Starting phenix.real_space_refine on Mon Sep 14 15:22:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c9r_30314/09_2026/7c9r_30314.cif" } resolution = 2.82 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= 0.009 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: 8 Type Number sf(0) Gaussians Ca 17 9.91 5 Fe 5 7.16 5 P 25 5.49 5 Mg 37 5.21 5 S 156 5.16 5 C 20089 2.51 5 N 4062 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29228 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2433 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 285} Chain: "L" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2161 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain: "M" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2535 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 296} Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2017 Classifications: {'peptide': 257} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 236} Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 66} Chain: "B" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "D" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "G" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "I" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 588 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "K" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 588 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 628 Classifications: {'peptide': 78} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 71} Chain: "R" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 579 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "T" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "5" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 589 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "8" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "9" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 74} Chain: "0" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "C" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {' CA': 1, ' MG': 1, 'DGA': 1, 'HEM': 4, 'PGV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-2': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 328 Unusual residues: {'8K6': 1, 'BCL': 2, 'BPH': 1, 'PGV': 1, 'UQ8': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UQ8:plan-6': 2, 'UQ8:plan-7': 2, 'UQ8:plan-8': 2, 'UQ8:plan-9': 2} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 290 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-2': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'H4X': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 204 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 319 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 2, 'PGV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2, 'PGV:plan-2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 265 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 2, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 190 Unusual residues: {' CA': 1, 'BCL': 2, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-2': 1, 'CDL:plan-3': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 11 Chain: "Z" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 239 Unusual residues: {' CA': 1, '8K6': 1, 'BCL': 2, 'H4X': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "6" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "0" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CB1 DGA C 407 " occ=0.70 ... (30 atoms not shown) pdb=" OA1 DGA C 407 " occ=0.70 Time building chain proxies: 6.25, per 1000 atoms: 0.21 Number of scatterers: 29228 At special positions: 0 Unit cell: (141.12, 126, 140.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 17 19.99 S 156 16.00 P 25 15.00 Mg 37 11.99 O 4837 8.00 N 4062 7.00 C 20089 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=42, symmetry=0 Number of additional bonds: simple=42, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 999.0 milliseconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 11 sheets defined 66.2% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.971A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 121 through 141 removed outlier: 4.098A pdb=" N ILE C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.630A pdb=" N PHE C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.567A pdb=" N LEU C 243 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.570A pdb=" N GLN C 261 " --> pdb=" O ASP C 258 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 262 " --> pdb=" O TRP C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 263 through 264 No H-bonds generated for 'chain 'C' and resid 263 through 264' Processing helix chain 'C' and resid 265 through 283 removed outlier: 3.636A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 274 " --> pdb=" O TRP C 270 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.845A pdb=" N GLU C 289 " --> pdb=" O PRO C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.740A pdb=" N LYS C 296 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.633A pdb=" N VAL C 321 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.774A pdb=" N ASP C 326 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 327 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Proline residue: C 328 - end of helix removed outlier: 3.931A pdb=" N TYR C 331 " --> pdb=" O PRO C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 331' Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.661A pdb=" N VAL L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.603A pdb=" N PHE L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.644A pdb=" N HIS L 145 " --> pdb=" O ALA L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 164 removed outlier: 3.689A pdb=" N TRP L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.510A pdb=" N GLU L 213 " --> pdb=" O THR L 209 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 252 removed outlier: 4.454A pdb=" N HIS L 231 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 267 Processing helix chain 'M' and resid 37 through 44 removed outlier: 4.062A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 78 