Starting phenix.real_space_refine on Thu Mar 5 20:43:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.map" model { file = "/net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f0l_31400/03_2026/7f0l_31400.cif" } resolution = 2.94 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= 0.016 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 21 5.49 5 Mg 32 5.21 5 S 88 5.16 5 C 16545 2.51 5 N 3101 2.21 5 O 3670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23458 Number of models: 1 Model: "" Number of chains: 66 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "U" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 369 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 3, 'BPH': 1, 'LDA': 2, 'PGV': 3, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 497 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 284 Unusual residues: {'CDL': 2, 'LMT': 2, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 193 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'BCL': 1, 'LMT': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "5" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 141 Unusual residues: {'LDA': 2, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 5.94, per 1000 atoms: 0.25 Number of scatterers: 23458 At special positions: 0 Unit cell: (132.374, 114.87, 137.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 88 16.00 P 21 15.00 Mg 32 11.99 O 3670 8.00 N 3101 7.00 C 16545 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 875.1 milliseconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 72.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.610A pdb=" N ARG L 10 " --> pdb=" O ARG L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.575A pdb=" N VAL L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.589A pdb=" N GLY L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 112 removed outlier: 3.523A pdb=" N GLU L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.628A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.810A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.640A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 5.929A pdb=" N HIS L 168 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.549A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.899A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 262 No H-bonds generated for 'chain 'L' and resid 260 through 262' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.670A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.731A pdb=" N LEU M 116 " --> pdb=" O GLY M 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.612A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 180 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.623A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.861A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 34 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.510A pdb=" N LEU H 212 " --> pdb=" O SER H 209 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 239 through 244 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 4.280A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 45 removed outlier: 3.584A pdb=" N GLN B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.747A pdb=" N LYS D 6 " --> pdb=" O LYS D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 removed outlier: 3.565A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.514A pdb=" N SER D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.658A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 1 through 10 removed outlier: 3.967A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.864A pdb=" N LYS K 6 " --> pdb=" O LYS K 3 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 8 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 37 removed outlier: 3.584A pdb=" N VAL K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.685A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 52 removed outlier: 3.633A pdb=" N SER O 47 " --> pdb=" O TRP O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 removed outlier: 3.509A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 45 removed outlier: 3.602A pdb=" N VAL R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.837A pdb=" N VAL S 18 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 12 through 45 Processing helix chain 'V' and resid 2 through 10 removed outlier: 4.048A pdb=" N TYR V 5 " --> pdb=" O SER V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 38 Processing helix chain 'V' and resid 42 through 52 Processing helix chain 'W' and resid 12 through 45 removed outlier: 3.502A pdb=" N VAL W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 8 removed outlier: 3.802A pdb=" N TRP Y 8 " --> pdb=" O TYR Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 38 Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Z' and resid 12 through 45 Processing helix chain '1' and resid 3 through 10 removed outlier: 3.605A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 51 removed outlier: 3.543A pdb=" N ALA 1 48 " --> pdb=" O LEU 1 44 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 45 Processing helix chain '3' and resid 3 through 5 No H-bonds generated for 'chain '3' and resid 3 through 5' Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 52 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 3 through 10 removed outlier: 3.729A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 5 10 " --> pdb=" O ILE 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 38 Processing helix chain '5' and resid 42 through 51 Processing helix chain '6' and resid 12 through 45 Processing helix chain '7' and resid 6 through 11 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.550A pdb=" N PHE 7 17 " --> pdb=" O PRO 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 51 Processing helix chain '8' and resid 12 through 45 Processing helix chain 'X' and resid 18 through 54 Processing helix chain 'U' and resid 5 through 30 Processing helix chain 'U' and resid 31 through 48 removed outlier: 3.709A pdb=" N GLY U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.806A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.829A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.002A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA6, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.822A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL H 169 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA H 176 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.357A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3600 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: 3.47 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 6887 1.37 - 1.54: 17020 1.54 - 1.71: 113 1.71 - 1.88: 171 1.88 - 2.05: 128 Bond restraints: 24319 Sorted by residual: bond pdb=" CB7 CDL Y 102 " pdb=" OB8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 304 " pdb=" OA8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL H 305 " pdb=" OA8 CDL H 305 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL H 304 " pdb=" OB8 CDL H 304 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 ... (remaining 24314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 30783 3.72 - 7.45: 2092 7.45 - 11.17: 296 11.17 - 14.90: 55 14.90 - 18.62: 13 Bond angle restraints: 33239 Sorted by residual: angle pdb=" C51 CDL M 811 " pdb=" CB5 CDL M 811 " pdb=" OB6 CDL M 811 " ideal model delta sigma weight residual 111.33 122.29 -10.96 1.32e+00 5.72e-01 6.87e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.28 -13.71 1.83e+00 2.99e-01 5.63e+01 angle pdb=" C1D BCL 8 102 " pdb=" C2D BCL 8 102 " pdb=" CMD BCL 8 102 " ideal model delta sigma weight residual 125.57 139.06 -13.49 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL M 803 " pdb=" C2D BCL M 803 " pdb=" CMD BCL M 803 " ideal model delta sigma weight residual 125.57 139.05 -13.48 1.83e+00 2.99e-01 5.44e+01 angle pdb=" C1D BCL A 703 " pdb=" C2D BCL A 703 " pdb=" CMD BCL A 703 " ideal model delta sigma weight residual 125.57 138.97 -13.40 1.83e+00 2.99e-01 5.37e+01 ... (remaining 33234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 13144 35.96 - 71.92: 650 71.92 - 107.89: 127 107.89 - 143.85: 52 143.85 - 179.81: 8 Dihedral angle restraints: 13981 sinusoidal: 7399 harmonic: 6582 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.66 -179.34 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 1 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CBD BCL M 803 " pdb=" CGD BCL M 803 " pdb=" O2D BCL M 803 " pdb=" CED BCL M 803 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 1 5.00e+00 4.00e-02 9.90e+01 ... (remaining 13978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2645 0.057 - 0.115: 511 0.115 - 0.172: 123 0.172 - 0.230: 41 0.230 - 0.287: 15 Chirality restraints: 3335 Sorted by residual: chirality pdb=" C05 PGV Q 103 " pdb=" C04 PGV Q 103 " pdb=" C06 PGV Q 103 " pdb=" O05 PGV Q 103 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV X 101 " pdb=" C04 PGV X 101 " pdb=" C06 PGV X 101 " pdb=" O05 PGV X 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3332 not shown) Planarity restraints: 3930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A BCL 8 102 " -0.080 3.20e-02 9.77e+02 2.46e-01 2.95e+02 pdb=" C4A BCL 8 102 " -0.035 3.20e-02 9.77e+02 pdb=" CHA BCL 8 102 " 0.264 3.20e-02 9.77e+02 pdb=" CHB BCL 8 102 " 0.252 3.20e-02 9.77e+02 pdb=" NA BCL 8 102 " -0.402 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1 BPH M 804 " 0.178 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" C2 BPH M 804 " -0.223 2.00e-02 2.50e+03 pdb=" C3 BPH M 804 " -0.077 2.00e-02 2.50e+03 pdb=" C4 BPH M 804 " -0.020 2.00e-02 2.50e+03 pdb=" C5 BPH M 804 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " -0.271 3.00e-02 1.11e+03 2.17e-01 2.61e+02 pdb=" CBA BCL W 101 " -0.178 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " 0.069 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.027 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " 0.353 3.00e-02 1.11e+03 ... (remaining 3927 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 148 2.57 - 3.15: 17150 3.15 - 3.74: 36713 3.74 - 4.32: 56462 4.32 - 4.90: 91637 Nonbonded interactions: 202110 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 805 " model vdw 1.988 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 805 " model vdw 2.084 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 805 " model vdw 2.167 2.340 nonbonded pdb=" O1B LMT H 301 " pdb=" O6' LMT H 301 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" O ARG E 45 " model vdw 2.191 3.040 ... (remaining 202105 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 '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '7' and (resid 4 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.980 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.020 0.542 24351 Z= 1.171 Angle : 1.896 18.619 33239 Z= 0.803 Chirality : 0.056 0.287 3335 Planarity : 0.016 0.246 3930 Dihedral : 22.127 179.811 9751 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.93 % Allowed : 4.72 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2199 helix: 0.29 (0.12), residues: 1500 sheet: -0.43 (1.15), residues: 24 loop : -0.30 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 53 TYR 0.011 0.002 TYR R 8 PHE 0.011 0.001 PHE H 10 TRP 0.012 0.002 TRP M 252 HIS 0.008 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.01885 (24319) covalent geometry : angle 1.89554 (33239) hydrogen bonds : bond 0.22690 ( 1269) hydrogen bonds : angle 6.74408 ( 3600) Misc. bond : bond 0.22272 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 0.717 Fit side-chains REVERT: L 102 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8799 (mt) REVERT: L 248 MET cc_start: 0.8663 (mmm) cc_final: 0.8450 (mmm) REVERT: M 263 GLU cc_start: 0.8522 (tt0) cc_final: 0.8095 (tt0) REVERT: M 292 ASP cc_start: 0.7462 (p0) cc_final: 0.7245 (p0) REVERT: H 30 TYR cc_start: 0.8642 (t80) cc_final: 0.8438 (t80) REVERT: H 52 ASN cc_start: 0.8675 (p0) cc_final: 0.8258 (p0) REVERT: H 128 HIS cc_start: 0.7854 (m-70) cc_final: 0.7498 (m170) REVERT: H 182 GLU cc_start: 0.7962 (tt0) cc_final: 0.7620 (tt0) REVERT: A 6 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8279 (mtmt) REVERT: B 11 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 17 GLN cc_start: 0.8325 (mt0) cc_final: 0.7954 (mt0) REVERT: G 14 GLU cc_start: 0.7372 (pm20) cc_final: 0.7151 (pm20) REVERT: I 5 TYR cc_start: 0.8568 (p90) cc_final: 0.8353 (p90) REVERT: K 12 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7666 (t0) REVERT: O 15 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6440 (mtp85) REVERT: O 