Starting phenix.real_space_refine on Mon Sep 14 00:52:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.map" model { file = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z5r_11080/09_2026/6z5r_11080.cif" } resolution = 2.8 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 38 5.49 5 Mg 36 5.21 5 S 57 5.16 5 C 17903 2.51 5 N 3290 2.21 5 O 3723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s 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: 25048 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 394 Chain: "E" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 394 Chain: "G" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "J" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 392 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "H" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1862 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 220} Chain: "L" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2185 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain: "M" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2433 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 285} Chain: "R" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "T" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "V" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "P" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "Y" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 387 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Z" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "A" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 394 Chain: "1" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "3" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "5" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Conformer: "B" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} bond proxies already assigned to first conformer: 402 Chain: "7" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 394 Chain: "9" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 394 Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'6PL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 205 Unusual residues: {'6PL': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'6PL': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 366 Unusual residues: {'BCL': 2, 'CDL': 2, 'CRT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "I" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'6PL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'6PL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'6PL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'6PL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 610 Unusual residues: {'6PL': 2, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'U10': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 576 Unusual residues: {' FE': 1, '6PL': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'QAK': 1, 'U10': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'6PL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'6PL': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'6PL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'6PL': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 158 Unusual residues: {'6PL': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'6PL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'6PL': 1, 'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'6PL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'6PL': 1, 'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 184 Unusual residues: {'6PL': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'6PL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 227 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'6PL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'6PL': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N APHE D 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 26 " occ=0.50 residue: pdb=" N APHE F 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE F 26 " occ=0.50 residue: pdb=" N APHE K 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE K 26 " occ=0.50 residue: pdb=" N APHE O 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE O 26 " occ=0.50 residue: pdb=" N APHE S 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE S 26 " occ=0.50 residue: pdb=" N APHE U 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE U 26 " occ=0.50 residue: pdb=" N APHE Q 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE Q 26 " occ=0.50 residue: pdb=" N APHE Z 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE Z 26 " occ=0.50 residue: pdb=" N APHE B 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 26 " occ=0.50 residue: pdb=" N APHE 2 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE 2 26 " occ=0.50 residue: pdb=" N APHE 4 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE 4 26 " occ=0.50 residue: pdb=" N APHE 6 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE 6 26 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 5.61, per 1000 atoms: 0.22 Number of scatterers: 25048 At special positions: 0 Unit cell: (130.995, 117.15, 140.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 57 16.00 P 38 15.00 Mg 36 11.99 O 3723 8.00 N 3290 7.00 C 17903 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4384 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 6 sheets defined 66.