angle 0.81360 (42300) hydrogen bonds : bond 0.04391 ( 1494) hydrogen bonds : angle 3.32832 ( 4344) Misc. bond : bond 0.04663 ( 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 408 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 388 time to evaluate : 1.027 Fit side-chains REVERT: B 38 PHE cc_start: 0.8661 (m-80) cc_final: 0.8433 (m-80) REVERT: C 1 MET cc_start: 0.6807 (tpt) cc_final: 0.6366 (tpt) REVERT: E 11 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.8230 (ttt-90) REVERT: F 14 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7299 (mt-10) REVERT: I 12 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7452 (mtp85) REVERT: J 23 MET cc_start: 0.8364 (mmm) cc_final: 0.7941 (mmm) REVERT: J 38 PHE cc_start: 0.8556 (m-80) cc_final: 0.8304 (m-80) REVERT: K 1 MET cc_start: 0.6737 (tpt) cc_final: 0.6180 (tpt) REVERT: K 8 LEU cc_start: 0.8431 (mt) cc_final: 0.8182 (mp) REVERT: K 11 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7464 (mtp85) REVERT: M 12 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7828 (mtp85) REVERT: N 10 LEU cc_start: 0.7709 (tp) cc_final: 0.7430 (tp) REVERT: N 24 GLN cc_start: 0.7773 (mt0) cc_final: 0.7116 (tt0) REVERT: N 27 LEU cc_start: 0.8223 (mp) cc_final: 0.7813 (tp) REVERT: O 12 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6970 (mtp-110) REVERT: O 16 LEU cc_start: 0.8721 (tp) cc_final: 0.8509 (tt) REVERT: Q 12 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7397 (mtp85) REVERT: R 12 ASP cc_start: 0.7197 (m-30) cc_final: 0.6724 (m-30) REVERT: R 14 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7201 (mt-10) REVERT: R 23 MET cc_start: 0.8499 (mmm) cc_final: 0.8211 (mmm) REVERT: T 14 GLU cc_start: 0.7224 (tt0) cc_final: 0.6976 (tt0) REVERT: V 10 LEU cc_start: 0.7601 (tp) cc_final: 0.7241 (tp) REVERT: V 14 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7218 (mt-10) REVERT: V 24 GLN cc_start: 0.7901 (mt0) cc_final: 0.7344 (tt0) REVERT: Z 10 LEU cc_start: 0.7630 (tp) cc_final: 0.7353 (tp) REVERT: Z 14 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7207 (mt-10) REVERT: Z 20 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (t) REVERT: Z 24 GLN cc_start: 0.7812 (mt0) cc_final: 0.7527 (mt0) REVERT: Z 51 GLU cc_start: 0.7239 (pm20) cc_final: 0.6992 (pm20) REVERT: 4 24 GLN cc_start: 0.7796 (mt0) cc_final: 0.7168 (tt0) REVERT: 5 1 MET cc_start: 0.6846 (tpt) cc_final: 0.6631 (tpt) REVERT: 5 6 LYS cc_start: 0.8025 (mttt) cc_final: 0.7771 (mtmt) REVERT: 5 8 LEU cc_start: 0.8340 (mt) cc_final: 0.7987 (mp) REVERT: 6 16 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: 8 12 ASP cc_start: 0.7168 (m-30) cc_final: 0.6721 (m-30) REVERT: 8 24 GLN cc_start: 0.7765 (mt0) cc_final: 0.7439 (mt0) REVERT: 9 21 MET cc_start: 0.8926 (mmm) cc_final: 0.8715 (mmt) REVERT: a 2 ASN cc_start: 0.6329 (m-40) cc_final: 0.6112 (p0) REVERT: a 3 GLN cc_start: 0.6951 (mm110) cc_final: 0.6361 (mm-40) REVERT: f 28 GLU cc_start: 0.7620 (tp30) cc_final: 0.7334 (tp30) REVERT: h 32 TYR cc_start: 0.8194 (m-80) cc_final: 0.7898 (m-80) outliers start: 20 outliers final: 4 residues processed: 405 average time/residue: 0.9353 time to fit residues: 428.3510 Evaluate side-chains 365 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 358 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain 6 residue 16 LYS Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN c 37 ASN e 2 ASN g 2 ASN i 2 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123722 restraints weight = 28673.746| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.84 r_work: 0.3257 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.007 0.162 30708 Z= 0.259 Angle : 1.023 17.825 42300 Z= 0.363 Chirality : 0.048 0.395 4266 Planarity : 0.005 0.038 4743 Dihedral : 22.873 179.987 8811 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.05 % Allowed : 10.44 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.16), residues: 2421 helix: 2.96 (0.11), residues: 1629 sheet: None (None), residues: 