Starting phenix.real_space_refine on Sun Sep 13 05:11:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.cif" model { file = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yq7_6828/09_2026/5yq7_6828.map" } resolution = 4.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 Mg 48 5.21 5 S 51 5.16 5 C 14179 2.51 5 N 2791 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 20009 Number of models: 1 Model: "" Number of chains: 68 Chain: "E" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "0" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2292 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 291} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 90 Chain: "8" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "6" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "4" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 319 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "2" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 326 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2041 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 21, 'TRANS': 271} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "I" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "W" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 312 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 326 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 318 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 325 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "9" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "7" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "5" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "3" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "1" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 245 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "X" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 288} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 5, 'TRP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "E" 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: "B" 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: "0" 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: "L" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 266 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'MQE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "8" 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: "6" 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: "4" 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" 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: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" 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: "G" 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: "W" 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: "U" 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: "T" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" 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: "Q" 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 264 Unusual residues: {'BCL': 1, 'BPH': 2, 'MQE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.32, per 1000 atoms: 0.22 Number of scatterers: 20009 At special positions: 0 Unit cell: (137.76, 142.24, 129.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 51 16.00 Mg 48 11.99 O 2935 8.00 N 2791 7.00 C 14179 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 693.7 milliseconds 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 62.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'E' and resid 22 through 51 removed outlier: 3.589A pdb=" N HIS E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 51 " --> pdb=" O CYS E 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 51 removed outlier: 4.102A pdb=" N HIS B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) Processing helix chain '0' and resid 22 through 51 removed outlier: 3.795A pdb=" N HIS 0 26 " --> pdb=" O GLN 0 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 0 31 " --> pdb=" O ASP 0 27 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP 0 50 " --> pdb=" O LEU 0 46 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR 0 51 " --> pdb=" O CYS 0 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 29 Proline residue: L 17 - end of helix removed outlier: 4.049A pdb=" N SER L 26 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 33 Processing helix chain 'L' and resid 38 through 45 removed outlier: 3.980A pdb=" N PHE L 42 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 45 " --> pdb=" O GLU L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 93 Processing helix chain 'L' and resid 123 through 150 removed outlier: 3.583A pdb=" N LEU L 127 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 172 removed outlier: 3.938A pdb=" N ILE L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.604A pdb=" N ALA L 177 " --> pdb=" O LEU L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.874A pdb=" N TRP L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 234 removed outlier: 4.043A pdb=" N THR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 252 removed outlier: 3.566A pdb=" N ASN L 252 " --> pdb=" O VAL L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 284 removed outlier: 3.926A pdb=" N VAL L 266 " --> pdb=" O GLY L 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA L 272 " --> pdb=" O PHE L 268 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER L 274 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU L 280 " --> pdb=" O LEU L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 297 Processing helix