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 1 through 7 Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.574A pdb=" N THR C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 43 Processing helix chain 'E' and resid 1 through 7 Processing helix chain 'E' and resid 9 through 35 removed outlier: 3.654A pdb=" N VAL E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 Processing helix chain 'G' and resid 1 through 7 Processing helix chain 'G' and resid 9 through 34 Processing helix chain 'I' and resid 10 through 43 Processing helix chain 'J' and resid 3 through 8 Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.536A pdb=" N THR J 35 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 43 Processing helix chain 'N' and resid 1 through 7 Processing helix chain 'N' and resid 9 through 35 removed outlier: 3.572A pdb=" N THR N 35 " --> pdb=" O ILE N 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 43 Processing helix chain 'H' and resid 8 through 32 Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.826A pdb=" N ASP H 79 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 121 through 125 removed outlier: 4.323A pdb=" N ASP H 124 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 211 through 218 removed outlier: 3.871A pdb=" N PHE H 215 " --> pdb=" O GLY H 212 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA H 216 " --> pdb=" O ASP H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 246 removed outlier: 3.528A pdb=" N TYR H 239 " --> pdb=" O ILE H 235 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY H 242 " --> pdb=" O TYR H 238 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR H 243 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 56 removed outlier: 3.897A pdb=" N VAL L 37 " --> pdb=" O GLY L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.601A pdb=" N ILE L 65 " --> pdb=" O LEU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.561A pdb=" N GLN L 88 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.792A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.951A 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 Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.797A pdb=" N ASP L 156 " --> pdb=" O PHE L 152 " (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: 3.698A pdb=" N PHE L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 251 removed outlier: 4.022A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 271 removed outlier: 3.824A pdb=" N ARG L 270 " --> pdb=" O TRP L 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.910A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 78 removed outlier: 3.812A pdb=" N VAL M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 removed outlier: 3.927A pdb=" N GLY M 103 " --> pdb=" O PRO M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 139 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.994A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.798A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.696A pdb=" N LEU M 183 " --> pdb=" O VAL M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 235 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.646A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 287 removed outlier: 4.017A pdb=" N CYS M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) Proline residue: M 277 - end of helix Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'R' and resid 3 through 8 removed outlier: 3.734A pdb=" N LEU R 7 " --> pdb=" O ARG R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 35 removed outlier: 3.503A pdb=" N THR R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 43 Processing helix chain 'T' and resid 1 through 7 Processing helix chain 'T' and resid 9 through 35 removed outlier: 3.623A pdb=" N PHE T 18 " --> pdb=" O LEU T 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL T 19 " --> pdb=" O VAL T 15 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR T 35 " --> pdb=" O ILE T 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 43 Processing helix chain 'V' and resid 3 through 8 removed outlier: 3.943A pdb=" N LEU V 7 " --> pdb=" O ARG V 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 35 removed outlier: 3.559A pdb=" N THR V 35 " --> pdb=" O ILE V 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 43 Processing helix chain 'P' and resid 1 through 7 Processing helix chain 'P' and resid 9 through 34 removed outlier: 4.134A pdb=" N VAL P 15 " --> pdb=" O ARG P 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 43 removed outlier: 3.775A pdb=" N LYS Q 15 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.617A pdb=" N LEU Y 17 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 43 removed outlier: 3.506A pdb=" N LYS Z 15 " --> pdb=" O GLU Z 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.833A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 34 removed outlier: 4.082A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 removed outlier: 3.802A pdb=" N ALA B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 removed outlier: 3.841A pdb=" N LEU 1 7 " --> pdb=" O ARG 1 3 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 35 removed outlier: 4.925A pdb=" N VAL 1 15 " --> pdb=" O ARG 1 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR 1 35 " --> pdb=" O ILE 1 31 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 43 Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 9 through 35 removed outlier: 4.092A pdb=" N VAL 