45 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7099 (mm-30) REVERT: P 25 SER cc_start: 0.8657 (t) cc_final: 0.8374 (p) REVERT: P 29 LEU cc_start: 0.8610 (tp) cc_final: 0.7944 (tp) REVERT: Q 5 TYR cc_start: 0.8225 (p90) cc_final: 0.7913 (p90) REVERT: Q 6 LYS cc_start: 0.8043 (mttm) cc_final: 0.7751 (mttt) REVERT: V 6 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7070 (mmmt) REVERT: V 45 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7594 (mm-30) REVERT: Z 15 GLN cc_start: 0.7782 (mt0) cc_final: 0.7455 (mt0) REVERT: Z 45 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7906 (ttt-90) REVERT: 2 18 GLU cc_start: 0.7005 (tp30) cc_final: 0.6530 (tp30) REVERT: 3 5 TYR cc_start: 0.7517 (p90) cc_final: 0.7273 (p90) REVERT: 3 27 LEU cc_start: 0.8707 (tp) cc_final: 0.8470 (tp) REVERT: 5 18 VAL cc_start: 0.8043 (t) cc_final: 0.7841 (t) REVERT: 5 30 MET cc_start: 0.8055 (ttp) cc_final: 0.7844 (ttp) REVERT: 6 13 ASP cc_start: 0.6134 (t0) cc_final: 0.5275 (t0) REVERT: 6 15 GLN cc_start: 0.5722 (mt0) cc_final: 0.5114 (mm110) REVERT: 7 30 MET cc_start: 0.7313 (mmt) cc_final: 0.7023 (mmt) REVERT: 7 51 TYR cc_start: 0.7620 (m-80) cc_final: 0.7362 (m-80) REVERT: U 24 MET cc_start: 0.7676 (ptp) cc_final: 0.7325 (ptp) outliers start: 36 outliers final: 19 residues processed: 378 average time/residue: 0.5709 time to fit residues: 250.1402 Evaluate side-chains 320 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 272 MET Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain X residue 17 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 301 HIS H 52 ASN G 17 GLN K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 17 GLN V 20 GLN 5 52 ASN X 66 ASN U 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101112 restraints weight = 27780.077| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.22 r_work: 0.2849 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24351 Z= 0.142 Angle : 0.742 14.610 33239 Z= 0.287 Chirality : 0.040 0.490 3335 Planarity : 0.004 0.053 3930 Dihedral : 19.654 179.231 5879 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 10.50 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.18), residues: 2199 helix: 1.99 (0.12), residues: 1523 sheet: 0.38 (0.95), residues: 34 loop : -0.24 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 45 TYR 0.011 0.001 TYR R 8 PHE 0.013 0.001 PHE M 189 TRP 0.012 0.001 TRP M 252 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00325 (24319) covalent geometry : angle 0.74153 (33239) hydrogen bonds : bond 0.05314 ( 1269) hydrogen bonds : angle 3.73448 ( 3600) Misc. bond : bond 0.00233 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 0.805 Fit side-chains REVERT: L 102 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8640 (mt) REVERT: L 248 MET cc_start: 0.8779 (mmm) cc_final: 0.8512 (mmm) REVERT: M 86 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8652 (tp) REVERT: M 210 TYR cc_start: 0.8753 (m-10) cc_final: 0.8497 (m-10) REVERT: M 216 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8793 (t80) REVERT: H 30 TYR cc_start: 0.8632 (t80) cc_final: 0.8285 (t80) REVERT: H 128 HIS cc_start: 0.7564 (m-70) cc_final: 0.7229 (m170) REVERT: H 175 MET cc_start: 0.8676 (ptm) cc_final: 0.8366 (ptp) REVERT: H 182 GLU cc_start: 0.8534 (tt0) cc_final: 0.7888 (tt0) REVERT: B 11 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8192 (mp) REVERT: B 17 GLN cc_start: 0.8160 (mt0) cc_final: 0.7794 (mt0) REVERT: B 24 MET cc_start: 0.8483 (tpp) cc_final: 0.8169 (mmt) REVERT: G 6 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.2795 (mt) REVERT: G 43 ILE cc_start: 0.8663 (mt) cc_final: 0.8404 (mm) REVERT: K 6 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8317 (mmtp) REVERT: N 24 MET cc_start: 0.8567 (mmp) cc_final: 0.8063 (mmt) REVERT: O 6 LYS cc_start: 0.8191 (mtmp) cc_final: 0.7939 (mtmm) REVERT: O 45 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7530 (mm-30) REVERT: P 25 SER cc_start: 0.8610 (t) cc_final: 0.8121 (p) REVERT: P 29 LEU cc_start: 0.8267 (tp) cc_final: 0.7631 (tp) REVERT: Q 3 LYS cc_start: 0.8046 (mttp) cc_final: 0.7321 (mttp) REVERT: S 3 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7837 (mtpp) REVERT: T 8 TYR cc_start: 0.7218 (m-80) cc_final: 0.6881 (m-80) REVERT: V 45 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8156 (mm-30) REVERT: W 24 MET cc_start: 0.8028 (mmm) cc_final: 0.7745 (mmm) REVERT: Z 15 GLN cc_start: 0.7446 (mt0) cc_final: 0.7068 (mt0) REVERT: 3 5 TYR cc_start: 0.7198 (p90) cc_final: 0.6846 (p90) REVERT: 5 30 MET cc_start: 0.8093 (ttp) cc_final: 0.7827 (ttp) REVERT: 5 53 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7492 (mtm180) REVERT: 6 11 LEU cc_start: 0.6319 (mm) cc_final: 0.6037 (mp) REVERT: 6 13 ASP cc_start: 0.6142 (t0) cc_final: 0.5657 (t70) REVERT: 7 51 TYR cc_start: 0.7314 (m-80) cc_final: 0.6859 (m-80) REVERT: 8 39 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7712 (tp) REVERT: X 29 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7937 (ttmt) REVERT: X 53 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6459 (mtt90) REVERT: X 59 GLU cc_start: 0.6194 (mp0) cc_final: 0.5755 (mp0) REVERT: U 24 MET cc_start: 0.7523 (ptp) cc_final: 0.7286 (ptp) outliers start: 55 outliers final: 17 residues processed: 343 average time/residue: 0.5426 time to fit residues: 217.8834 Evaluate side-chains 307 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 282 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain 2 residue 11 LEU Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 28 ASN H 44 ASN F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098874 restraints weight = 27891.763| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.28 r_work: 0.2779 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24351 Z= 0.166 Angle : 0.714 18.008 33239 Z= 0.278 Chirality : 0.040 0.500 3335 Planarity : 0.004 0.050 3930 Dihedral : 18.008 179.748 5857 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.89 % Allowed : 12.49 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2199 helix: 2.22 (0.12), residues: 1518 sheet: 0.43 (0.94), residues: 34 loop : -0.39 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 45 TYR 0.012 0.001 TYR V 5 PHE 0.013 0.001 PHE H 20 TRP 0.013 0.001 TRP M 252 HIS 0.007 0.001 HIS I 32 Details of bonding type rmsd