0 loop : 0.66 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 11 TYR 0.012 0.002 TYR 9 46 PHE 0.022 0.003 PHE l 41 TRP 0.017 0.002 TRP 5 5 HIS 0.011 0.003 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00632 (30636) covalent geometry : angle 1.02344 (42300) hydrogen bonds : bond 0.05365 ( 1494) hydrogen bonds : angle 3.65582 ( 4344) Misc. bond : bond 0.03448 ( 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 400 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 378 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8136 (tpp) cc_final: 0.7544 (tpp) REVERT: C 1 MET cc_start: 0.6989 (tpt) cc_final: 0.6445 (tpt) REVERT: E 11 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.8277 (ttt-90) REVERT: F 14 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7377 (mt-10) REVERT: I 12 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7527 (mtp85) REVERT: J 23 MET cc_start: 0.8268 (mmm) cc_final: 0.7718 (mmm) REVERT: J 38 PHE cc_start: 0.8555 (m-80) cc_final: 0.8307 (m-80) REVERT: K 1 MET cc_start: 0.6838 (tpt) cc_final: 0.6338 (tpt) REVERT: K 8 LEU cc_start: 0.8460 (mt) cc_final: 0.8256 (mp) REVERT: K 11 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7532 (mtp85) REVERT: N 24 GLN cc_start: 0.7793 (mt0) cc_final: 0.7442 (mt0) REVERT: O 12 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7341 (mtp180) REVERT: O 16 LEU cc_start: 0.8727 (tp) cc_final: 0.8485 (tt) REVERT: R 11 SER cc_start: 0.7983 (p) cc_final: 0.7379 (t) REVERT: R 12 ASP cc_start: 0.7358 (m-30) cc_final: 0.6958 (m-30) REVERT: U 1 MET cc_start: 0.8056 (tpp) cc_final: 0.7448 (tpp) REVERT: V 10 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7418 (tp) REVERT: V 14 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7250 (mt-10) REVERT: V 24 GLN cc_start: 0.7911 (mt0) cc_final: 0.7386 (tt0) REVERT: Z 14 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7111 (mt-10) REVERT: Z 24 GLN cc_start: 0.7842 (mt0) cc_final: 0.7556 (mt0) REVERT: Z 51 GLU cc_start: 0.7248 (pm20) cc_final: 0.6994 (pm20) REVERT: 1 11 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7529 (ttm-80) REVERT: 2 16 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7968 (mttm) REVERT: 5 1 MET cc_start: 0.6861 (tpt) cc_final: 0.6552 (tpt) REVERT: 5 6 LYS cc_start: 0.8061 (mttt) cc_final: 0.7775 (mtmt) REVERT: 5 8 LEU cc_start: 0.8409 (mt) cc_final: 0.8102 (mp) REVERT: 6 16 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8053 (mttt) REVERT: 8 12 ASP cc_start: 0.7064 (m-30) cc_final: 0.6742 (m-30) REVERT: 8 24 GLN cc_start: 0.7752 (mt0) cc_final: 0.7444 (mt0) REVERT: e 46 GLU cc_start: 0.8435 (tp30) cc_final: 0.8108 (tp30) REVERT: h 32 TYR cc_start: 0.8280 (m-80) cc_final: 0.8020 (m-80) outliers start: 22 outliers final: 8 residues processed: 389 average time/residue: 0.9180 time to fit residues: 402.1372 Evaluate side-chains 375 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 363 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU 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 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 103 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 135 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN c 37 ASN e 2 ASN g 2 ASN i 2 ASN k 2 ASN m 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128450 restraints weight = 28655.995| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.83 r_work: 0.3331 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 30708 Z= 0.128 Angle : 0.810 15.411 42300 Z= 0.284 Chirality : 0.042 0.389 4266 Planarity : 0.004 0.039 4743 Dihedral : 21.170 179.938 8811 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.67 % Allowed : 11.