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.836A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 160 removed outlier: 3.896A pdb=" N TRP M 148 " --> pdb=" O THR M 144 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.680A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 removed outlier: 3.559A pdb=" N TYR M 193 " --> pdb=" O ILE M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 removed outlier: 3.517A pdb=" N VAL M 226 " --> pdb=" O THR M 222 " (cutoff:3.500A) 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: 3.826A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 286 removed outlier: 3.890A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU M 286 " --> pdb=" O LEU M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 11 through 24 removed outlier: 3.752A pdb=" N VAL H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 215 through 220 removed outlier: 3.636A pdb=" N ASN H 219 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 249 removed outlier: 3.829A pdb=" N GLY H 245 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 247 " --> pdb=" O GLY H 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 removed outlier: 4.438A pdb=" N HIS A 10 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 13 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 42 Processing helix chain 'A' and resid 55 through 62 removed outlier: 3.520A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.894A pdb=" N MET A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.518A pdb=" N HIS D 10 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 42 Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.525A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'E' and resid 10 through 43 Processing helix chain 'F' and resid 6 through 15 removed outlier: 4.526A pdb=" N HIS F 10 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP F 13 " --> pdb=" O HIS F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 42 Processing helix chain 'F' and resid 55 through 62 removed outlier: 3.522A pdb=" N THR F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'G' and resid 10 through 43 Processing helix chain 'I' and resid 7 through 15 removed outlier: 4.265A pdb=" N HIS I 10 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP I 13 " --> pdb=" O HIS I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 42 Processing helix chain 'I' and resid 55 through 62 removed outlier: 3.532A pdb=" N THR I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'K' and resid 7 through 15 removed outlier: 4.184A pdb=" N HIS K 10 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP K 13 " --> pdb=" O HIS K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 42 Processing helix chain 'K' and resid 55 through 62 removed outlier: 3.523A pdb=" N THR K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 72 Processing helix chain 'N' and resid 10 through 43 Processing helix chain 'O' and resid 8 through 15 removed outlier: 3.721A pdb=" N TRP O 13 " --> pdb=" O HIS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 42 Processing helix chain 'O' and resid 55 through 62 removed outlier: 3.528A pdb=" N THR O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 72 Processing helix chain 'P' and resid 10 through 43 Processing helix chain 'Q' and resid 8 through 15 removed outlier: 3.699A pdb=" N TRP Q 13 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 42 removed outlier: 3.644A pdb=" N SER Q 27 " --> pdb=" O LEU Q 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 43 Processing helix chain 'S' and resid 7 through 15 removed outlier: 4.398A pdb=" N HIS S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP S 13 " --> pdb=" O HIS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 42 Processing helix chain 'S' and resid 55 through 62 removed outlier: 3.509A pdb=" N THR S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 72 removed outlier: 3.957A pdb=" N ALA S 72 " --> pdb=" O GLU S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 43 Processing helix chain 'U' and resid 3 through 15 removed outlier: 4.438A pdb=" N PHE U 6 " --> pdb=" O ALA U 3 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP U 7 " --> pdb=" O LYS U 4 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY U 8 " --> pdb=" O SER U 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET U 9 " --> pdb=" O PHE U 6 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS U 10 " --> pdb=" O ASP U 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP U 13 " --> pdb=" O HIS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 42 Processing helix chain 'U' and resid 55 through 62 removed outlier: 3.523A pdb=" N THR U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 74 Processing helix chain 'V' and resid 10 through 43 Processing helix chain 'W' and resid 7 through 15 removed outlier: 4.386A pdb=" N HIS W 10 " --> pdb=" O ASP W 7 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP W 13 " --> pdb=" O HIS W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 42 Processing helix chain 'W' and resid 55 through 62 removed outlier: 3.524A pdb=" N THR W 62 " --> pdb=" O LEU W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 72 Processing helix chain 'X' and resid 10 through 43 Processing helix chain 'Y' and resid 3 through 15 removed outlier: 4.456A pdb=" N PHE Y 6 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP Y 7 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY Y 8 " --> pdb=" O SER Y 5 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET Y 9 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS Y 10 " --> pdb=" O ASP Y 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP Y 13 " --> pdb=" O HIS Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 55 through 62 removed outlier: 3.517A pdb=" N THR Y 62 " --> pdb=" O LEU Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 72 Processing helix chain 'Z' and resid 10 through 43 Processing helix chain '1' and resid 6 through 15 removed outlier: 3.548A pdb=" N MET 1 9 " --> pdb=" O PHE 1 6 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS 1 10 " --> pdb=" O ASP 1 7 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP 1 13 " --> pdb=" O HIS 1 10 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 42 Processing helix chain '1' and resid 55 through 62 removed outlier: 3.523A pdb=" N THR 1 62 " --> pdb=" O LEU 1 58 " (cutoff:3.500A) Processing helix chain '1' and resid 63 through 73 removed outlier: 3.624A pdb=" N ALA 1 72 " --> pdb=" O GLU 1 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU 1 73 " --> pdb=" O MET 1 69 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 43 Processing helix chain '3' and resid 7 through 15 removed outlier: 4.352A pdb=" N HIS 3 10 " --> pdb=" O ASP 3 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP 3 13 " --> pdb=" O HIS 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 42 Processing helix chain '3' and resid 55 through 62 removed outlier: 3.522A pdb=" N THR 3 62 " --> pdb=" O LEU 3 58 " (cutoff:3.500A) Processing helix chain '3' and resid 63 through 74 removed outlier: 3.665A pdb=" N LYS 3 74 " --> pdb=" O LYS 3 70 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 43 Processing helix chain '5' and resid 3 through 15 removed outlier: 4.322A pdb=" N PHE 5 6 " --> pdb=" O ALA 5 3 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP 5 7 " --> pdb=" O LYS 5 4 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY 5 8 " --> pdb=" O SER 5 5 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET 5 9 " --> pdb=" O PHE 5 6 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS 5 10 " --> pdb=" O ASP 5 7 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP 5 13 " --> pdb=" O HIS 5 10 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 42 Processing helix chain '5' and resid 55 through 62 removed outlier: 3.532A pdb=" N THR 5 62 " --> pdb=" O LEU 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 75 removed outlier: 3.692A pdb=" N LYS 5 74 " --> pdb=" O LYS 5 70 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 5 75 " --> pdb=" O ALA 5 71 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 43 Processing helix chain '7' and resid 6 through 15 removed outlier: 4.508A pdb=" N HIS 7 10 " --> pdb=" O ASP 7 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP 7 13 " --> pdb=" O HIS 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 17 through 42 Processing helix chain '7' and resid 55 through 62 removed outlier: 3.530A pdb=" N THR 7 62 " --> pdb=" O LEU 7 58 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 74 removed outlier: 3.994A pdb=" N LYS 7 74 " --> pdb=" O LYS 7 70 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 43 Processing helix chain '9' and resid 3 through 7 removed outlier: 4.039A pdb=" N PHE 9 6 " --> pdb=" O SER 9 3 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA 9 7 " --> pdb=" O ASP 9 4 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 3 through 7' Processing helix chain '9' and resid 8 through 15 removed outlier: 3.516A pdb=" N LYS 9 11 " --> pdb=" O GLY 9 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 9 15 " --> pdb=" O LEU 9 12 " (cutoff:3.500A) Processing helix chain '9' and resid 17 through 42 removed outlier: 3.551A pdb=" N THR 9 21 " --> pdb=" O ASP 9 17 " (cutoff:3.500A) Processing helix chain '0' and resid 10 through 43 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AA7, first strand: chain 'H' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 4.523A pdb=" N GLY H 165 " --> pdb=" O VAL H 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.794A pdb=" N GLU H 183 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR H 181 " --> pdb=" O ILE H 170 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL H 172 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 200 through 202 1428 hydrogen bonds defined for protein. 3969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 7738 1.35 - 1.54: 20376 1.54 - 1.72: 1704 1.72 - 1.91: 300 1.91 - 2.10: 159 Bond restraints: 30277 Sorted by residual: bond pdb=" CZ ARG C 219 " pdb=" NH2 ARG C 219 " ideal model delta sigma weight residual 1.330 1.587 -0.257 1.30e-02 5.92e+03 3.90e+02 bond pdb=" NE ARG C 219 " pdb=" CZ ARG C 219 " ideal model delta sigma weight residual 1.326 1.480 -0.154 1.10e-02 8.26e+03 1.96e+02 bond pdb=" CZ TYR B 42 " pdb=" OH TYR B 42 " ideal model delta sigma weight residual 1.376 1.615 -0.239 2.10e-02 2.27e+03 1.30e+02 bond pdb=" C11 LMT P 102 " pdb=" C12 LMT P 102 " ideal model delta sigma weight residual 1.522 1.737 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C11 LMT T 102 " pdb=" C12 LMT T 102 " ideal model delta sigma weight residual 1.522 1.731 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 30272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 39469 5.14 - 10.28: 1815 10.28 - 15.42: 192 15.42 - 20.55: 30 20.55 - 25.69: 4 Bond angle restraints: 41510 Sorted by residual: angle pdb=" CBD BCL L 304 " pdb=" CGD BCL L 304 " pdb=" O2D BCL L 304 " ideal model delta sigma weight residual 113.47 139.16 -25.69 2.65e+00 1.43e-01 9.44e+01 angle pdb=" C11 CDL H 302 " pdb=" CA5 CDL H 302 " pdb=" OA6 CDL H 302 " ideal model delta sigma weight residual 111.33 122.66 -11.33 1.32e+00 5.72e-01 7.35e+01 angle pdb=" O1D BCL L 304 " pdb=" CGD BCL L 304 " pdb=" O2D BCL L 304 " ideal model delta sigma weight residual 121.14 97.96 23.18 2.84e+00 1.24e-01 6.65e+01 angle pdb=" C3 BCL K 108 " pdb=" C5 BCL K 108 " pdb=" C6 BCL K 108 " ideal model delta sigma weight residual 115.95 95.79 20.16 2.79e+00 1.29e-01 5.22e+01 angle pdb=" C10 LMT 2 103 " pdb=" C11 LMT 2 103 " pdb=" C12 LMT 2 103 " ideal model delta sigma weight residual 112.79 134.31 -21.52 3.00e+00 1.11e-01 5.15e+01 ... (remaining 41505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.95: 15181 28.95 - 57.90: 1132 57.90 - 86.85: 154 86.85 - 115.80: 25 115.80 - 144.75: 3 Dihedral angle restraints: 16495 sinusoidal: 7872 harmonic: 8623 Sorted by residual: dihedral pdb=" C1 BCL Q 103 " pdb=" CGA BCL Q 103 " pdb=" O2A BCL Q 103 " pdb=" CBA BCL Q 103 " ideal model delta sinusoidal sigma weight residual 180.00 93.04 86.96 1 6.00e+00 2.78e-02 2.53e+02 dihedral pdb=" C1 BCL 9 103 " pdb=" CGA BCL 9 103 " pdb=" O2A BCL 9 103 " pdb=" CBA BCL 9 103 " ideal model delta sinusoidal sigma weight