covalent geometry : bond 0.00397 (24319) covalent geometry : angle 0.71403 (33239) hydrogen bonds : bond 0.05110 ( 1269) hydrogen bonds : angle 3.62765 ( 3600) Misc. bond : bond 0.00275 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.764 Fit side-chains REVERT: L 102 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (mt) REVERT: L 248 MET cc_start: 0.8904 (mmm) cc_final: 0.8646 (mmm) REVERT: M 86 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8702 (tp) REVERT: M 210 TYR cc_start: 0.8801 (m-10) cc_final: 0.8541 (m-10) REVERT: M 216 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8896 (t80) REVERT: M 233 ARG cc_start: 0.7777 (ptt180) cc_final: 0.7576 (mtm180) REVERT: H 30 TYR cc_start: 0.8756 (t80) cc_final: 0.8455 (t80) REVERT: H 128 HIS cc_start: 0.7692 (m-70) cc_final: 0.7396 (m170) REVERT: H 182 GLU cc_start: 0.8636 (tt0) cc_final: 0.8036 (tt0) REVERT: B 17 GLN cc_start: 0.8153 (mt0) cc_final: 0.7757 (mt0) REVERT: B 24 MET cc_start: 0.8649 (tpp) cc_final: 0.8239 (mmt) REVERT: G 6 LEU cc_start: 0.3367 (OUTLIER) cc_final: 0.2854 (mt) REVERT: G 43 ILE cc_start: 0.8603 (mt) cc_final: 0.8374 (mm) REVERT: K 3 LYS cc_start: 0.7708 (mtmm) cc_final: 0.6801 (mptt) REVERT: N 24 MET cc_start: 0.8716 (mmp) cc_final: 0.8243 (mmt) REVERT: O 6 LYS cc_start: 0.8337 (mtmp) cc_final: 0.7579 (mttm) REVERT: P 25 SER cc_start: 0.8789 (t) cc_final: 0.8367 (p) REVERT: P 29 LEU cc_start: 0.8456 (tp) cc_final: 0.7826 (tp) REVERT: Q 3 LYS cc_start: 0.8127 (mttp) cc_final: 0.7388 (mttt) REVERT: Q 5 TYR cc_start: 0.8387 (p90) cc_final: 0.8026 (p90) REVERT: Q 20 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7434 (mm-40) REVERT: R 18 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: S 3 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8013 (mtpp) REVERT: T 8 TYR cc_start: 0.7273 (m-80) cc_final: 0.6893 (m-80) REVERT: V 45 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8225 (mm-30) REVERT: Z 15 GLN cc_start: 0.7849 (mt0) cc_final: 0.7339 (mt0) REVERT: 3 5 TYR cc_start: 0.7367 (p90) cc_final: 0.7062 (p90) REVERT: 5 30 MET cc_start: 0.8241 (ttp) cc_final: 0.7958 (ttp) REVERT: 5 53 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7561 (mtm180) REVERT: 6 13 ASP cc_start: 0.6132 (t0) cc_final: 0.5474 (t70) REVERT: 6 15 GLN cc_start: 0.6045 (mt0) cc_final: 0.5425 (mm110) REVERT: 7 51 TYR cc_start: 0.7460 (m-80) cc_final: 0.7064 (m-80) REVERT: 8 39 LEU cc_start: 0.7962 (tt) cc_final: 0.7568 (tp) REVERT: X 53 ARG cc_start: 0.7384 (mtm110) cc_final: 0.6677 (mtt90) REVERT: X 54 MET cc_start: 0.7863 (ptm) cc_final: 0.7464 (ptt) REVERT: X 59 GLU cc_start: 0.6585 (mp0) cc_final: 0.6230 (mp0) REVERT: U 24 MET cc_start: 0.7588 (ptp) cc_final: 0.7337 (ptp) outliers start: 54 outliers final: 33 residues processed: 339 average time/residue: 0.5272 time to fit residues: 209.9302 Evaluate side-chains 329 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 184 optimal weight: 0.0170 chunk 131 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 GLN 5 52 ASN X 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100543 restraints weight = 27755.594| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.11 r_work: 0.2829 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24351 Z= 0.155 Angle : 0.692 18.102 33239 Z= 0.268 Chirality : 0.039 0.526 3335 Planarity : 0.004 0.051 3930 Dihedral : 17.397 179.730 5855 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.75 % Allowed : 13.50 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.18), residues: 2199 helix: 2.35 (0.12), residues: 1518 sheet: 0.48 (0.95), residues: 34 loop : -0.46 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 247 TYR 0.014 0.001 TYR O 5 PHE 0.026 0.001 PHE U 27 TRP 0.013 0.001 TRP M 252 HIS 0.006 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00369 (24319) covalent geometry : angle 0.69187 (33239) hydrogen bonds : bond 0.04793 ( 1269) hydrogen bonds : angle 3.51453 ( 3600) Misc. bond : bond 0.00253 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 0.738 Fit side-chains REVERT: L 102 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8703 (mt) REVERT: L 248 MET cc_start: 0.8869 (mmm) cc_final: 0.8593 (mmm) REVERT: M 20 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: M 86 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8668 (tp) REVERT: M 210 TYR cc_start: 0.8741 (m-10) cc_final: 0.8460 (m-10) REVERT: M 216 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8870 (t80) REVERT: H 30 TYR cc_start: 0.8673 (t80) cc_final: 0.8367 (t80) REVERT: H 128 HIS cc_start: 0.7709 (m-70) cc_final: 0.7460 (m170) REVERT: H 182 GLU cc_start: 0.8629 (tt0) cc_final: 0.8006 (tt0) REVERT: B 17 GLN cc_start: 0.8119 (mt0) cc_final: 0.7746 (mt0) REVERT: B 24 MET cc_start: 0.8610 (tpp) cc_final: 0.8209 (mmt) REVERT: F 15 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7989 (mtp-110) REVERT: G 6 LEU cc_start: 0.3318 (OUTLIER) cc_final: 0.2816 (mt) REVERT: G 43 ILE cc_start: 0.8592 (mt) cc_final: 0.8354 (mm) REVERT: N 24 MET cc_start: 0.8621 (mmp) cc_final: 0.8155 (mmp) REVERT: O 6 LYS cc_start: 0.8295 (mtmp) cc_final: 0.7555 (mttm) REVERT: P 25 SER cc_start: 0.8693 (t) cc_final: 0.8279 (p) REVERT: P 29 LEU cc_start: 0.8358 (tp) cc_final: 0.7738 (tp) REVERT: Q 3 LYS cc_start: 0.8056 (mttp) cc_final: 0.7321 (mttt) REVERT: Q 5 TYR cc_start: 0.8271 (p90) cc_final: 0.7868 (p90) REVERT: Q 20 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7414 (mm-40) REVERT: R 18 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: S 3 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8003 (mtpp) REVERT: T 8 TYR cc_start: 0.7272 (m-80) cc_final: 0.6863 (m-80) REVERT: T 35 ILE cc_start: 0.8699 (mt) cc_final: 0.8456 (mm) REVERT: V 45 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8132 (mm-30) REVERT: Z 15 GLN cc_start: 0.7785 (mt0) cc_final: 0.7348 (mt0) REVERT: 2 29 LEU cc_start: 0.8573 (tp) cc_final: 0.8354 (tt) REVERT: 3 5 TYR cc_start: 0.7293 (p90) cc_final: 0.6978 (p90) REVERT: 5 30 MET cc_start: 0.8185 (ttp) cc_final: 0.7966 (ttp) REVERT: 5 53 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7512 (mtm180) REVERT: 6 15 GLN cc_start: 0.6000 (mt0) cc_final: 0.5325 (mm110) REVERT: 7 51 TYR cc_start: 0.7441 (m-80) cc_final: 0.7067 (m-80) REVERT: 8 39 LEU cc_start: 0.7891 (tt) cc_final: 0.7646 (tp) REVERT: X 53 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6602 (mtt90) REVERT: X 59 GLU cc_start: 0.6457 (mp0) cc_final: 0.6038 (mp0) REVERT: U 24 MET cc_start: 0.7641 (ptp) cc_final: 0.7369 (ptp) REVERT: U 27 PHE cc_start: 0.7754 (t80) cc_final: 0.7513 (t80) outliers start: 70 outliers final: 34 residues processed: 346 average time/residue: 0.5414 time to fit residues: 218.9593 Evaluate side-chains 325 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 3 residue 29 VAL Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.099268 restraints weight = 27759.141| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.10 r_work: 0.2801 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24351 Z= 0.220 Angle : 0.784 18.005 33239 Z= 0.304 Chirality : 0.042 0.534 3335 Planarity : 0.004 0.054 3930 Dihedral : 17.800 179.763 5855 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.70 % Allowed : 14.