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.93 (0.16), residues: 2421 helix: 3.43 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 12 TYR 0.007 0.001 TYR d 32 PHE 0.011 0.001 PHE Z 29 TRP 0.016 0.001 TRP k 40 HIS 0.004 0.001 HIS l 30 Details of bonding type rmsd covalent geometry : bond 0.00295 (30636) covalent geometry : angle 0.81049 (42300) hydrogen bonds : bond 0.04372 ( 1494) hydrogen bonds : angle 3.28947 ( 4344) Misc. bond : bond 0.04734 ( 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 393 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 379 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6882 (tpt) cc_final: 0.6558 (tpt) REVERT: E 11 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.8234 (ttt-90) REVERT: F 14 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7327 (mt-10) REVERT: H 16 LYS cc_start: 0.8209 (mptp) cc_final: 0.7908 (mttt) REVERT: I 12 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7487 (mtp85) REVERT: J 23 MET cc_start: 0.8363 (mmm) cc_final: 0.7947 (mmm) REVERT: J 38 PHE cc_start: 0.8551 (m-80) cc_final: 0.8272 (m-80) REVERT: K 1 MET cc_start: 0.6762 (tpt) cc_final: 0.6239 (tpt) REVERT: K 8 LEU cc_start: 0.8464 (mt) cc_final: 0.8220 (mp) REVERT: K 11 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7513 (mtp85) REVERT: M 12 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7800 (mtp85) REVERT: N 24 GLN cc_start: 0.7790 (mt0) cc_final: 0.7408 (mt0) REVERT: N 27 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7804 (tp) REVERT: O 11 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7552 (ttm-80) REVERT: O 12 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6970 (mtp-110) REVERT: O 16 LEU cc_start: 0.8725 (tp) cc_final: 0.8512 (tt) REVERT: Q 12 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7395 (mtp85) REVERT: R 12 ASP cc_start: 0.7141 (m-30) cc_final: 0.6751 (m-30) REVERT: R 14 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7199 (mt-10) REVERT: R 23 MET cc_start: 0.8513 (mmm) cc_final: 0.8222 (mmm) REVERT: T 14 GLU cc_start: 0.7242 (tt0) cc_final: 0.6996 (tt0) REVERT: V 10 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7286 (tp) REVERT: V 14 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7279 (mt-10) REVERT: V 24 GLN cc_start: 0.7893 (mt0) cc_final: 0.7353 (tt0) REVERT: W 11 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7603 (ttm-80) REVERT: Z 14 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7189 (mt-10) REVERT: Z 20 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8343 (t) REVERT: Z 24 GLN cc_start: 0.7706 (mt0) cc_final: 0.7422 (mt0) REVERT: Z 51 GLU cc_start: 0.7246 (pm20) cc_final: 0.6992 (pm20) REVERT: 1 11 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7214 (ttm170) REVERT: 5 1 MET cc_start: 0.6892 (tpt) cc_final: 0.6664 (tpt) REVERT: 5 6 LYS cc_start: 0.8029 (mttt) cc_final: 0.7769 (mtmt) REVERT: 5 8 LEU cc_start: 0.8340 (mt) cc_final: 0.7993 (mp) REVERT: 6 16 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8056 (mttt) REVERT: 8 12 ASP cc_start: 0.7145 (m-30) cc_final: 0.6759 (m-30) REVERT: 8 24 GLN cc_start: 0.7757 (mt0) cc_final: 0.7427 (mt0) REVERT: f 28 GLU cc_start: 0.7566 (tp30) cc_final: 0.7318 (tp30) REVERT: h 32 TYR cc_start: 0.8193 (m-80) cc_final: 0.7908 (m-80) outliers start: 14 outliers final: 4 residues processed: 386 average time/residue: 0.8016 time to fit residues: 349.8261 Evaluate side-chains 369 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 360 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain 6 residue 16 LYS 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 58 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 196 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125966 restraints weight = 28456.189| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.83 r_work: 0.3292 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 30708 Z= 0.165 Angle : 0.864 15.900 42300 Z= 0.308 Chirality : 0.043 0.388 4266 Planarity : 0.004 0.039 4743 Dihedral : 21.428 179.973 8811 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.77 % Allowed : 11.