residual 180.00 124.51 55.49 1 6.00e+00 2.78e-02 1.16e+02 dihedral pdb=" C1 BCL M 402 " pdb=" CGA BCL M 402 " pdb=" O2A BCL M 402 " pdb=" CBA BCL M 402 " ideal model delta sinusoidal sigma weight residual 180.00 129.78 50.22 1 6.00e+00 2.78e-02 9.61e+01 ... (remaining 16492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 3674 0.183 - 0.366: 497 0.366 - 0.549: 58 0.549 - 0.732: 6 0.732 - 0.915: 2 Chirality restraints: 4237 Sorted by residual: chirality pdb=" CA PHE H 3 " pdb=" N PHE H 3 " pdb=" C PHE H 3 " pdb=" CB PHE H 3 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CG LEU J 41 " pdb=" CB LEU J 41 " pdb=" CD1 LEU J 41 " pdb=" CD2 LEU J 41 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB VAL S 65 " pdb=" CA VAL S 65 " pdb=" CG1 VAL S 65 " pdb=" CG2 VAL S 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.95e+00 ... (remaining 4234 not shown) Planarity restraints: 4905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL Q 103 " -0.376 3.00e-02 1.11e+03 3.12e-01 5.42e+02 pdb=" CBA BCL Q 103 " -0.121 3.00e-02 1.11e+03 pdb=" CGA BCL Q 103 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL Q 103 " -0.140 3.00e-02 1.11e+03 pdb=" O2A BCL Q 103 " 0.552 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BPH M 404 " 0.223 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" C2 BPH M 404 " -0.311 2.00e-02 2.50e+03 pdb=" C3 BPH M 404 " -0.060 2.00e-02 2.50e+03 pdb=" C4 BPH M 404 " 0.153 2.00e-02 2.50e+03 pdb=" C5 BPH M 404 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 9 103 " 0.318 3.00e-02 1.11e+03 2.56e-01 3.65e+02 pdb=" CBA BCL 9 103 " 0.196 3.00e-02 1.11e+03 pdb=" CGA BCL 9 103 " -0.088 3.00e-02 1.11e+03 pdb=" O1A BCL 9 103 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL 9 103 " -0.425 3.00e-02 1.11e+03 ... (remaining 4902 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 175 2.53 - 3.12: 19490 3.12 - 3.72: 41609 3.72 - 4.31: 67291 4.31 - 4.90: 110916 Nonbonded interactions: 239481 Sorted by model distance: nonbonded pdb=" CED BCL L 304 " pdb=" O1D BCL L 304 " model vdw 1.938 2.768 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.053 2.260 nonbonded pdb=" OD2 ASP H 93 " pdb=" NH1 ARG 9 19 " model vdw 2.098 3.120 nonbonded pdb=" O HIS 5 10 " pdb=" OG SER 6 14 " model vdw 2.142 3.040 nonbonded pdb=" O06 PGV 3 101 " pdb=" O12 PGV 3 101 " model vdw 2.164 3.040 ... (remaining 239476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '2' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '4' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '6' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '8' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'B' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'E' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'G' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'J' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'N' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'P' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'R' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'T' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'V' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'X' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'Z' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) } ncs_group { reference = (chain '1' and resid 3 through 72) selection = (chain '3' and resid 3 through 72) selection = (chain '5' and resid 3 through 72) selection = (chain '7' and resid 3 through 72) selection = (chain 'A' and resid 3 through 72) selection = (chain 'D' and resid 3 through 72) selection = (chain 'F' and resid 3 through 72) selection = (chain 'I' and resid 3 through 72) selection = (chain 'K' and resid 3 through 72) selection = (chain 'O' and resid 3 through 72) selection = (chain 'S' and resid 3 through 72) selection = (chain 'U' and resid 3 through 72) selection = (chain 'W' and resid 3 through 72) selection = (chain 'Y' and resid 3 through 72) } 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.900 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.681 30319 Z= 1.822 Angle : 2.353 25.693 41510 Z= 1.131 Chirality : 0.129 0.915 4237 Planarity : 0.019 0.312 4905 Dihedral : 19.386 144.754 10925 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 0.43 % Allowed : 4.53 % Favored : 95.04 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.57 (0.15), residues: 2937 helix: 0.58 (0.12), residues: 1713 sheet: -1.91 (0.66), residues: 55 loop : -1.76 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.125 0.004 ARG C 219 TYR 0.088 0.014 TYR B 42 PHE 0.084 0.012 PHE L 152 TRP 0.158 0.015 TRP L 273 HIS 0.051 0.008 HIS D 37 Details of bonding type rmsd/Z covalent geometry : bond 0.02165 / 1.09 (30277) covalent geometry : angle 2.35345 / 1.13 (41510) hydrogen bonds : bond 0.16948 / 11.29 ( 1426) hydrogen bonds : angle 4.91523 / 3.44 ( 3969) Misc. bond : bond 0.40241 / 23.19 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 432 time to evaluate : 0.817 Fit side-chains REVERT: L 200 ASN cc_start: 0.9305 (m-40) cc_final: 0.9013 (m110) REVERT: L 203 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8282 (ttpt) REVERT: M 135 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8248 (mtpt) REVERT: A 17 ASN cc_start: 0.9386 (t0) cc_final: 0.9135 (t0) REVERT: A 69 MET cc_start: 0.6981 (ttt) cc_final: 0.6529 (tmm) REVERT: G 22 MET cc_start: 0.9230 (mmt) cc_final: 0.8998 (mmm) REVERT: I 14 MET cc_start: 0.8986 (mtm) cc_final: 0.8753 (mtp) REVERT: K 4 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7424 (pmtt) REVERT: P 25 MET cc_start: 0.9187 (ttp) cc_final: 0.8960 (ttp) REVERT: S 69 MET cc_start: 0.5704 (mtt) cc_final: 0.5197 (ttp) REVERT: 5 69 MET cc_start: 0.8492 (mtt) cc_final: 0.8204 (mtm) outliers start: 11 outliers final: 4 residues processed: 442 average time/residue: 0.6755 time to fit residues: 349.5460 Evaluate side-chains 368 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 364 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain B residue 20 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN C 42 GLN C 215 ASN C 275 ASN L 88 GLN L 145 HIS M 259 ASN H 42 GLN H 46 GLN O 29 GLN Q 29 GLN Y 29 