chain 'L' and resid 302 through 306 Processing helix chain '8' and resid 22 through 48 removed outlier: 3.563A pdb=" N HIS 8 26 " --> pdb=" O GLN 8 22 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE 8 38 " --> pdb=" O TYR 8 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE 8 39 " --> pdb=" O GLY 8 35 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP 8 48 " --> pdb=" O HIS 8 44 " (cutoff:3.500A) Processing helix chain '6' and resid 22 through 51 removed outlier: 3.616A pdb=" N HIS 6 26 " --> pdb=" O GLN 6 22 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE 6 38 " --> pdb=" O TYR 6 34 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE 6 39 " --> pdb=" O GLY 6 35 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 6 40 " --> pdb=" O GLY 6 36 " (cutoff:3.500A) Processing helix chain '4' and resid 22 through 47 removed outlier: 3.769A pdb=" N HIS 4 26 " --> pdb=" O GLN 4 22 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE 4 38 " --> pdb=" O TYR 4 34 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE 4 39 " --> pdb=" O GLY 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 51 removed outlier: 4.032A pdb=" N THR 4 51 " --> pdb=" O TRP 4 48 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 48 through 51' Processing helix chain '2' and resid 22 through 48 removed outlier: 3.515A pdb=" N TYR 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY 2 35 " --> pdb=" O LYS 2 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 47 removed outlier: 3.860A pdb=" N HIS K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 removed outlier: 4.408A pdb=" N ILE C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.836A pdb=" N ILE C 58 " --> pdb=" O GLN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 removed outlier: 3.619A pdb=" N LEU C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA C 76 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 135 through 153 removed outlier: 3.631A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 149 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 removed outlier: 4.190A pdb=" N THR C 157 " --> pdb=" O GLN C 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 219 through 236 removed outlier: 4.039A pdb=" N GLU C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.975A pdb=" N VAL C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 48 removed outlier: 3.731A pdb=" N HIS I 26 " --> pdb=" O GLN I 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 47 removed outlier: 3.725A pdb=" N HIS G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 48 removed outlier: 3.598A pdb=" N HIS W 26 " --> pdb=" O GLN W 22 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS W 31 " --> pdb=" O ASP W 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 48 removed outlier: 3.636A pdb=" N TRP U 48 " --> pdb=" O HIS U 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 34 removed outlier: 3.574A pdb=" N VAL T 12 " --> pdb=" O PHE T 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 51 removed outlier: 3.635A pdb=" N ILE S 42 " --> pdb=" O ILE S 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 48 removed outlier: 3.829A pdb=" N ASP Q 27 " --> pdb=" O TRP Q 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP Q 48 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 47 removed outlier: 4.330A pdb=" N HIS O 26 " --> pdb=" O GLN O 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 32 removed outlier: 3.616A pdb=" N VAL V 12 " --> pdb=" O PHE V 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 33 removed outlier: 3.762A pdb=" N SER R 33 " --> pdb=" O VAL R 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.636A pdb=" N SER P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 34 Processing helix chain 'J' and resid 8 through 34 removed outlier: 4.009A pdb=" N SER J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 33 removed outlier: 4.205A pdb=" N SER H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 12 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.870A pdb=" N VAL F 12 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.581A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 34 removed outlier: 4.035A pdb=" N VAL 9 12 " --> pdb=" O PHE 9 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 9 13 " --> pdb=" O ARG 9 9 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 33 removed outlier: 3.859A pdb=" N SER 7 33 " --> pdb=" O VAL 7 29 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 34 removed outlier: 3.716A pdb=" N THR 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU 5 31 " --> pdb=" O HIS 5 27 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 34 Processing helix chain '1' and resid 7 through 31 removed outlier: 3.621A pdb=" N VAL 1 14 " --> pdb=" O THR 1 10 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER 1 15 " --> pdb=" O SER 1 11 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR 1 16 " --> pdb=" O VAL 1 12 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 1 17 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.625A pdb=" N UNK Y 5 " --> pdb=" O UNK Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 23 removed outlier: 3.800A pdb=" N UNK Y 23 " --> pdb=" O UNK Y 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 23 removed outlier: 4.283A pdb=" N UNK X 23 " --> pdb=" O UNK X 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 366 Processing helix chain 'M' and resid 379 through 398 removed outlier: 3.685A pdb=" N ASP M 396 " --> pdb=" O ILE M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 438 through 463 removed outlier: 3.948A pdb=" N THR M 