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.17), residues: 2199 helix: 2.14 (0.12), residues: 1518 sheet: 0.40 (0.93), residues: 34 loop : -0.56 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 247 TYR 0.013 0.002 TYR 5 5 PHE 0.016 0.002 PHE H 20 TRP 0.015 0.002 TRP M 252 HIS 0.008 0.002 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00540 (24319) covalent geometry : angle 0.78447 (33239) hydrogen bonds : bond 0.05245 ( 1269) hydrogen bonds : angle 3.63238 ( 3600) Misc. bond : bond 0.00340 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 294 time to evaluate : 0.797 Fit side-chains REVERT: L 102 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8771 (mt) REVERT: L 248 MET cc_start: 0.8899 (mmm) cc_final: 0.8685 (mmm) REVERT: M 20 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8250 (mtp) REVERT: M 210 TYR cc_start: 0.8774 (m-10) cc_final: 0.8529 (m-10) REVERT: M 216 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8896 (t80) REVERT: H 30 TYR cc_start: 0.8700 (t80) cc_final: 0.8404 (t80) REVERT: H 43 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: H 128 HIS cc_start: 0.7675 (m-70) cc_final: 0.7455 (m170) REVERT: H 182 GLU cc_start: 0.8608 (tt0) cc_final: 0.7983 (tt0) REVERT: B 17 GLN cc_start: 0.8143 (mt0) cc_final: 0.7894 (mt0) REVERT: B 24 MET cc_start: 0.8643 (tpp) cc_final: 0.8226 (mmt) REVERT: G 43 ILE cc_start: 0.8637 (mt) cc_final: 0.8371 (mm) REVERT: K 12 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7555 (t0) REVERT: O 6 LYS cc_start: 0.8354 (mtmp) cc_final: 0.7634 (mttm) REVERT: P 25 SER cc_start: 0.8694 (t) cc_final: 0.8204 (p) REVERT: P 29 LEU cc_start: 0.8380 (tp) cc_final: 0.7794 (tp) REVERT: Q 3 LYS cc_start: 0.8088 (mttp) cc_final: 0.7341 (mttt) REVERT: Q 5 TYR cc_start: 0.8268 (p90) cc_final: 0.7877 (p90) REVERT: Q 20 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7394 (mm-40) REVERT: R 18 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: S 3 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7960 (mtpp) REVERT: T 35 ILE cc_start: 0.8649 (mt) cc_final: 0.8428 (mm) REVERT: V 45 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8043 (mm-30) REVERT: Z 15 GLN cc_start: 0.7774 (mt0) cc_final: 0.7336 (mt0) REVERT: 3 5 TYR cc_start: 0.7272 (p90) cc_final: 0.6957 (p90) REVERT: 5 15 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.4570 (tmt170) REVERT: 5 30 MET cc_start: 0.8202 (ttp) cc_final: 0.7937 (ttp) REVERT: 5 53 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7517 (mtm180) REVERT: 6 13 ASP cc_start: 0.5876 (t0) cc_final: 0.5165 (t70) REVERT: 6 15 GLN cc_start: 0.6034 (mt0) cc_final: 0.5375 (mm110) REVERT: 7 51 TYR cc_start: 0.7477 (m-80) cc_final: 0.7042 (m-80) REVERT: 8 30 PHE cc_start: 0.6368 (t80) cc_final: 0.6083 (t80) REVERT: 8 39 LEU cc_start: 0.7983 (tt) cc_final: 0.7762 (tp) REVERT: X 53 ARG cc_start: 0.7268 (mtm110) cc_final: 0.6606 (mtt90) REVERT: X 59 GLU cc_start: 0.6504 (mp0) cc_final: 0.6169 (mp0) REVERT: U 24 MET cc_start: 0.7607 (ptp) cc_final: 0.7330 (ptp) REVERT: U 27 PHE cc_start: 0.7759 (t80) cc_final: 0.7540 (t80) outliers start: 69 outliers final: 44 residues processed: 338 average time/residue: 0.5196 time to fit residues: 205.8418 Evaluate side-chains 333 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 29 VAL Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 7 ILE Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain 8 residue 24 MET Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 54 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.101322 restraints weight = 27767.155| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.26 r_work: 0.2825 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24351 Z= 0.127 Angle : 0.656 17.612 33239 Z= 0.254 Chirality : 0.037 0.520 3335 Planarity : 0.003 0.051 3930 Dihedral : 16.934 179.782 5854 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.73 % Allowed : 15.49 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.18), residues: 2199 helix: 2.50 (0.12), residues: 1517 sheet: 0.48 (0.95), residues: 34 loop : -0.51 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 247 TYR 0.010 0.001 TYR L 73 PHE 0.012 0.001 PHE U 27 TRP 0.013 0.001 TRP M 252 HIS 0.004 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00293 (24319) covalent geometry : angle 0.65574 (33239) hydrogen bonds : bond 0.04466 ( 1269) hydrogen bonds : angle 3.42035 ( 3600) Misc. bond : bond 0.00201 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 300 time to evaluate : 0.751 Fit side-chains REVERT: L 102 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8668 (mt) REVERT: L 248 MET cc_start: 0.8879 (mmm) cc_final: 0.8577 (mmm) REVERT: M 20 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: M 60 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8346 (mm) REVERT: M 86 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8680 (tp) REVERT: M 210 TYR cc_start: 0.8751 (m-10) cc_final: 0.8517 (m-10) REVERT: M 236 GLU cc_start: 0.7762 (tp30) cc_final: 0.7363 (tp30) REVERT: H 30 TYR cc_start: 0.8682 (t80) cc_final: 0.8340 (t80) REVERT: H 43 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: H 52 ASN cc_start: 0.8788 (p0) cc_final: 0.8401 (p0) REVERT: H 122 GLU cc_start: 0.7508 (tt0) cc_final: 0.7171 (tt0) REVERT: H 128 HIS cc_start: 0.7718 (m-70) cc_final: 0.7471 (m170) REVERT: H 182 GLU cc_start: 0.8657 (tt0) cc_final: 0.8041 (tt0) REVERT: B 17 GLN cc_start: 0.8137 (mt0) cc_final: 