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.75 (0.16), residues: 2421 helix: 3.29 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.74 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 12 TYR 0.008 0.001 TYR E 8 PHE 0.013 0.002 PHE 8 29 TRP 0.014 0.001 TRP k 40 HIS 0.006 0.002 HIS 4 37 Details of bonding type rmsd covalent geometry : bond 0.00392 (30636) covalent geometry : angle 0.86429 (42300) hydrogen bonds : bond 0.04768 ( 1494) hydrogen bonds : angle 3.37916 ( 4344) Misc. bond : bond 0.03873 ( 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 386 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 370 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 38 PHE cc_start: 0.8686 (m-80) cc_final: 0.8449 (m-80) REVERT: C 1 MET cc_start: 0.6929 (tpt) cc_final: 0.6480 (tpt) REVERT: E 11 ARG cc_start: 0.8569 (ttt-90) cc_final: 0.8248 (ttt-90) REVERT: F 14 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7273 (mt-10) REVERT: H 16 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7860 (mttt) REVERT: I 12 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7478 (mtp85) REVERT: J 23 MET cc_start: 0.8318 (mmm) cc_final: 0.7779 (mmm) REVERT: J 38 PHE cc_start: 0.8558 (m-80) cc_final: 0.8286 (m-80) REVERT: K 1 MET cc_start: 0.6739 (tpt) cc_final: 0.6262 (tpt) REVERT: K 8 LEU cc_start: 0.8429 (mt) cc_final: 0.8198 (mp) REVERT: K 11 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7532 (mtp85) REVERT: N 24 GLN cc_start: 0.7774 (mt0) cc_final: 0.7475 (mt0) REVERT: O 11 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7628 (ttm-80) REVERT: O 12 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6977 (mtp-110) REVERT: O 16 LEU cc_start: 0.8762 (tp) cc_final: 0.8535 (tt) REVERT: Q 12 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7440 (mtp85) REVERT: R 12 ASP cc_start: 0.7212 (m-30) cc_final: 0.6855 (m-30) REVERT: R 23 MET cc_start: 0.8515 (mmm) cc_final: 0.8309 (mmm) REVERT: V 10 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7357 (tp) REVERT: V 14 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7211 (mt-10) REVERT: V 24 GLN cc_start: 0.7936 (mt0) cc_final: 0.7399 (tt0) REVERT: Z 14 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7101 (mt-10) REVERT: Z 20 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (t) REVERT: Z 24 GLN cc_start: 0.7745 (mt0) cc_final: 0.7457 (mt0) REVERT: Z 51 GLU cc_start: 0.7273 (pm20) cc_final: 0.7019 (pm20) REVERT: 1 11 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7246 (ttm170) REVERT: 5 1 MET cc_start: 0.6876 (tpt) cc_final: 0.6666 (tpt) REVERT: 5 6 LYS cc_start: 0.8050 (mttt) cc_final: 0.7788 (mtmt) REVERT: 5 8 LEU cc_start: 0.8390 (mt) cc_final: 0.8071 (mp) REVERT: 6 16 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8055 (mttt) REVERT: 8 12 ASP cc_start: 0.7118 (m-30) cc_final: 0.6786 (m-30) REVERT: 8 24 GLN cc_start: 0.7763 (mt0) cc_final: 0.7500 (mt0) REVERT: f 28 GLU cc_start: 0.7608 (tp30) cc_final: 0.7370 (tp30) REVERT: h 32 TYR cc_start: 0.8227 (m-80) cc_final: 0.7986 (m-80) outliers start: 16 outliers final: 8 residues processed: 376 average time/residue: 0.8010 time to fit residues: 339.8155 Evaluate side-chains 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 363 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 20 SER 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 p residue 55 SER Chi-restraints excluded: chain r residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 206 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125222 restraints weight = 28566.908| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.84 r_work: 0.3281 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 30708 Z= 0.189 Angle : 0.909 16.381 42300 Z= 0.325 Chirality : 0.045 0.396 4266 Planarity : 0.004 0.040 4743 Dihedral : 21.706 179.946 8811 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.72 % Allowed : 11.54 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.54 (0.16), residues: 2421 helix: 3.11 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.70 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 12 TYR 0.009 0.002 TYR n 32 PHE 0.015 0.002 PHE l 41 TRP 0.014 