GLN 3 29 GLN 7 2 ASN 7 29 GLN 9 49 ASN 9 86 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.087287 restraints weight = 35572.651| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.14 r_work: 0.2711 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30319 Z= 0.138 Angle : 0.734 13.130 41510 Z= 0.288 Chirality : 0.040 0.146 4237 Planarity : 0.004 0.050 4905 Dihedral : 16.001 148.331 5452 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.60 % Allowed : 10.03 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 1.32 (0.16), residues: 2937 helix: 2.17 (0.13), residues: 1739 sheet: -1.27 (0.72), residues: 55 loop : -1.11 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 19 TYR 0.012 0.001 TYR H 85 PHE 0.020 0.002 PHE H 3 TRP 0.013 0.001 TRP L 244 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30277) covalent geometry : angle 0.73414 / 0.29 (41510) hydrogen bonds : bond 0.06320 / 4.17 ( 1426) hydrogen bonds : angle 3.60972 / 2.54 ( 3969) Misc. bond : bond 0.01280 / 0.63 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 387 time to evaluate : 0.717 Fit side-chains REVERT: C 230 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: L 213 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8673 (mt-10) REVERT: L 249 MET cc_start: 0.8802 (mmm) cc_final: 0.8551 (tpt) REVERT: M 135 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8172 (mptt) REVERT: M 160 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8110 (pt) REVERT: M 216 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8857 (t80) REVERT: A 69 MET cc_start: 0.7131 (ttt) cc_final: 0.6720 (tmm) REVERT: I 14 MET cc_start: 0.9002 (mtm) cc_final: 0.8767 (mtp) REVERT: K 4 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7583 (pmtt) REVERT: O 70 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7876 (mtpt) REVERT: S 69 MET cc_start: 0.6455 (mtt) cc_final: 0.5980 (ttp) REVERT: W 14 MET cc_start: 0.8730 (mtp) cc_final: 0.8448 (mtt) REVERT: 1 16 MET cc_start: 0.7666 (mtt) cc_final: 0.7421 (mtm) REVERT: 1 29 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8681 (mm-40) REVERT: 4 15 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7951 (mtpp) REVERT: 4 22 MET cc_start: 0.8954 (mmt) cc_final: 0.8680 (mmm) REVERT: 6 22 MET cc_start: 0.8937 (mmt) cc_final: 0.8700 (mmt) REVERT: 7 51 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8514 (mt0) outliers start: 41 outliers final: 12 residues processed: 406 average time/residue: 0.6640 time to fit residues: 317.1609 Evaluate side-chains 362 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 344 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 70 LYS Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain W residue 49 ASP Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN C 189 ASN ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 HIS M 9 ASN H 162 GLN W 59 GLN Y 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.083452 restraints weight = 35758.692| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.14 r_work: 0.2606 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30319 Z= 0.233 Angle : 0.812 14.923 41510 Z= 0.330 Chirality : 0.046 0.148 4237 Planarity : 0.005 0.067 4905 Dihedral : 15.628 146.885 5448 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 10.97 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 1.61 (0.16), residues: 2937 helix: 2.35 (0.12), residues: 1717 sheet: -1.12 (0.74), residues: 55 loop : -0.84 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 9 19 TYR 0.015 0.002 TYR M 198 PHE 0.023 0.002 PHE H 3 TRP 0.014 0.002 TRP M 92 HIS 0.011 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.23 (30277) covalent geometry : angle 0.81181 / 0.33 (41510) hydrogen bonds : bond 0.07942 / 5.27 ( 1426) hydrogen bonds : angle 3.60345 / 2.53 ( 3969) Misc. bond : bond 0.01792 / 0.80 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 1.032 Fit side-chains REVERT: M 25 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (mttp) REVERT: M 160 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8215 (pt) REVERT: A 69 MET cc_start: 0.7372 (ttt) cc_final: 0.6865 (tmm) REVERT: B 15 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8205 (ttmt) REVERT: F 49 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: K 4 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7625 (pmtt) REVERT: S 69 MET cc_start: 0.6594 (mtt) cc_final: 0.5856 (ttp) REVERT: W 14 MET cc_start: 0.8858 (mtp) cc_final: 0.8535 (mtt) REVERT: 1 16 MET cc_start: 0.7706 (mtt) cc_final: 0.7465 (mtm) REVERT: 4 15 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: 4 22 MET cc_start: 0.9071 (mmt) cc_final: 0.8813 (mmm) REVERT: 6 6 THR cc_start: 0.8135 (t) cc_final: 0.7878 (m) REVERT: 7 11 LYS cc_start: 0.8729 (mttp) cc_final: 0.8501 (mttt) REVERT: 7 51 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: 0 41 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8518 (tp) outliers start: 60 outliers final: 24 residues processed: 374 average time/residue: 0.6857 time to fit residues: 300.5123 Evaluate side-chains 371 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 340 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 41 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 187 optimal weight: 0.0470 chunk 208 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 5 ASN L 88 GLN L 200 ASN H 252 ASN Y 29 GLN 3 29 GLN 5 29 GLN 9 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.086210 restraints weight = 35507.088| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.15 r_work: 0.2680 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30319 Z= 0.144 Angle : 0.682 14.166 41510 Z= 0.274 Chirality : 0.040 0.142 4237 Planarity : 0.004 0.051 4905 Dihedral : 14.484 146.750 5448 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 11.83 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.03 (0.16), residues: 2937 helix: 2.71 (0.12), residues: 1725 sheet: -0.87 (0.75), residues: 55 loop : -0.72 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 19 TYR 0.010 0.001 TYR M 193 PHE 0.016 0.001 PHE H 95 TRP 0.012 0.001 TRP 5 13 HIS 0.009 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (30277) covalent