0.7735 (mt0) REVERT: B 24 MET cc_start: 0.8603 (tpp) cc_final: 0.8197 (mmt) REVERT: G 6 LEU cc_start: 0.3305 (OUTLIER) cc_final: 0.2905 (pp) REVERT: G 43 ILE cc_start: 0.8556 (mt) cc_final: 0.8336 (mm) REVERT: K 6 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8356 (mmtp) REVERT: O 6 LYS cc_start: 0.8212 (mtmp) cc_final: 0.7594 (mttm) REVERT: O 11 PHE cc_start: 0.7514 (m-80) cc_final: 0.7289 (m-80) REVERT: P 25 SER cc_start: 0.8680 (t) cc_final: 0.8297 (p) REVERT: P 29 LEU cc_start: 0.8363 (tp) cc_final: 0.7744 (tp) REVERT: Q 3 LYS cc_start: 0.8135 (mttp) cc_final: 0.7394 (mttt) REVERT: Q 5 TYR cc_start: 0.8245 (p90) cc_final: 0.7826 (p90) REVERT: R 18 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: S 3 LYS cc_start: 0.8459 (ttmm) cc_final: 0.7991 (mtpp) REVERT: T 35 ILE cc_start: 0.8663 (mt) cc_final: 0.8453 (mm) REVERT: V 45 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8210 (mm-30) REVERT: Z 15 GLN cc_start: 0.7758 (mt0) cc_final: 0.7261 (mt0) REVERT: 2 29 LEU cc_start: 0.8450 (tp) cc_final: 0.8230 (tt) REVERT: 3 5 TYR cc_start: 0.7287 (p90) cc_final: 0.6967 (p90) REVERT: 5 15 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.4528 (tmt170) REVERT: 5 30 MET cc_start: 0.8189 (ttp) cc_final: 0.7947 (ttp) REVERT: 5 53 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7568 (ttm170) REVERT: 6 13 ASP cc_start: 0.5793 (t0) cc_final: 0.5020 (t70) REVERT: 6 15 GLN cc_start: 0.5985 (mt0) cc_final: 0.5396 (mm110) REVERT: 7 51 TYR cc_start: 0.7428 (m-80) cc_final: 0.7047 (m-80) REVERT: 8 30 PHE cc_start: 0.6369 (t80) cc_final: 0.6015 (t80) REVERT: X 53 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6693 (mtt90) REVERT: X 59 GLU cc_start: 0.6459 (mp0) cc_final: 0.6126 (mp0) REVERT: U 24 MET cc_start: 0.7706 (ptp) cc_final: 0.7430 (ptp) REVERT: U 27 PHE cc_start: 0.7742 (t80) cc_final: 0.7433 (t80) outliers start: 51 outliers final: 25 residues processed: 329 average time/residue: 0.5412 time to fit residues: 208.3110 Evaluate side-chains 320 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 66 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100786 restraints weight = 27684.961| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.24 r_work: 0.2814 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24351 Z= 0.142 Angle : 0.675 17.263 33239 Z= 0.262 Chirality : 0.038 0.535 3335 Planarity : 0.003 0.052 3930 Dihedral : 16.820 179.731 5852 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.89 % Allowed : 15.59 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.18), residues: 2199 helix: 2.50 (0.12), residues: 1517 sheet: 0.56 (0.96), residues: 34 loop : -0.53 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.010 0.001 TYR L 73 PHE 0.013 0.001 PHE H 20 TRP 0.013 0.001 TRP M 252 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00337 (24319) covalent geometry : angle 0.67510 (33239) hydrogen bonds : bond 0.04576 ( 1269) hydrogen bonds : angle 3.42729 ( 3600) Misc. bond : bond 0.00231 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 0.662 Fit side-chains REVERT: L 102 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8690 (mt) REVERT: L 248 MET cc_start: 0.8898 (mmm) cc_final: 0.8597 (mmm) REVERT: M 20 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: M 60 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8246 (mm) REVERT: M 86 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8672 (tp) REVERT: M 210 TYR cc_start: 0.8752 (m-10) cc_final: 0.8507 (m-10) REVERT: M 216 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8724 (t80) REVERT: H 30 TYR cc_start: 0.8688 (t80) cc_final: 0.8368 (t80) REVERT: H 43 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: H 52 ASN cc_start: 0.8806 (p0) cc_final: 0.8428 (p0) REVERT: H 128 HIS cc_start: 0.7712 (m-70) cc_final: 0.7507 (m170) REVERT: H 182 GLU cc_start: 0.8655 (tt0) cc_final: 0.8029 (tt0) REVERT: B 17 GLN cc_start: 0.8141 (mt0) cc_final: 0.7773 (mt0) REVERT: B 24 MET cc_start: 0.8620 (tpp) cc_final: 0.8207 (mmt) REVERT: G 6 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2922 (pp) REVERT: G 43 ILE cc_start: 0.8543 (mt) cc_final: 0.8315 (mm) REVERT: N 24 MET cc_start: 0.8651 (mmt) cc_final: 0.8309 (mmt) REVERT: O 6 LYS cc_start: 0.8278 (mtmp) cc_final: 0.7654 (mttm) REVERT: O 11 PHE cc_start: 0.7516 (m-80) cc_final: 0.7286 (m-80) REVERT: P 25 SER cc_start: 0.8685 (t) cc_final: 0.8311 (p) REVERT: P 29 LEU cc_start: 0.8360 (tp) cc_final: 0.7712 (tp) REVERT: Q 3 LYS cc_start: 0.8146 (mttp) cc_final: 0.7404 (mttt) REVERT: Q 5 TYR cc_start: 0.8285 (p90) cc_final: 0.7884 (p90) REVERT: R 18 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: S 3 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8016 (mtpp) REVERT: T 35 ILE cc_start: 0.8659 (mt) cc_final: 0.8439 (mm) REVERT: V 45 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8123 (mm-30) REVERT: Z 15 GLN cc_start: 0.7774 (mt0) cc_final: 0.7351 (mt0) REVERT: 2 29 LEU cc_start: 0.8501 (tp) cc_final: 0.8296 (tt) REVERT: 3 5 TYR cc_start: 0.7261 (p90) cc_final: 0.7031 (p90) REVERT: 5 15 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.4541 (tmt170) REVERT: 5 30 MET cc_start: 0.8188 (ttp) cc_final: 0.7947 (ttp) REVERT: 5 53 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7620 (ttm170) REVERT: 6 13 ASP cc_start: 0.5886 (t0) cc_final: 0.5152 (t70) REVERT: 7 51 TYR cc_start: 0.7399 (m-80) cc_final: 0.7019 (m-80) REVERT: 8 30 PHE cc_start: 0.6379 (t80) cc_final: 0.6047 (t80) REVERT: 8 39 LEU cc_start: 0.7713 (tp) cc_final: 0.7421 (tt) REVERT: X 53 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6626 (mtt90) REVERT: X 59 GLU cc_start: 0.6468 (mp0) cc_final: 0.6146 (mp0) REVERT: U 24 MET cc_start: 0.7637 (ptp) cc_final: 0.7349 (ptp) REVERT: U 27 PHE cc_start: 0.7781 (t80) cc_final: 0.7519 (t80) outliers start: 54 outliers final: 28 residues processed: 323 average time/residue: 0.5111 time to fit residues: 193.9150 Evaluate side-chains 325 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 202 optimal weight: 0.4980 chunk 93 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100005 restraints weight = 27744.634| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.24 r_work: 0.2804 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24351 Z= 0.159 Angle : 0.699 17.245 33239 Z= 0.271 Chirality : 0.039 0.543 3335 