0.002 TRP k 40 HIS 0.007 0.002 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00453 (30636) covalent geometry : angle 0.90914 (42300) hydrogen bonds : bond 0.04958 ( 1494) hydrogen bonds : angle 3.47955 ( 4344) Misc. bond : bond 0.03726 ( 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 387 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 372 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6905 (tpt) cc_final: 0.6460 (tpt) REVERT: E 11 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8268 (ttt-90) REVERT: F 11 SER cc_start: 0.7999 (p) cc_final: 0.7516 (t) REVERT: F 14 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7389 (mt-10) REVERT: I 12 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7498 (mtp85) REVERT: J 23 MET cc_start: 0.8302 (mmm) cc_final: 0.7755 (mmm) REVERT: J 38 PHE cc_start: 0.8554 (m-80) cc_final: 0.8285 (m-80) REVERT: K 1 MET cc_start: 0.6817 (tpt) cc_final: 0.6284 (tpt) REVERT: K 8 LEU cc_start: 0.8456 (mt) cc_final: 0.8238 (mp) REVERT: K 11 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7517 (mtp85) REVERT: M 11 ARG cc_start: 0.8615 (ttt-90) cc_final: 0.8253 (ttt180) REVERT: M 12 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7813 (mtp85) REVERT: N 24 GLN cc_start: 0.7777 (mt0) cc_final: 0.7490 (mt0) REVERT: O 11 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7648 (ttm-80) REVERT: O 12 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6957 (mtp-110) REVERT: O 16 LEU cc_start: 0.8746 (tp) cc_final: 0.8521 (tt) REVERT: Q 12 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7446 (mtp85) REVERT: R 12 ASP cc_start: 0.7257 (m-30) cc_final: 0.6917 (m-30) REVERT: R 23 MET cc_start: 0.8476 (mmm) cc_final: 0.8113 (mmm) REVERT: V 10 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7377 (tp) REVERT: V 14 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7210 (mt-10) REVERT: V 24 GLN cc_start: 0.7927 (mt0) cc_final: 0.7387 (tt0) REVERT: Z 14 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7154 (mt-10) REVERT: Z 20 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8349 (t) REVERT: Z 24 GLN cc_start: 0.7835 (mt0) cc_final: 0.7539 (mt0) REVERT: Z 51 GLU cc_start: 0.7300 (pm20) cc_final: 0.7044 (pm20) REVERT: 4 11 SER cc_start: 0.8072 (p) cc_final: 0.7585 (t) REVERT: 5 1 MET cc_start: 0.6800 (tpt) cc_final: 0.6600 (tpt) REVERT: 5 6 LYS cc_start: 0.8053 (mttt) cc_final: 0.7783 (mtmt) REVERT: 5 8 LEU cc_start: 0.8402 (mt) cc_final: 0.8086 (mp) REVERT: 8 12 ASP cc_start: 0.7095 (m-30) cc_final: 0.6781 (m-30) REVERT: 8 24 GLN cc_start: 0.7775 (mt0) cc_final: 0.7535 (mt0) REVERT: a 2 ASN cc_start: 0.6789 (p0) cc_final: 0.6559 (p0) REVERT: f 28 GLU cc_start: 0.7603 (tp30) cc_final: 0.7342 (tp30) REVERT: h 32 TYR cc_start: 0.8237 (m-80) cc_final: 0.7979 (m-80) outliers start: 15 outliers final: 8 residues processed: 379 average time/residue: 0.9683 time to fit residues: 413.5774 Evaluate side-chains 378 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 367 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 20 SER 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 p residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 60 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124605 restraints weight = 28482.690| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 0.83 r_work: 0.3273 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 30708 Z= 0.212 Angle : 0.948 15.973 42300 Z= 0.340 Chirality : 0.046 0.396 4266 Planarity : 0.005 0.049 4743 Dihedral : 21.854 179.986 8811 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.43 % Allowed : 11.83 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.38 (0.16), residues: 2421 helix: 2.98 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.66 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 12 TYR 0.012 0.002 TYR n 32 PHE 0.017 0.002 PHE l 41 TRP 0.014 0.002 TRP k 40 HIS 0.008 0.002 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00512 (30636) covalent geometry : angle 0.94771 (42300) hydrogen bonds : bond 0.05093 ( 1494) hydrogen bonds : angle 3.53076 ( 4344) Misc. bond : bond 0.03662 ( 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 380 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 371 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6994 (tpt) cc_final: 0.6526 (tpt) REVERT: E 11 ARG cc_start: 0.8591 (ttt-90) cc_final: 0.8332 (ttt-90) REVERT: F 11 SER cc_start: 0.7997 (p) cc_final: 0.7597 (t) REVERT: F 14 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7383 (mt-10) REVERT: I 12 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7509 (mtp85) REVERT: J 23 MET cc_start: 0.8304 (mmm) cc_final: 0.7748 (mmm) REVERT: J 38 PHE cc_start: 0.8542 (m-80) cc_final: 0.8268 (m-80) REVERT: K 1 MET cc_start: 0.6737 (tpt) cc_final: 0.6220 (tpt) REVERT: K 8 LEU cc_start: 0.8442 (mt) cc_final: 0.8226 (mp) REVERT: K 11 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7530 (mtp85) REVERT: M 12 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7828 (mtp85) REVERT: N 24 GLN cc_start: 0.7776 (mt0) cc_final: 0.7489 (mt0) REVERT: O 11 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7667 (ttm-80) REVERT: O 12 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7026 (mtp-110) REVERT: Q 12 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7441 (mtp85) REVERT: R 12 ASP cc_start: 0.7259 (m-30) cc_final: 0.6934 (m-30) REVERT: U 1 MET cc_start: 0.8112 (tpp) cc_final: 0.7397 (tpp) REVERT: V 10 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (tp) REVERT: V 14 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7218 (mt-10) REVERT: V 24 GLN cc_start: 0.7928 (mt0) cc_final: 0.7393 (tt0) REVERT: Z 14 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7150 (mt-10) REVERT: Z 24 GLN cc_start: 0.7830 (mt0) cc_final: 0.7543 (mt0) REVERT: Z 51 GLU cc_start: 0.7271 (pm20) cc_final: 0.7017 (pm20) REVERT: 4 11 SER cc_start: 0.8068 (p) cc_final: 0.7644 (t) REVERT: 5 1 MET cc_start: 0.6826 (tpt) cc_final: 0.6526 (tpt) REVERT: 5 6 LYS cc_start: 0.8008 (mttt) cc_final: 0.7744 (mtmt) REVERT: 5 8 LEU cc_start: 0.8403 (mt) cc_final: 0.8087 (mp) REVERT: 8 12 ASP cc_start: 0.7114 (m-30) cc_final: 0.6818 (m-30) REVERT: 8 24 GLN cc_start: 0.7775 (mt0) cc_final: 0.7534 (mt0) REVERT: f 28 GLU cc_start: 0.7586 (tp30) cc_final: 0.7303 (tp30) REVERT: h 32 TYR cc_start: 0.8239 (m-80) cc_final: 0.7971 (m-80) outliers start: 9 outliers final: 7 residues processed: 374 average time/residue: 0.9785 time to fit residues: 412.1906 Evaluate side-chains 374 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 365 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 12 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain m residue 9 VAL Chi-restraints excluded: chain p residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN e 2 ASN g 2 ASN i 2 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127419 restraints weight = 28624.731| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.83 r_work: 0.3317 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2303 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= 0.139 Angle : 0.821 14.362 42300 Z= 0.293 Chirality : 0.042 0.384 4266 Planarity : 0.004 0.046 4743 Dihedral : 20.894 179.974 8811 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.62 % Allowed : 11.83 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.16), residues: 2421 helix: 3.31 (0.10), residues: 1638 sheet: None (None), residues: 0 loop : 0.73 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 12 TYR 0.011 0.001 TYR n 32 PHE 0.012 0.001 PHE Z 29 TRP 0.016 0.001 TRP k 40 HIS 0.004 0.001 HIS 4 37 Details of bonding type rmsd covalent geometry : bond 0.00323 (30636) covalent geometry : angle 0.82147 (42300) hydrogen bonds : bond 0.04495 ( 1494) hydrogen bonds : angle 3.31192 ( 4344) Misc. bond : bond 0.04525 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11900.70 seconds wall clock time: 203 minutes 49.69 seconds (12229.69 seconds total)