geometry : angle 0.68226 / 0.27 (41510) hydrogen bonds : bond 0.06276 / 4.15 ( 1426) hydrogen bonds : angle 3.39165 / 2.38 ( 3969) Misc. bond : bond 0.01731 / 0.75 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 1.257 Fit side-chains REVERT: C 230 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8405 (mt-10) REVERT: M 135 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7139 (mttt) REVERT: M 160 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8107 (pt) REVERT: A 69 MET cc_start: 0.7288 (ttt) cc_final: 0.6829 (tmm) REVERT: B 15 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8078 (ttmt) REVERT: K 4 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7655 (pmtt) REVERT: R 15 LYS cc_start: 0.8289 (tttp) cc_final: 0.7869 (ttpt) REVERT: S 69 MET cc_start: 0.6667 (mtt) cc_final: 0.5930 (ttp) REVERT: W 14 MET cc_start: 0.8726 (mtp) cc_final: 0.8450 (mtt) REVERT: 1 16 MET cc_start: 0.7654 (mtt) cc_final: 0.7375 (mtm) REVERT: 4 22 MET cc_start: 0.8985 (mmt) cc_final: 0.8714 (mmm) REVERT: 5 38 MET cc_start: 0.8898 (ttp) cc_final: 0.8689 (ttm) REVERT: 7 42 SER cc_start: 0.8830 (m) cc_final: 0.8582 (t) REVERT: 7 51 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8440 (mt0) outliers start: 45 outliers final: 21 residues processed: 371 average time/residue: 0.6905 time to fit residues: 300.1219 Evaluate side-chains 360 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 335 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 155 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN H 252 ASN O 57 GLN Y 29 GLN 3 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.082979 restraints weight = 35788.984| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.14 r_work: 0.2651 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 30319 Z= 0.211 Angle : 0.766 14.610 41510 Z= 0.311 Chirality : 0.044 0.149 4237 Planarity : 0.004 0.057 4905 Dihedral : 14.708 147.534 5448 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.34 % Allowed : 11.75 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 1.82 (0.16), residues: 2937 helix: 2.47 (0.12), residues: 1746 sheet: -0.86 (0.77), residues: 55 loop : -0.76 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 9 19 TYR 0.014 0.002 TYR M 198 PHE 0.019 0.002 PHE H 3 TRP 0.013 0.002 TRP 7 13 HIS 0.011 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.21 (30277) covalent geometry : angle 0.76639 / 0.31 (41510) hydrogen bonds : bond 0.07436 / 4.93 ( 1426) hydrogen bonds : angle 3.48533 / 2.44 ( 3969) Misc. bond : bond 0.02623 / 0.98 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 343 time to evaluate : 0.917 Fit side-chains REVERT: M 135 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7307 (mttt) REVERT: M 160 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8193 (pt) REVERT: H 81 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 69 MET cc_start: 0.7316 (ttt) cc_final: 0.6788 (tmm) REVERT: B 15 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: K 4 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7666 (pmtt) REVERT: S 69 MET cc_start: 0.6754 (mtt) cc_final: 0.5955 (ttp) REVERT: W 14 MET cc_start: 0.8850 (mtp) cc_final: 0.8538 (mtt) REVERT: 1 16 MET cc_start: 0.7605 (mtt) cc_final: 0.7337 (mtm) REVERT: 7 11 LYS cc_start: 0.8675 (mttp) cc_final: 0.8389 (mttt) REVERT: 7 42 SER cc_start: 0.9007 (m) cc_final: 0.8737 (t) REVERT: 7 51 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: 0 41 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8500 (tp) outliers start: 60 outliers final: 28 residues processed: 373 average time/residue: 0.6809 time to fit residues: 297.6975 Evaluate side-chains 373 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Chi-restraints excluded: chain 0 residue 6 THR Chi-restraints excluded: chain 0 residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 286 optimal weight: 0.0060 chunk 235 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 ASN ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN H 252 ASN Y 29 GLN 3 29 GLN 9 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.085375 restraints weight = 35681.964| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.15 r_work: 0.2685 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 30319 Z= 0.160 Angle : 0.701 13.791 41510 Z= 0.283 Chirality : 0.041 0.144 4237 Planarity : 0.004 0.053 4905 Dihedral : 14.191 147.620 5448 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.11 % Allowed : 12.22 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.05 (0.16), residues: 2937 helix: 2.69 (0.12), residues: 1741 sheet: -0.78 (0.75), residues: 55 loop : -0.69 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 19 TYR 0.010 0.002 TYR M 198 PHE 0.017 0.002 PHE 5 31 TRP 0.013 0.001 TRP S 13 HIS 0.010 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (30277) covalent geometry : angle 0.70135 / 0.28 (41510) hydrogen bonds : bond 0.06590 / 4.36 ( 1426) hydrogen bonds : angle 3.38912 / 2.37 ( 3969) Misc. bond : bond 0.02780 / 1.02 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 1.015 Fit side-chains REVERT: L 213 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8707 (mt-10) REVERT: M 135 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7210 (mttt) REVERT: M 160 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8148 (pt) REVERT: H 81 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: A 69 MET cc_start: 0.7302 (ttt) cc_final: 0.6757 (tmm) REVERT: B 15 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8098 (ttmt) REVERT: D 49 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8801 (m-30) REVERT: E 41 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8654 (mp) REVERT: K 4 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7645 (pmtt) REVERT: K 38 MET cc_start: 0.8335 (mmt) cc_final: 0.7895 (mmt) REVERT: S 69 MET cc_start: 0.6824 (mtt) cc_final: 0.6036 (ttp) REVERT: W 14 MET cc_start: 0.8800 (mtp) cc_final: 0.8524 (mtt) REVERT: 1 16 MET cc_start: 0.7551 (mtt) cc_final: 0.7269 (mtm) REVERT: 4 22 MET cc_start: 0.9017 (mmt) cc_final: 0.8750 (mmm) REVERT: 5 16 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (ttp) REVERT: 7 