3 15 " --> pdb=" O ARG 3 11 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU 3 16 " --> pdb=" O ARG 3 12 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 43 Processing helix chain '5' and resid 1 through 7 Processing helix chain '5' and resid 9 through 35 removed outlier: 3.553A pdb=" N THR 5 35 " --> pdb=" O ILE 5 31 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 43 Processing helix chain '7' and resid 3 through 8 Processing helix chain '7' and resid 9 through 35 removed outlier: 4.349A pdb=" N VAL 7 15 " --> pdb=" O ARG 7 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR 7 35 " --> pdb=" O ILE 7 31 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 43 Processing helix chain '9' and resid 3 through 8 Processing helix chain '9' and resid 9 through 34 removed outlier: 4.080A pdb=" N VAL 9 15 " --> pdb=" O ARG 9 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU 9 16 " --> pdb=" O ARG 9 12 " (cutoff:3.500A) Processing helix chain '0' and resid 10 through 43 Processing sheet with id=AA1, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA2, first strand: chain 'H' and resid 85 through 87 Processing sheet with id=AA3, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.591A pdb=" N GLU H 179 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL H 166 " --> pdb=" O TYR H 177 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR H 177 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL H 168 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA H 175 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 131 removed outlier: 3.705A pdb=" N GLY H 161 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA6, first strand: chain 'M' and resid 35 through 36 1222 hydrogen bonds defined for protein. 3518 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: 4.29 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 6890 1.37 - 1.54: 18664 1.54 - 1.71: 224 1.71 - 1.88: 103 1.88 - 2.05: 144 Bond restraints: 26025 Sorted by residual: bond pdb=" CZ2 QAK M 407 " pdb=" C4 QAK M 407 " ideal model delta sigma weight residual 1.330 1.551 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CE3 QAK M 407 " pdb=" CZ3 QAK M 407 " ideal model delta sigma weight residual 1.330 1.536 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" NA BCL L 308 " pdb="MG BCL L 308 " ideal model delta sigma weight residual 2.170 1.996 0.174 2.40e-02 1.74e+03 5.27e+01 bond pdb=" NA BCL M 404 " pdb="MG BCL M 404 " ideal model delta sigma weight residual 2.170 1.999 0.171 2.40e-02 1.74e+03 5.07e+01 bond pdb=" NA BCL N 102 " pdb="MG BCL N 102 " ideal model delta sigma weight residual 2.170 2.001 0.169 2.40e-02 1.74e+03 4.94e+01 ... (remaining 26020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 33364 3.63 - 7.26: 1824 7.26 - 10.89: 229 10.89 - 14.52: 58 14.52 - 18.15: 19 Bond angle restraints: 35494 Sorted by residual: angle pdb=" C1D BCL 9 102 " pdb=" C2D BCL 9 102 " pdb=" CMD BCL 9 102 " ideal model delta sigma weight residual 125.57 139.45 -13.88 1.83e+00 2.99e-01 5.76e+01 angle pdb=" C1D BCL 5 101 " pdb=" C2D BCL 5 101 " pdb=" CMD BCL 5 101 " ideal model delta sigma weight residual 125.57 139.43 -13.86 1.83e+00 2.99e-01 5.75e+01 angle pdb=" C1D BCL T 100 " pdb=" C2D BCL T 100 " pdb=" CMD BCL T 100 " ideal model delta sigma weight residual 125.57 139.42 -13.84 1.83e+00 2.99e-01 5.73e+01 angle pdb=" C1D BCL G 103 " pdb=" C2D BCL G 103 " pdb=" CMD BCL G 103 " ideal model delta sigma weight residual 125.57 139.37 -13.80 1.83e+00 2.99e-01 5.70e+01 angle pdb=" C1D BCL Y 101 " pdb=" C2D BCL Y 101 " pdb=" CMD BCL Y 101 " ideal model delta sigma weight residual 125.57 139.35 -13.78 1.83e+00 2.99e-01 5.68e+01 ... (remaining 35489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 13163 36.00 - 72.00: 616 72.00 - 107.99: 11 107.99 - 143.99: 3 143.99 - 179.99: 33 Dihedral angle restraints: 13826 sinusoidal: 7065 harmonic: 6761 Sorted by residual: dihedral pdb=" C1 BCL U 100 " pdb=" C2 BCL U 100 " pdb=" C3 BCL U 100 " pdb=" C5 BCL U 100 " ideal model delta sinusoidal sigma weight residual 180.00 0.01 179.99 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 1 102 " pdb=" C2 BCL 1 102 " pdb=" C3 BCL 1 102 " pdb=" C5 BCL 1 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.02 -179.98 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL B 102 " pdb=" C2 BCL B 102 " pdb=" C3 BCL B 102 " pdb=" C5 BCL B 102 " ideal model delta sinusoidal sigma weight residual 180.00 0.02 179.98 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 13823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 3423 1.059 - 2.119: 0 2.119 - 3.178: 0 3.178 - 4.237: 0 4.237 - 5.297: 7 Chirality restraints: 3430 Sorted by residual: chirality pdb=" C14 QAK M 407 " pdb=" C13 QAK M 407 " pdb=" C15 QAK M 407 " pdb=" C37 QAK M 407 " both_signs ideal model delta sigma weight residual False -2.57 2.73 -5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" C24 QAK M 407 " pdb=" C23 QAK M 407 " pdb=" C25 QAK M 407 " pdb=" C26 QAK M 407 " both_signs ideal model delta sigma weight residual False 2.58 -2.61 5.19 2.00e-01 2.50e+01 6.74e+02 chirality pdb=" C13 BPH L 302 " pdb=" C12 BPH L 302 " pdb=" C14 BPH L 302 " pdb=" C15 BPH L 302 " both_signs ideal model delta sigma weight residual False 2.60 -2.57 5.17 2.00e-01 2.50e+01 6.68e+02 ... (remaining 3427 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.315 3.00e-02 1.11e+03 2.52e-01 3.52e+02 