Planarity : 0.004 0.053 3930 Dihedral : 16.906 179.764 5851 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.05 % Allowed : 15.59 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.17), residues: 2199 helix: 2.43 (0.12), residues: 1517 sheet: 0.57 (0.96), residues: 34 loop : -0.57 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.012 0.001 TYR V 5 PHE 0.014 0.001 PHE H 20 TRP 0.013 0.001 TRP M 157 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00382 (24319) covalent geometry : angle 0.69907 (33239) hydrogen bonds : bond 0.04727 ( 1269) hydrogen bonds : angle 3.47441 ( 3600) Misc. bond : bond 0.00250 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.714 Fit side-chains REVERT: L 102 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8698 (mt) REVERT: L 248 MET cc_start: 0.8924 (mmm) cc_final: 0.8661 (mmm) REVERT: M 20 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: M 60 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8284 (mm) REVERT: M 86 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8673 (tp) REVERT: M 210 TYR cc_start: 0.8759 (m-10) cc_final: 0.8508 (m-10) REVERT: H 30 TYR cc_start: 0.8691 (t80) cc_final: 0.8373 (t80) REVERT: H 43 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: H 52 ASN cc_start: 0.8687 (p0) cc_final: 0.8334 (p0) REVERT: H 182 GLU cc_start: 0.8674 (tt0) cc_final: 0.8056 (tt0) REVERT: B 17 GLN cc_start: 0.8147 (mt0) cc_final: 0.7776 (mt0) REVERT: B 24 MET cc_start: 0.8623 (tpp) cc_final: 0.8208 (mmt) REVERT: G 6 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.2795 (mt) REVERT: G 43 ILE cc_start: 0.8565 (mt) cc_final: 0.8342 (mm) REVERT: N 24 MET cc_start: 0.8629 (mmt) cc_final: 0.8272 (mmt) REVERT: O 6 LYS cc_start: 0.8344 (mtmp) cc_final: 0.7666 (mttm) REVERT: O 11 PHE cc_start: 0.7524 (m-80) cc_final: 0.7300 (m-80) REVERT: P 25 SER cc_start: 0.8656 (t) cc_final: 0.8274 (p) REVERT: P 29 LEU cc_start: 0.8389 (tp) cc_final: 0.7780 (tp) REVERT: Q 3 LYS cc_start: 0.8156 (mttp) cc_final: 0.7412 (mttt) REVERT: Q 5 TYR cc_start: 0.8294 (p90) cc_final: 0.7900 (p90) REVERT: R 18 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: S 3 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8020 (mtpp) REVERT: T 35 ILE cc_start: 0.8656 (mt) cc_final: 0.8439 (mm) REVERT: V 45 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8089 (mm-30) REVERT: Z 15 GLN cc_start: 0.7875 (mt0) cc_final: 0.7452 (mt0) REVERT: 2 29 LEU cc_start: 0.8503 (tp) cc_final: 0.8296 (tt) REVERT: 3 5 TYR cc_start: 0.7266 (p90) cc_final: 0.7028 (p90) REVERT: 5 15 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.4567 (tmt170) REVERT: 5 30 MET cc_start: 0.8187 (ttp) cc_final: 0.7946 (ttp) REVERT: 5 53 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: 6 13 ASP cc_start: 0.6004 (t0) cc_final: 0.5320 (t70) REVERT: 7 51 TYR cc_start: 0.7508 (m-80) cc_final: 0.7140 (m-80) REVERT: 8 30 PHE cc_start: 0.6363 (t80) cc_final: 0.6030 (t80) REVERT: 8 39 LEU cc_start: 0.7711 (tp) cc_final: 0.7412 (tt) REVERT: X 59 GLU cc_start: 0.6507 (mp0) cc_final: 0.6255 (mp0) REVERT: U 24 MET cc_start: 0.7631 (ptp) cc_final: 0.7364 (ptp) outliers start: 57 outliers final: 34 residues processed: 322 average time/residue: 0.5320 time to fit residues: 200.2842 Evaluate side-chains 321 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 15 ARG Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 52 ASN Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103163 restraints weight = 27716.784| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.24 r_work: 0.2860 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24351 Z= 0.109 Angle : 0.624 16.773 33239 Z= 0.244 Chirality : 0.037 0.549 3335 Planarity : 0.003 0.051 3930 Dihedral : 16.175 179.728 5851 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.25 % Allowed : 16.51 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.18), residues: 2199 helix: 2.67 (0.12), residues: 1519 sheet: 0.69 (0.98), residues: 34 loop : -0.50 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 45 TYR 0.011 0.001 TYR V 5 PHE 0.010 0.001 PHE B 30 TRP 0.015 0.001 TRP P 28 HIS 0.004 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00243 (24319) covalent geometry : angle 0.62405 (33239) hydrogen bonds : bond 0.04212 ( 1269) hydrogen bonds : angle 3.32926 ( 3600) Misc. bond : bond 0.00149 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.689 Fit side-chains REVERT: L 248 MET cc_start: 0.8880 (mmm) cc_final: 0.8603 (mmm) REVERT: M 20 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8239 (mtp) REVERT: M 60 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8336 (mm) REVERT: M 86 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8671 (tp) REVERT: M 210 TYR cc_start: 0.8724 (m-10) cc_final: 0.8458 (m-10) REVERT: M 236 GLU cc_start: 0.7757 (tp30) cc_final: 0.7310 (tp30) REVERT: H 30 TYR cc_start: 0.8717 (t80) cc_final: 0.8354 (t80) REVERT: H 43 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: H 52 ASN cc_start: 0.8698 (p0) cc_final: 0.8374 (p0) REVERT: H 60 LYS cc_start: 0.7644 (mmpt) cc_final: 0.6930 (mttp) REVERT: H 122 GLU cc_start: 0.7598 (tt0) cc_final: 0.7280 (tt0) REVERT: H 130 LYS cc_start: 0.8113 (tttm) cc_final: 0.7824 (tttt) REVERT: H 182 GLU cc_start: 0.8648 (tt0) cc_final: 0.8065 (tt0) REVERT: B 17 GLN cc_start: 0.8131 (mt0) cc_final: 0.7770 (mt0) REVERT: B 24 MET cc_start: 0.8595 (tpp) cc_final: 0.8210 (mmt) REVERT: G 6 LEU cc_start: 0.3300 (OUTLIER) cc_final: 0.2900 (pp) REVERT: G 43 ILE cc_start: 0.8530 (mt) cc_final: 0.8299 (mm) REVERT: K 6 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8270 (mmtp) REVERT: O 6 LYS cc_start: 0.8212 (mtmp) cc_final: 0.7461 (mttt) REVERT: P 25 SER cc_start: 0.8560 (t) cc_final: 0.8330 (p) REVERT: P 29 LEU cc_start: 0.8351 (tp) cc_final: 0.7698 (tp) REVERT: Q 3 LYS cc_start: 0.8119 (mttp) cc_final: 0.7376 (mttt) REVERT: Q 5 TYR cc_start: 0.8287 (p90) cc_final: 0.7895 (p90) REVERT: Q 37 SER cc_start: 0.8929 (m) cc_final: 0.8442 (t) REVERT: R 18 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: S 3 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8041 (mtpp) REVERT: T 35 ILE cc_start: 0.8572 (mt) cc_final: 0.8363 (mm) REVERT: V 45 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8153 (mm-30) REVERT: Z 15 GLN cc_start: 0.7812 (mt0) cc_final: 0.7336 (mt0) REVERT: 2 29 LEU