42 SER cc_start: 0.8907 (m) cc_final: 0.8645 (t) REVERT: 7 51 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8440 (mt0) outliers start: 54 outliers final: 31 residues processed: 372 average time/residue: 0.6966 time to fit residues: 303.2661 Evaluate side-chains 377 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 201 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN H 42 GLN H 252 ASN Y 29 GLN 3 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.085053 restraints weight = 35573.700| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.17 r_work: 0.2639 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 30319 Z= 0.170 Angle : 0.711 13.802 41510 Z= 0.287 Chirality : 0.041 0.145 4237 Planarity : 0.004 0.054 4905 Dihedral : 14.060 146.949 5448 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.91 % Allowed : 12.76 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.07 (0.16), residues: 2937 helix: 2.69 (0.12), residues: 1741 sheet: -0.75 (0.75), residues: 55 loop : -0.67 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 19 TYR 0.012 0.002 TYR M 198 PHE 0.017 0.002 PHE 5 31 TRP 0.012 0.001 TRP S 13 HIS 0.010 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (30277) covalent geometry : angle 0.71061 / 0.29 (41510) hydrogen bonds : bond 0.06705 / 4.44 ( 1426) hydrogen bonds : angle 3.38521 / 2.37 ( 3969) Misc. bond : bond 0.02799 / 1.05 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 0.949 Fit side-chains REVERT: C 230 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8433 (mt-10) REVERT: L 213 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8709 (mt-10) REVERT: M 135 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7303 (mttt) REVERT: M 160 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8160 (pt) REVERT: H 81 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: A 16 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8879 (mtt) REVERT: A 69 MET cc_start: 0.7290 (ttt) cc_final: 0.6710 (tmm) REVERT: B 15 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8147 (ttmt) REVERT: D 49 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: E 41 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8689 (mp) REVERT: K 4 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7706 (pmtt) REVERT: S 69 MET cc_start: 0.6837 (mtt) cc_final: 0.6053 (ttp) REVERT: W 14 MET cc_start: 0.8846 (mtp) cc_final: 0.8575 (mtt) REVERT: 1 16 MET cc_start: 0.7485 (mtt) cc_final: 0.7208 (mtm) REVERT: 5 16 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8653 (ttp) REVERT: 7 42 SER cc_start: 0.8941 (m) cc_final: 0.8719 (t) REVERT: 7 51 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: 0 41 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8460 (tp) outliers start: 49 outliers final: 31 residues processed: 367 average time/residue: 0.6851 time to fit residues: 294.7046 Evaluate side-chains 379 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 7 residue 51 GLN Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Chi-restraints excluded: chain 0 residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 289 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 253 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 200 ASN H 252 ASN Y 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.087400 restraints weight = 35586.754| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.14 r_work: 0.2710 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 30319 Z= 0.133 Angle : 0.656 13.980 41510 Z= 0.263 Chirality : 0.039 0.141 4237 Planarity : 0.004 0.054 4905 Dihedral : 13.519 144.490 5448 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.68 % Allowed : 13.19 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.30 (0.16), residues: 2937 helix: 2.89 (0.12), residues: 1743 sheet: -0.71 (0.74), residues: 55 loop : -0.60 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 132 TYR 0.010 0.001 TYR S 56 PHE 0.017 0.001 PHE 5 31 TRP 0.012 0.001 TRP S 13 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (30277) covalent geometry : angle 0.65644 / 0.26 (41510) hydrogen bonds : bond 0.05814 / 3.84 ( 1426) hydrogen bonds : angle 3.27051 / 2.28 ( 3969) Misc. bond : bond 0.02733 / 1.02 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 0.942 Fit side-chains REVERT: C 230 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8389 (mt-10) REVERT: L 213 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8714 (mt-10) REVERT: M 68 LEU cc_start: 0.8649 (mt) cc_final: 0.8356 (mt) REVERT: M 135 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7087 (mttt) REVERT: M 160 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8028 (pt) REVERT: H 81 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: A 16 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8840 (mtt) REVERT: A 69 MET cc_start: 0.7236 (ttt) cc_final: 0.6660 (tmm) REVERT: F 49 ASP cc_start: 0.9045 (m-30) cc_final: 0.8468 (m-30) REVERT: K 4 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7627 (pmtt) REVERT: K 38 MET cc_start: 0.8279 (mmt) cc_final: 0.7848 (mmt) REVERT: P 25 MET cc_start: 0.9032 (ttp) cc_final: 0.8818 (ttp) REVERT: Q 12 MET cc_start: 0.8850 (ttp) cc_final: 0.8595 (ptm) REVERT: S 69 MET cc_start: 0.6816 (mtt) cc_final: 0.6078 (ttp) REVERT: U 38 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.7740 (mpt) REVERT: W 14 MET cc_start: 0.8783 (mtp) cc_final: 0.8536 (mtt) REVERT: 1 16 MET cc_start: 0.7391 (mtt) cc_final: 0.7101 (mtm) REVERT: 4 22 MET cc_start: 0.8979 (mmt) cc_final: 0.8719 (mmm) REVERT: 5 16 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8636 (ttp) REVERT: 7 42 SER cc_start: 0.8816 (m) cc_final: 0.8602 (t) REVERT: 0 9 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7739 (mp) outliers start: 43 outliers final: 28 residues processed: 369 average time/residue: 0.6724 time to fit residues: 292.1508 Evaluate side-chains 379 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 38 MET Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Chi-restraints excluded: chain 0 residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 118 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 250 