pdb=" CBA BCL E 101 " 0.195 3.00e-02 1.11e+03 pdb=" CGA BCL E 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL E 101 " -0.015 3.00e-02 1.11e+03 pdb=" O2A BCL E 101 " -0.417 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 308 " -0.313 3.00e-02 1.11e+03 2.51e-01 3.50e+02 pdb=" CBA BCL L 308 " -0.191 3.00e-02 1.11e+03 pdb=" CGA BCL L 308 " 0.075 3.00e-02 1.11e+03 pdb=" O1A BCL L 308 " 0.011 3.00e-02 1.11e+03 pdb=" O2A BCL L 308 " 0.419 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL N 101 " -0.291 3.00e-02 1.11e+03 2.32e-01 2.98e+02 pdb=" CBA BCL N 101 " -0.187 3.00e-02 1.11e+03 pdb=" CGA BCL N 101 " 0.072 3.00e-02 1.11e+03 pdb=" O1A BCL N 101 " 0.028 3.00e-02 1.11e+03 pdb=" O2A BCL N 101 " 0.378 3.00e-02 1.11e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 131 2.57 - 3.15: 17820 3.15 - 3.73: 37703 3.73 - 4.32: 59092 4.32 - 4.90: 94841 Nonbonded interactions: 209587 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 403 " model vdw 1.982 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 403 " model vdw 2.099 2.260 nonbonded pdb=" O2' LMT J 102 " pdb=" O31 6PL L 305 " model vdw 2.159 3.040 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 403 " model vdw 2.171 2.340 nonbonded pdb=" O ALA 6 32 " pdb=" ND1 HIS 6 36 " model vdw 2.192 3.120 ... (remaining 209582 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 6 through 25 or resid 27 through 52)) selection = (chain '2' and (resid 6 through 25 or resid 27 through 52)) selection = (chain '4' and (resid 6 through 25 or resid 27 through 52)) selection = (chain '6' and (resid 6 through 25 or resid 27 through 52)) selection = (chain '8' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'B' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'D' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'F' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'I' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'K' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'O' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'Q' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'S' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'U' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'X' and (resid 6 through 25 or resid 27 through 52)) selection = (chain 'Z' and (resid 6 through 25 or resid 27 through 52)) } ncs_group { reference = (chain '1' and resid 2 through 45) selection = (chain '3' and resid 2 through 45) selection = (chain '5' and resid 2 through 45) selection = (chain '7' and resid 2 through 45) selection = (chain '9' and resid 2 through 45) selection = (chain 'A' and resid 2 through 45) selection = (chain 'C' and resid 2 through 45) selection = (chain 'E' and resid 2 through 45) selection = (chain 'G' and resid 2 through 45) selection = (chain 'J' and resid 2 through 45) selection = (chain 'N' and resid 2 through 45) selection = (chain 'P' and resid 2 through 45) selection = (chain 'R' and resid 2 through 45) selection = (chain 'T' and resid 2 through 45) selection = (chain 'V' and resid 2 through 45) selection = (chain 'Y' and resid 2 through 45) } 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=0.50 max=1.00 mean=0.99 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.500 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.024 0.691 26047 Z= 1.739 Angle : 1.763 18.151 35494 Z= 0.779 Chirality : 0.238 5.297 3430 Planarity : 0.018 0.252 4068 Dihedral : 20.201 179.990 9442 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2293 helix: 1.39 (0.12), residues: 1386 sheet: -0.84 (0.87), residues: 33 loop : -2.03 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 43 TYR 0.011 0.001 TYR M 198 PHE 0.064 0.002 PHE M 216 TRP 0.025 0.002 TRP L 275 HIS 0.007 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.01900 / 0.84 (26025) covalent geometry : angle 1.76259 / 0.78 (35494) hydrogen bonds : bond 0.12264 / 7.74 ( 1220) hydrogen bonds : angle 4.19989 / 3.03 ( 3518) Misc. bond : bond 0.52460 / 28.73 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 218 MET cc_start: 0.8987 (mtp) cc_final: 0.8577 (mtm) REVERT: M 256 MET cc_start: 0.9402 (ptt) cc_final: 0.9053 (ptt) REVERT: 2 23 THR cc_start: 0.8854 (p) cc_final: 0.8646 (p) REVERT: 3 3 ARG cc_start: 0.8392 (mtt90) cc_final: 0.8177 (mtt90) REVERT: 8 25 PHE cc_start: 0.8382 (t80) cc_final: 0.7901 (t80) REVERT: 0 15 LYS cc_start: 0.8656 (mttp) cc_final: 0.8445 (mttp) outliers start: 0 outliers final: 1 residues processed: 289 average time/residue: 0.7851 time to fit residues: 254.7394 Evaluate side-chains 198 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 4 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 HIS F 18 HIS I 18 HIS K 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN L 160 ASN L 267 ASN L 271 ASN M 12 GLN S 18 HIS U 18 HIS Q 18 HIS B 18 HIS 2 18 HIS 4 18 HIS 6 18 HIS 8 18 HIS 0 18 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.054403 restraints weight = 226469.857| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.63 r_work: 0.2617 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26047 Z= 0.137 Angle : 0.682 12.713 35494 Z= 0.275 Chirality : 0.038 0.325 3430 Planarity : 0.005 0.052 4068 Dihedral : 21.932 179.999 5336 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 10.90 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.66 (0.17), residues: 2293 helix: 2.61 (0.13), residues: 1396 sheet: -0.85 (0.76), residues: 43 loop : -1.50 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 3 TYR 0.010 0.001 TYR M 198 PHE 0.034 0.001 PHE M 216 TRP 0.014 0.001 TRP U 45 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (26025) covalent geometry : angle 0.68156 / 0.28 (35494) hydrogen bonds : bond 0.05350 / 3.50 ( 1220) hydrogen bonds : angle 3.44482 / 2.48 ( 3518) Misc. bond : bond 0.00214 / 0.12 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8585 (mttp) cc_final: 0.8277 (mmtp) REVERT: M 33 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6976 (tm-30) REVERT: M 218 MET cc_start: 0.9230 (mtp) cc_final: 0.8953 (mtm) REVERT: Q 13 GLU cc_start: 0.7816 (pm20) cc_final: 0.7485 (pm20) REVERT: 1 12 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7560 (mtp-110) REVERT: 4 16 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7956 (mm-30) REVERT: 8 25 PHE cc_start: 0.8765 (t80) cc_final: 0.8182 (t80) REVERT: 0 15 LYS cc_start: 0.8894 (mttp) cc_final: 0.8654 (mttp) outliers start: 28 outliers final: 11 residues processed: 237 average time/residue: 0.7828 time to fit residues: 208.1114 Evaluate side-chains 209 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain 2 residue 10 SER Chi-restraints excluded: chain 7 residue 9 ASP Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 18 HIS M 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053630 restraints weight = 228859.890| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.63 r_work: 0.2595 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26047 Z= 0.159 Angle : 0.687 12.360 35494 Z= 0.280 Chirality : 0.039 0.208 3430 Planarity : 0.004 0.052 4068 Dihedral : 21.526 179.996 5334 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.74 % Allowed : 11.66 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.17), residues: 2293 helix: 2.83 (0.13), residues: 1401 sheet: -0.61 (0.77), residues: 43 loop : -1.35 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 3 TYR 0.011 0.001 TYR M 198 PHE 0.026 0.002 PHE M 216 TRP 0.014 0.001 TRP U 45 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (26025) covalent geometry : angle 0.68685 / 0.28 (35494) hydrogen bonds : bond 0.05593 / 3.66 ( 1220) hydrogen bonds : angle 3.39797 / 2.46 ( 3518) Misc. bond : bond 0.00256 / 0.14 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8536 (mttp) cc_final: 0.8228 (mmtp) REVERT: O 43 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8418 (ttp-110) REVERT: L 83 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: M 33 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6995 (tm-30) REVERT: M 218 MET cc_start: 0.9284 (mtp) cc_final: 0.9016 (mtm) REVERT: V 3 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8665 (ttm-80) REVERT: X 11 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7485 (tm-30) REVERT: Z 16 GLU cc_start: 0.8378 (tt0) cc_final: 0.7587 (tt0) REVERT: B 6 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6482 (pp) REVERT: 8 25 PHE cc_start: 0.8781 (t80) cc_final: 0.8228 (t80) REVERT: 0 15 LYS cc_start: 0.8932 (mttp) cc_final: 0.8669 (mttp) outliers start: 34 outliers final: 13 residues processed: 232 average time/residue: 0.8015 time to fit residues: 209.2145 Evaluate side-chains 207 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 7 residue 9 ASP Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 0 residue 20 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053550 restraints weight = 233679.173| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.65 r_work: 0.2591 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26047 Z= 0.155 Angle : 0.677 13.002 35494 Z= 0.275 Chirality : 0.039 0.276 3430 Planarity : 0.004 0.053 4068 Dihedral : 21.324 179.990 5334 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.05 % Allowed : 11.97 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.20 (0.18), residues: 2293 helix: 3.00 (0.13), residues: 1393 sheet: -0.48 (0.78), residues: 43 loop : -1.20 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 3 TYR 0.011 0.001 TYR M 198 PHE 0.019 0.002 PHE M 216 TRP 0.018 0.001 TRP 7 2 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (26025) covalent geometry : angle 0.67692 / 0.27 (35494) hydrogen bonds : bond 0.05462 / 3.58 ( 1220) hydrogen bonds : angle 3.35650 / 2.43 ( 3518) Misc. bond : bond 0.00273 / 0.15 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8500 (mttp) cc_final: 0.8167 (mmtp) REVERT: O 15 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8680 (mptp) REVERT: O 43 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8409 (ttp-110) REVERT: H 233 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8889 (t0) REVERT: M 33 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6962 (tm-30) REVERT: M 218 MET cc_start: 0.9295 (mtp) cc_final: 0.9012 (mtm) REVERT: V 3 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8689 (ttm-80) REVERT: X 11 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7596 (tm-30) REVERT: Z 16 GLU cc_start: 0.8427 (tt0) cc_final: 0.7567 (tt0) REVERT: B 6 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6524 (pp) REVERT: 6 16 GLU cc_start: 0.8777 (tt0) cc_final: 0.8417 (tt0) REVERT: 8 25 PHE cc_start: 0.8720 (t80) cc_final: 0.8205 (t80) outliers start: 40 outliers final: 17 residues processed: 231 average time/residue: 0.8282 time to fit residues: 215.0813 Evaluate side-chains 214 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 7 residue 9 