cc_start: 0.8400 (tp) cc_final: 0.8158 (tt) REVERT: 3 5 TYR cc_start: 0.7304 (p90) cc_final: 0.7047 (p90) REVERT: 5 30 MET cc_start: 0.8184 (ttp) cc_final: 0.7938 (ttp) REVERT: 5 53 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7659 (ttm170) REVERT: 6 15 GLN cc_start: 0.5935 (mt0) cc_final: 0.5320 (mm110) REVERT: 7 51 TYR cc_start: 0.7324 (m-80) cc_final: 0.6955 (m-80) REVERT: 8 30 PHE cc_start: 0.6399 (t80) cc_final: 0.6057 (t80) REVERT: 8 39 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7338 (tt) REVERT: X 53 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6646 (mtt90) REVERT: X 54 MET cc_start: 0.7849 (ptm) cc_final: 0.7478 (ptt) REVERT: X 59 GLU cc_start: 0.6528 (mp0) cc_final: 0.6270 (mp0) REVERT: U 24 MET cc_start: 0.7615 (ptp) cc_final: 0.7333 (ptp) outliers start: 42 outliers final: 26 residues processed: 322 average time/residue: 0.5334 time to fit residues: 201.8287 Evaluate side-chains 318 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 117 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101220 restraints weight = 27766.694| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.23 r_work: 0.2824 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24351 Z= 0.148 Angle : 0.681 16.622 33239 Z= 0.267 Chirality : 0.038 0.556 3335 Planarity : 0.003 0.053 3930 Dihedral : 16.403 179.708 5851 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.20 % Allowed : 17.15 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.17), residues: 2199 helix: 2.56 (0.12), residues: 1519 sheet: 0.67 (0.97), residues: 34 loop : -0.55 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.015 0.001 TYR V 5 PHE 0.014 0.001 PHE H 20 TRP 0.017 0.001 TRP P 28 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00353 (24319) covalent geometry : angle 0.68073 (33239) hydrogen bonds : bond 0.04563 ( 1269) hydrogen bonds : angle 3.41692 ( 3600) Misc. bond : bond 0.00236 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.762 Fit side-chains REVERT: L 102 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8711 (mt) REVERT: L 248 MET cc_start: 0.8904 (mmm) cc_final: 0.8580 (mmm) REVERT: M 13 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7232 (ttm170) REVERT: M 20 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: M 60 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8272 (mm) REVERT: M 86 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8677 (tp) REVERT: M 210 TYR cc_start: 0.8748 (m-10) cc_final: 0.8482 (m-10) REVERT: H 30 TYR cc_start: 0.8708 (t80) cc_final: 0.8412 (t80) REVERT: H 43 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: H 52 ASN cc_start: 0.8778 (p0) cc_final: 0.8422 (p0) REVERT: H 60 LYS cc_start: 0.7631 (mmpt) cc_final: 0.6921 (mttp) REVERT: H 182 GLU cc_start: 0.8646 (tt0) cc_final: 0.8062 (tt0) REVERT: B 17 GLN cc_start: 0.8157 (mt0) cc_final: 0.7784 (mt0) REVERT: B 24 MET cc_start: 0.8624 (tpp) cc_final: 0.8230 (mmt) REVERT: F 15 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7946 (mtp-110) REVERT: G 6 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2921 (pp) REVERT: G 43 ILE cc_start: 0.8550 (mt) cc_final: 0.8313 (mm) REVERT: N 24 MET cc_start: 0.8660 (mmt) cc_final: 0.8370 (mmt) REVERT: O 6 LYS cc_start: 0.8144 (mtmp) cc_final: 0.7506 (mttm) REVERT: P 25 SER cc_start: 0.8654 (t) cc_final: 0.8324 (p) REVERT: P 29 LEU cc_start: 0.8385 (tp) cc_final: 0.7794 (tp) REVERT: Q 3 LYS cc_start: 0.8178 (mttp) cc_final: 0.7385 (mttt) REVERT: Q 5 TYR cc_start: 0.8285 (p90) cc_final: 0.7831 (p90) REVERT: R 18 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: S 3 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8022 (mtpp) REVERT: T 35 ILE cc_start: 0.8661 (mt) cc_final: 0.8448 (mm) REVERT: V 6 LYS cc_start: 0.7299 (tptp) cc_final: 0.6961 (tptm) REVERT: V 45 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8057 (mm-30) REVERT: Z 15 GLN cc_start: 0.7862 (mt0) cc_final: 0.7412 (mt0) REVERT: 2 29 LEU cc_start: 0.8499 (tp) cc_final: 0.8271 (tt) REVERT: 3 5 TYR cc_start: 0.7272 (p90) cc_final: 0.7038 (p90) REVERT: 5 30 MET cc_start: 0.8197 (ttp) cc_final: 0.7979 (ttp) REVERT: 5 53 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7638 (ttm170) REVERT: 6 11 LEU cc_start: 0.6653 (mm) cc_final: 0.6288 (mp) REVERT: 6 13 ASP cc_start: 0.5805 (t0) cc_final: 0.4996 (t70) REVERT: 6 15 GLN cc_start: 0.5993 (mt0) cc_final: 0.5352 (mm110) REVERT: 7 51 TYR cc_start: 0.7465 (m-80) cc_final: 0.7065 (m-80) REVERT: 8 30 PHE cc_start: 0.6336 (t80) cc_final: 0.6029 (t80) REVERT: 8 39 LEU cc_start: 0.7740 (tp) cc_final: 0.7446 (tt) REVERT: X 59 GLU cc_start: 0.6557 (mp0) cc_final: 0.6319 (mp0) REVERT: U 24 MET cc_start: 0.7604 (ptp) cc_final: 0.7334 (ptp) outliers start: 41 outliers final: 26 residues processed: 312 average time/residue: 0.5498 time to fit residues: 200.6788 Evaluate side-chains 313 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 197 PHE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain 3 residue 10 ILE Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 5 residue 40 SER Chi-restraints excluded: chain 5 residue 53 ARG Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 54 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 125 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 ASN X 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100087 restraints weight = 27744.462| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.10 r_work: 0.2820 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24351 Z= 0.185 Angle : 0.744 16.791 33239 Z= 0.291 Chirality : 0.040 0.558 3335 Planarity : 0.004 0.055 3930 Dihedral : 16.879 179.758 5851 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.63 % Allowed : 16.67 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.17), residues: 2199 helix: 2.39 (0.12), residues: 1516 sheet: 0.59 (0.96), residues: 34 loop : -0.60 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.017 0.002 TYR 1 5 PHE 0.015 0.001 PHE H 20 TRP 0.018 0.002 TRP P 28 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00452 (24319) covalent geometry : angle 0.74365 (33239) hydrogen bonds : bond 0.04937 ( 1269) hydrogen bonds : angle 3.51904 ( 3600) Misc. bond : bond 0.00284 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7399.72 seconds wall clock time: 126 minutes 45.86 seconds (7605.86 seconds total)