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN H 162 GLN H 252 ASN Y 29 GLN 1 29 GLN 3 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.084499 restraints weight = 35557.752| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.11 r_work: 0.2663 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 30319 Z= 0.207 Angle : 0.755 14.402 41510 Z= 0.306 Chirality : 0.044 0.149 4237 Planarity : 0.004 0.053 4905 Dihedral : 14.127 145.962 5448 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.91 % Allowed : 13.23 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 1.99 (0.16), residues: 2937 helix: 2.61 (0.12), residues: 1747 sheet: -0.74 (0.75), residues: 55 loop : -0.70 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 128 TYR 0.014 0.002 TYR M 198 PHE 0.025 0.002 PHE M 216 TRP 0.012 0.002 TRP 7 13 HIS 0.012 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (30277) covalent geometry : angle 0.75533 / 0.31 (41510) hydrogen bonds : bond 0.07247 / 4.80 ( 1426) hydrogen bonds : angle 3.42165 / 2.39 ( 3969) Misc. bond : bond 0.03381 / 1.24 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 1.047 Fit side-chains REVERT: L 213 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8695 (mt-10) REVERT: M 135 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7270 (mttt) REVERT: M 160 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8119 (pt) REVERT: H 81 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: A 16 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8802 (mtt) REVERT: A 69 MET cc_start: 0.7290 (ttt) cc_final: 0.6649 (tmm) REVERT: D 49 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8840 (m-30) REVERT: K 4 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7717 (pmtt) REVERT: K 38 MET cc_start: 0.8316 (mmt) cc_final: 0.7881 (mmt) REVERT: S 69 MET cc_start: 0.6912 (mtt) cc_final: 0.6099 (ttp) REVERT: U 38 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7789 (mpt) REVERT: W 14 MET cc_start: 0.8823 (mtp) cc_final: 0.8526 (mtt) REVERT: 1 16 MET cc_start: 0.7360 (mtt) cc_final: 0.7080 (mtm) REVERT: 7 11 LYS cc_start: 0.8624 (mttp) cc_final: 0.8334 (mttt) REVERT: 7 42 SER cc_start: 0.8954 (m) cc_final: 0.8709 (t) outliers start: 49 outliers final: 29 residues processed: 363 average time/residue: 0.6528 time to fit residues: 278.6584 Evaluate side-chains 368 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 273 TRP Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 38 MET Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 266 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 275 optimal weight: 0.3980 chunk 271 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 ASN L 200 ASN H 229 GLN H 252 ASN Y 29 GLN 5 29 GLN 9 49 ASN 9 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.089163 restraints weight = 35701.311| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.14 r_work: 0.2778 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 30319 Z= 0.109 Angle : 0.620 14.421 41510 Z= 0.245 Chirality : 0.037 0.138 4237 Planarity : 0.004 0.052 4905 Dihedral : 13.042 141.352 5448 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.01 % Allowed : 14.13 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.54 (0.16), residues: 2937 helix: 3.07 (0.12), residues: 1741 sheet: -0.69 (0.73), residues: 55 loop : -0.47 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 132 TYR 0.009 0.001 TYR M 193 PHE 0.019 0.001 PHE 5 31 TRP 0.013 0.001 TRP S 13 HIS 0.006 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (30277) covalent geometry : angle 0.62023 / 0.25 (41510) hydrogen bonds : bond 0.04934 / 3.25 ( 1426) hydrogen bonds : angle 3.17814 / 2.22 ( 3969) Misc. bond : bond 0.02681 / 1.02 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 0.725 Fit side-chains REVERT: L 213 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8653 (mt-10) REVERT: M 68 LEU cc_start: 0.8660 (mt) cc_final: 0.8396 (mt) REVERT: M 135 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7056 (mttt) REVERT: M 160 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8174 (pt) REVERT: M 249 MET cc_start: 0.9395 (mtp) cc_final: 0.9156 (mtt) REVERT: A 16 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8821 (mtt) REVERT: A 69 MET cc_start: 0.7241 (ttt) cc_final: 0.6665 (tmm) REVERT: F 49 ASP cc_start: 0.9011 (m-30) cc_final: 0.8424 (m-30) REVERT: K 4 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7587 (pmtt) REVERT: K 38 MET cc_start: 0.8295 (mmt) cc_final: 0.7926 (mmt) REVERT: S 69 MET cc_start: 0.6864 (mtt) cc_final: 0.6151 (ttp) REVERT: 1 16 MET cc_start: 0.7286 (mtt) cc_final: 0.7004 (mtm) REVERT: 4 22 MET cc_start: 0.8966 (mmt) cc_final: 0.8695 (mmm) outliers start: 26 outliers final: 18 residues processed: 367 average time/residue: 0.6445 time to fit residues: 278.7887 Evaluate side-chains 357 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 336 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 177 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN H 252 ASN Y 29 GLN 3 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.086129 restraints weight = 35815.761| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.12 r_work: 0.2703 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 30319 Z= 0.151 Angle : 0.682 13.804 41510 Z= 0.273 Chirality : 0.040 0.143 4237 Planarity : 0.004 0.054 4905 Dihedral : 13.315 140.559 5448 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.17 % Allowed : 14.60 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % 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: 2.36 (0.16), residues: 2937 helix: 2.93 (0.12), residues: 1743 sheet: -0.74 (0.72), residues: 56 loop : -0.56 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.011 0.002 TYR S 56 PHE 0.021 0.002 PHE M 216 TRP 0.012 0.001 TRP S 13 HIS 0.010 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (30277) covalent geometry : angle 0.68213 / 0.27 (41510) hydrogen bonds : bond 0.06073 / 4.02 ( 1426) hydrogen bonds : angle 3.25020 / 2.27 ( 3969) Misc. bond : bond 0.03191 / 1.15 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9530.09 seconds wall clock time: 163 minutes 7.32 seconds (9787.32 seconds total)