ASP Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 9 residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 13 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052137 restraints weight = 267064.097| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.78 r_work: 0.2546 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 26047 Z= 0.225 Angle : 0.762 12.879 35494 Z= 0.311 Chirality : 0.043 0.310 3430 Planarity : 0.005 0.059 4068 Dihedral : 21.759 179.990 5334 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.71 % Allowed : 12.43 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.17), residues: 2293 helix: 2.77 (0.13), residues: 1413 sheet: -0.43 (0.79), residues: 43 loop : -1.18 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 43 TYR 0.015 0.002 TYR M 198 PHE 0.019 0.002 PHE M 216 TRP 0.021 0.002 TRP 1 2 HIS 0.009 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.22 (26025) covalent geometry : angle 0.76176 / 0.31 (35494) hydrogen bonds : bond 0.06401 / 4.20 ( 1220) hydrogen bonds : angle 3.51242 / 2.54 ( 3518) Misc. bond : bond 0.00359 / 0.19 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.959 Fit side-chains REVERT: O 43 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8432 (ttp-110) REVERT: H 233 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8890 (t0) REVERT: L 83 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: M 33 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6878 (tm-30) REVERT: M 218 MET cc_start: 0.9337 (mtp) cc_final: 0.9035 (mtm) REVERT: V 3 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8633 (ttm-80) REVERT: X 11 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7756 (tm-30) REVERT: Z 16 GLU cc_start: 0.8480 (tt0) cc_final: 0.7774 (tt0) REVERT: B 6 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6584 (pp) REVERT: 6 15 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8024 (mmtm) REVERT: 6 16 GLU cc_start: 0.8828 (tt0) cc_final: 0.8523 (tt0) REVERT: 8 25 PHE cc_start: 0.8774 (t80) cc_final: 0.8210 (t80) REVERT: 0 15 LYS cc_start: 0.8980 (mttp) cc_final: 0.8683 (mttp) outliers start: 53 outliers final: 23 residues processed: 227 average time/residue: 0.7969 time to fit residues: 204.5093 Evaluate side-chains 216 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 5 residue 19 VAL Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 0 residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 191 optimal weight: 0.0030 chunk 165 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 113 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.054620 restraints weight = 255660.675| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.78 r_work: 0.2618 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26047 Z= 0.117 Angle : 0.640 12.907 35494 Z= 0.261 Chirality : 0.037 0.300 3430 Planarity : 0.004 0.051 4068 Dihedral : 20.875 179.996 5334 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.79 % Allowed : 13.50 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.18), residues: 2293 helix: 3.14 (0.13), residues: 1392 sheet: -0.34 (0.78), residues: 43 loop : -1.00 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 7 3 TYR 0.011 0.001 TYR M 157 PHE 0.019 0.001 PHE X 26 TRP 0.015 0.001 TRP 1 2 HIS 0.004 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (26025) covalent geometry : angle 0.63974 / 0.26 (35494) hydrogen bonds : bond 0.04774 / 3.13 ( 1220) hydrogen bonds : angle 3.28030 / 2.37 ( 3518) Misc. bond : bond 0.00180 / 0.10 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8494 (mttp) cc_final: 0.8068 (mmtp) REVERT: O 43 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8458 (ttp-110) REVERT: H 233 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8840 (t0) REVERT: M 33 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6953 (tm-30) REVERT: M 218 MET cc_start: 0.9295 (mtp) cc_final: 0.8946 (mtm) REVERT: S 10 SER cc_start: 0.7011 (OUTLIER) cc_final: 0.6559 (p) REVERT: S 13 GLU cc_start: 0.7951 (pm20) cc_final: 0.7678 (pt0) REVERT: V 3 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8509 (ttm-80) REVERT: X 11 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7341 (tm-30) REVERT: X 15 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8347 (mmtp) REVERT: Q 13 GLU cc_start: 0.7889 (pm20) cc_final: 0.7624 (pm20) REVERT: A 14 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (mt) REVERT: 6 16 GLU cc_start: 0.8712 (tt0) cc_final: 0.8213 (tt0) REVERT: 6 48 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8787 (mtmm) REVERT: 8 9 LEU cc_start: 0.8820 (mp) cc_final: 0.8611 (mm) REVERT: 8 25 PHE cc_start: 0.8741 (t80) cc_final: 0.8227 (t80) REVERT: 9 2 TRP cc_start: 0.7519 (m100) cc_final: 0.7209 (t-100) REVERT: 0 15 LYS cc_start: 0.8955 (mttp) cc_final: 0.8637 (mttp) outliers start: 35 outliers final: 10 residues processed: 229 average time/residue: 0.7612 time to fit residues: 196.6071 Evaluate side-chains 213 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 6 residue 48 LYS Chi-restraints excluded: chain 7 residue 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053676 restraints weight = 239561.430| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.68 r_work: 0.2593 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26047 Z= 0.150 Angle : 0.677 12.370 35494 Z= 0.278 Chirality : 0.039 0.372 3430 Planarity : 0.004 0.053 4068 Dihedral : 20.940 179.995 5334 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.69 % Allowed : 14.12 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.45 (0.18), residues: 2293 helix: 3.11 (0.13), residues: 1392 sheet: -0.27 (0.79), residues: 43 loop : -0.92 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 7 3 TYR 0.011 0.001 TYR H 15 PHE 0.013 0.001 PHE 2 25 TRP 0.013 0.001 TRP D 45 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (26025) covalent geometry : angle 0.67735 / 0.28 (35494) hydrogen bonds : bond 0.05289 / 3.47 ( 1220) hydrogen bonds : angle 3.32011 / 2.40 ( 3518) Misc. bond : bond 0.00277 / 0.15 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8569 (mttp) cc_final: 0.8241 (mmtp) REVERT: O 43 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8377 (ttp-110) REVERT: H 233 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8857 (t0) REVERT: M 33 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6900 (tm-30) REVERT: M 214 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9017 (tp) REVERT: M 218 MET cc_start: 0.9329 (mtp) cc_final: 0.8938 (mtm) REVERT: S 10 SER cc_start: 0.6908 (OUTLIER) cc_final: 0.6485 (p) REVERT: V 3 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8564 (ttm-80) REVERT: X 11 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7392 (tm-30) REVERT: X 15 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8396 (mmtp) REVERT: Q 13 GLU cc_start: 0.7925 (pm20) cc_final: 0.7645 (pm20) REVERT: 6 16 GLU cc_start: 0.8750 (tt0) cc_final: 0.8422 (tt0) REVERT: 6 48 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8804 (mtmm) REVERT: 8 25 PHE cc_start: 0.8743 (t80) cc_final: 0.8210 (t80) REVERT: 9 2 TRP cc_start: 0.7581 (m100) cc_final: 0.7211 (t-100) REVERT: 0 15 LYS cc_start: 0.8982 (mttp) cc_final: 0.8671 (mttp) outliers start: 33 outliers final: 14 residues processed: 228 average time/residue: 0.7916 time to fit residues: 203.6075 Evaluate side-chains 218 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 6 residue 48 LYS Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 49 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053521 restraints weight = 247898.240| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.72 r_work: 0.2588 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26047 Z= 0.155 Angle : 0.682 12.324 35494 Z= 0.281 Chirality : 0.039 0.340 3430 Planarity : 0.004 0.069 4068 Dihedral : 20.939 179.990 5334 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 14.63 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.18), residues: 2293 helix: 3.08 (0.13), residues: 1396 sheet: -0.18 (0.80), residues: 42 loop : -0.89 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 9 12 TYR 0.011 0.001 TYR M 198 PHE 0.020 0.001 PHE X 26 TRP 0.013 0.001 TRP D 45 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (26025) covalent geometry : angle 0.68165 / 0.28 (35494) hydrogen bonds : bond 0.05387 / 3.53 ( 1220) hydrogen bonds : angle 3.34109 / 2.41 ( 3518) Misc. bond : bond 0.00284 / 0.15 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8516 (mttp) cc_final: 0.8058 (mmtp) REVERT: I 9 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9131 (mp) REVERT: O 43 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8391 (ttp-110) REVERT: H 233 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8848 (t0) REVERT: M 33 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6940 (tm-30) REVERT: M 214 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9020 (tp) REVERT: M 218 MET cc_start: 0.9331 (mtp) cc_final: 0.8940 (mtm) REVERT: V 3 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8534 (ttm-80) REVERT: X 11 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7404 (tm-30) REVERT: X 15 LYS cc_start: 0.8745 (mmtp) cc_final: 0.8386 (mmtp) REVERT: Q 13 GLU cc_start: 0.7928 (pm20) cc_final: 0.7680 (pm20) REVERT: 2 15 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8245 (ttmm) REVERT: 6 16 GLU cc_start: 0.8704 (tt0) cc_final: 0.8406 (tt0) REVERT: 6 48 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: 8 25 PHE cc_start: 0.8762 (t80) cc_final: 0.8222 (t80) REVERT: 0 15 LYS cc_start: 0.8988 (mttp) cc_final: 0.8691 (mttp) outliers start: 28 outliers final: 17 residues processed: 220 average time/residue: 0.8277 time to fit residues: 204.9067 Evaluate side-chains 216 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 6 residue 48 LYS Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 139 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053185 restraints weight = 229878.023| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.62 r_work: 0.2583 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26047 Z= 0.171 Angle : 0.704 12.855 35494 Z= 0.291 Chirality : 0.040 0.364 3430 Planarity : 0.004 0.055 4068 Dihedral : 21.077 179.998 5334 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.59 % Allowed : 14.48 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.41 (0.18), residues: 2293 helix: 3.04 (0.13), residues: 1396 sheet: -0.18 (0.81), residues: 42 loop : -0.89 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 9 12 TYR 0.013 0.001 TYR M 198 PHE 0.014 0.002 PHE 2 25 TRP 0.014 0.001 TRP D 45 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (26025) covalent geometry : angle 0.70438 / 0.29 (35494) hydrogen bonds : bond 0.05640 / 3.70 ( 1220) hydrogen bonds : angle 3.38533 / 2.44 ( 3518) Misc. bond : bond 0.00308 / 0.17 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8540 (mttp) cc_final: 0.8117 (mmtp) REVERT: I 9 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9123 (mp) REVERT: O 43 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8393 (ttp-110) REVERT: H 233 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8846 (t0) REVERT: M 33 GLN cc_start: 0.7170 (tm-30) cc_final: 0.6840 (tm-30) REVERT: M 214 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9023 (tp) REVERT: M 218 MET cc_start: 0.9333 (mtp) cc_final: 0.9031 (mtm) REVERT: V 3 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8668 (ttm-80) REVERT: X 11 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7417 (tm-30) REVERT: X 15 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8364 (mmtp) REVERT: Z 5 SER cc_start: 0.8096 (m) cc_final: 0.7482 (t) REVERT: Z 13 GLU cc_start: 0.8281 (pm20) cc_final: 0.8022 (pm20) REVERT: Z 16 GLU cc_start: 0.8455 (tt0) cc_final: 0.7736 (pt0) REVERT: 6 15 LYS cc_start: 0.8639 (mmmm) cc_final: 0.7982 (mmtm) REVERT: 6 16 GLU cc_start: 0.8704 (tt0) cc_final: 0.8409 (tt0) REVERT: 6 48 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8781 (mtmm) REVERT: 8 25 PHE cc_start: 0.8772 (t80) cc_final: 0.8230 (t80) REVERT: 9 2 TRP cc_start: 0.7737 (m100) cc_final: 0.7350 (t-100) REVERT: 0 15 LYS cc_start: 0.8977 (mttp) cc_final: 0.8680 (mttp) outliers start: 31 outliers final: 18 residues processed: 222 average time/residue: 0.8153 time to fit residues: 203.4515 Evaluate side-chains 215 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 27 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 6 residue 48 LYS Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.054374 restraints weight = 264950.770| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.79 r_work: 0.2603 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26047 Z= 0.133 Angle : 0.666 13.351 35494 Z= 0.276 Chirality : 0.038 0.366 3430 Planarity : 0.004 0.060 4068 Dihedral : 20.741 179.991 5334 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 14.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.56 (0.18), residues: 2293 helix: 3.19 (0.13), residues: 1392 sheet: -0.16 (0.81), residues: 42 loop : -0.85 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 45 TYR 0.010 0.001 TYR M 157 PHE 0.022 0.001 PHE X 26 TRP 0.012 0.001 TRP 0 45 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (26025) covalent geometry : angle 0.66602 / 0.28 (35494) hydrogen bonds : bond 0.05049 / 3.31 ( 1220) hydrogen bonds : angle 3.32294 / 2.39 ( 3518) Misc. bond : bond 0.00230 / 0.12 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 LYS cc_start: 0.8541 (mttp) cc_final: 0.8068 (mmtp) REVERT: I 9 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9132 (mp) REVERT: N 9 ASP cc_start: 0.8776 (t0) cc_final: 0.8568 (t0) REVERT: O 43 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8446 (ttp-110) REVERT: H 233 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8830 (t0) REVERT: M 33 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6925 (tm-30) REVERT: M 214 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9004 (tp) REVERT: M 216 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8722 (t80) REVERT: M 218 MET cc_start: 0.9324 (mtp) cc_final: 0.9028 (mtm) REVERT: V 3 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8637 (ttm-80) REVERT: X 11 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7376 (tm-30) REVERT: Z 5 SER cc_start: 0.8090 (m) cc_final: 0.7445 (t) REVERT: Z 13 GLU cc_start: 0.8240 (pm20) cc_final: 0.7994 (pm20) REVERT: Z 16 GLU cc_start: 0.8465 (tt0) cc_final: 0.7739 (pt0) REVERT: 6 16 GLU cc_start: 0.8669 (tt0) cc_final: 0.8315 (tt0) REVERT: 6 48 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8769 (mtmm) REVERT: 8 25 PHE cc_start: 0.8779 (t80) cc_final: 0.8230 (t80) REVERT: 9 2 TRP cc_start: 0.7550 (m100) cc_final: 0.7304 (t-100) REVERT: 0 15 LYS cc_start: 0.8988 (mttp) cc_final: 0.8684 (mttp) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.8015 time to fit residues: 194.6470 Evaluate side-chains 213 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain R residue 14 LEU Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain V residue 3 ARG Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 6 residue 48 LYS Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 8 residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 142 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055269 restraints weight = 197544.270| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.47 r_work: 0.2644 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26047 Z= 0.118 Angle : 0.649 13.892 35494 Z= 0.270 Chirality : 0.037 0.373 3430 Planarity : 0.004 0.053 4068 Dihedral : 20.406 179.991 5334 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.23 % Allowed : 14.99 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.69 (0.18), residues: 2293 helix: 3.28 (0.13), residues: 1392 sheet: -0.02 (0.82), residues: 42 loop : -0.77 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 7 3 TYR 0.010 0.001 TYR M 157 PHE 0.011 0.001 PHE Z 25 TRP 0.012 0.001 TRP U 45 HIS 0.004 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26025) covalent geometry : angle 0.64859 / 0.27 (35494) hydrogen bonds : bond 0.04609 / 3.04 ( 1220) hydrogen bonds : angle 3.26197 / 2.36 ( 3518) Misc. bond : bond 0.00190 / 0.10 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7463.32 seconds wall clock time: 128 minutes 5.74 seconds (7685.74 seconds total)