463 " --> pdb=" O ARG M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 485 removed outlier: 3.659A pdb=" N ALA M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 481 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 517 removed outlier: 4.372A pdb=" N ASN M 510 " --> pdb=" O LEU M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 550 removed outlier: 3.755A pdb=" N MET M 526 " --> pdb=" O ASN M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 577 removed outlier: 3.523A pdb=" N GLN M 569 " --> pdb=" O GLY M 565 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU M 573 " --> pdb=" O GLN M 569 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE M 574 " --> pdb=" O ARG M 570 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP M 575 " --> pdb=" O ALA M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 587 through 610 removed outlier: 4.229A pdb=" N THR M 599 " --> pdb=" O PHE M 595 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA M 600 " --> pdb=" O ALA M 596 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 609 " --> pdb=" O ILE M 605 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER M 610 " --> pdb=" O GLY M 606 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 930 hydrogen bonds defined for protein. 2751 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: 2.71 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 5403 1.36 - 1.56: 15242 1.56 - 1.77: 1 1.77 - 1.97: 84 1.97 - 2.17: 206 Bond restraints: 20936 Sorted by residual: bond pdb=" CAX KGD H 102 " pdb=" CAY KGD H 102 " ideal model delta sigma weight residual 1.336 1.549 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CAJ KGD 5 101 " pdb=" CAL KGD 5 101 " ideal model delta sigma weight residual 1.343 1.547 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CAX KGD 5 101 " pdb=" CAY KGD 5 101 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CAV MQE L1004 " pdb=" CBF MQE L1004 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CAZ MQE L1004 " pdb=" CBI MQE L1004 " ideal model delta sigma weight residual 1.336 1.538 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 20931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.13: 29264 9.13 - 18.26: 225 18.26 - 27.39: 8 27.39 - 36.52: 2 36.52 - 45.65: 4 Bond angle restraints: 29503 Sorted by residual: angle pdb=" C4 BCL W 101 " pdb=" C3 BCL W 101 " pdb=" C5 BCL W 101 " ideal model delta sigma weight residual 114.06 68.40 45.65 3.27e+00 9.35e-02 1.95e+02 angle pdb=" C4 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C5 BCL U 101 " ideal model delta sigma weight residual 114.06 68.96 45.10 3.27e+00 9.35e-02 1.90e+02 angle pdb=" C2 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C5 BCL U 101 " ideal model delta sigma weight residual 120.75 160.88 -40.13 3.08e+00 1.05e-01 1.69e+02 angle pdb=" C2 BCL W 101 " pdb=" C3 BCL W 101 " pdb=" C5 BCL W 101 " ideal model delta sigma weight residual 120.75 160.40 -39.65 3.08e+00 1.05e-01 1.65e+02 angle pdb=" C2 BCL U 101 " pdb=" C3 BCL U 101 " pdb=" C4 BCL U 101 " ideal model delta sigma weight residual 124.96 91.93 33.04 2.80e+00 1.28e-01 1.39e+02 ... (remaining 29498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 10038 35.99 - 71.98: 169 71.98 - 107.97: 38 107.97 - 143.96: 32 143.96 - 179.95: 3 Dihedral angle restraints: 10280 sinusoidal: 4088 harmonic: 6192 Sorted by residual: dihedral pdb=" C1 BCL 4 101 " pdb=" C2 BCL 4 101 " pdb=" C3 BCL 4 101 " pdb=" C5 BCL 4 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.05 -179.95 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.27 179.73 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual -180.00 -0.38 -179.62 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 10277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2744 0.073 - 0.146: 334 0.146 - 0.218: 19 0.218 - 0.291: 3 0.291 - 0.364: 2 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CA PHE H 8 " pdb=" N PHE H 8 " pdb=" C PHE H 8 " pdb=" CB PHE H 8 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBD BCL B 102 " pdb=" CAD BCL B 102 " pdb=" CGD BCL B 102 " pdb=" CHA BCL B 102 " both_signs ideal model delta sigma weight residual False 2.62 2.33 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C13 BPH M 703 " pdb=" C12 BPH M 703 " pdb=" C14 BPH M 703 " pdb=" C15 BPH M 703 " both_signs ideal model delta sigma weight residual False 2.60 2.84 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3099 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH M 703 " 0.010 2.00e-02 2.50e+03 5.93e-02 7.92e+01 pdb=" C1D BPH M 703 " 0.020 2.00e-02 2.50e+03 pdb=" C2D BPH M 703 " -0.027 2.00e-02 2.50e+03 pdb=" C3D BPH M 703 " -0.047 2.00e-02 2.50e+03 pdb=" C4D BPH M 703 " -0.030 2.00e-02 2.50e+03 pdb=" CAD BPH M 703 " 0.132 2.00e-02 2.50e+03 pdb=" CHA BPH M 703 " -0.055 2.00e-02 2.50e+03 pdb=" CHD BPH M 703 " 0.057 2.00e-02 2.50e+03 pdb=" CMD BPH M 703 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH L1003 " 0.005 2.00e-02 2.50e+03 5.01e-02 5.64e+01 pdb=" C1D BPH L1003 " 0.023 2.00e-02 2.50e+03 pdb=" C2D BPH L1003 " -0.019 2.00e-02 2.50e+03 pdb=" C3D BPH L1003 " -0.026 2.00e-02 2.50e+03 pdb=" C4D BPH L1003 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH L1003 " 0.108 2.00e-02 2.50e+03 pdb=" CHA BPH L1003 " -0.054 2.00e-02 2.50e+03 pdb=" CHD BPH L1003 " 0.047 2.00e-02 2.50e+03 pdb=" CMD BPH L1003 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BPH L1003 " -0.004 2.00e-02 2.50e+03 4.65e-02 4.86e+01 pdb=" C1B BPH L1003 " -0.025 2.00e-02 2.50e+03 pdb=" C2B BPH L1003 " 0.015 2.00e-02 2.50e+03 pdb=" C3B BPH L1003 " -0.005 2.00e-02 2.50e+03 pdb=" C4B BPH L1003 " 0.031 2.00e-02 2.50e+03 pdb=" CAB BPH L1003 " -0.085 2.00e-02 2.50e+03 pdb=" CHB BPH L1003 " -0.049 2.00e-02 2.50e+03 pdb=" CHC BPH L1003 " 0.044 2.00e-02 2.50e+03 pdb=" CMB BPH L1003 " 0.078 2.00e-02 2.50e+03 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 21 2.21 - 2.89: 7095 2.89 - 3.56: 28515 3.56 - 4.23: 39468 4.23 - 4.90: 65720 Nonbonded interactions: 140819 Sorted by model distance: nonbonded pdb=" CE1 HIS L 192 " pdb="MG BCL L1001 " model vdw 1.542 3.130 nonbonded pdb=" CE1 HIS G 44 " pdb="MG BCL G 101 " model vdw 1.689 3.130 nonbonded pdb=" CE1 HIS Q 44 " pdb="MG BCL Q 101 " model vdw 1.704 3.130 nonbonded pdb=" CE1 HIS C 244 " pdb="FE HEM C 503 " model vdw 1.729 3.220 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE L1005 " model vdw 1.784 2.260 ... (remaining 140814 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 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain '2' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain '4' and (resid 11 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 102)) selection = (chain '6' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain '8' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain 'B' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 102)) selection = (chain 'E' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 102)) selection = (chain 'G' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain 'I' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain 'K' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 102)) selection = (chain 'O' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 102)) selection = (chain 'Q' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 36 or (resid 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 45 or (res \ id 46 and (name N or name CA or name C or name O or name CB )) or resid 47 throu \ gh 102)) selection = (chain 'S' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 102)) selection = (chain 'U' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throu \ gh 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 102)) selection = (chain 'W' and (resid 11 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 102)) } ncs_group { reference = (chain '1' and (resid 5 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 40)) selection = (chain '3' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '5' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '7' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain '9' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'A' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'D' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'F' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'H' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'J' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 40)) selection = (chain 'N' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'P' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'R' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 throug \ h 40 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'T' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 21 or (resid 22 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'V' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 38 or (resi \ d 39 through 40 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 3 through 25) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 17.670 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.022 0.787 21001 Z= 1.430 Angle : 1.763 45.655 29503 Z= 0.668 Chirality : 0.049 0.364 3102 Planarity : 0.005 0.078 3485 Dihedral : 17.699 179.948 6254 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.65 % Favored : 85.15 % Rotamer: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.20 % 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: -4.34 (0.15), residues: 2041 helix: -1.59 (0.12), residues: 1222 sheet: None (None), residues: 0 loop : -5.04 (0.16), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 410 TYR 0.031 0.003 TYR 6 34 PHE 0.026 0.002 PHE C 242 TRP 0.044 0.003 TRP M 577 HIS 0.024 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.01943 / 0.96 (20936) covalent geometry : angle 1.76313 / 0.67 (29503) hydrogen bonds : bond 0.11656 / 7.81 ( 930) hydrogen bonds : angle 5.60307 / 4.18 ( 2751) Misc. bond : bond 0.19475 / 10.61 ( 65) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 776 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7866 (tm-30) REVERT: L 143 GLN cc_start: 0.9089 (mt0) cc_final: 0.8726 (tt0) REVERT: L 281 CYS cc_start: 0.8894 (t) cc_final: 0.8451 (t) REVERT: 4 53 TRP cc_start: 0.5858 (m100) cc_final: 0.5273 (m100) REVERT: K 38 ILE cc_start: 0.9174 (mt) cc_final: 0.8929 (mt) REVERT: C 229 MET cc_start: 0.9507 (mmp) cc_final: 0.9152 (mmt) REVERT: C 268 LYS cc_start: 0.9530 (tmtm) cc_final: 0.9287 (tttt) REVERT: I 47 CYS cc_start: 0.8799 (t) cc_final: 0.8461 (t) REVERT: G 31 LYS cc_start: 0.8518 (mttt) cc_final: 0.8299 (mttp) REVERT: T 18 LEU cc_start: 0.8950 (tt) cc_final: 0.8738 (tt) REVERT: O 30 VAL cc_start: 0.8906 (p) cc_final: 0.8622 (t) REVERT: H 15 SER cc_start: 0.9149 (t) cc_final: 0.8807 (p) REVERT: H 38 TRP cc_start: 0.8738 (t60) cc_final: 0.8392 (t60) REVERT: 7 33 SER cc_start: 0.8880 (t) cc_final: 0.8567 (m) REVERT: 1 18 LEU cc_start: 0.8856 (tp) cc_final: 0.8142 (tt) REVERT: 1 22 MET cc_start: 0.9237 (tpt) cc_final: 0.9030 (ptt) REVERT: M 341 GLU cc_start: 0.8899 (pt0) cc_final: 0.8622 (pm20) REVERT: M 391 PHE cc_start: 0.9263 (t80) cc_final: 0.8949 (t80) REVERT: M 414 ASN cc_start: 0.8423 (m-40) cc_final: 0.8079 (t0) REVERT: M 415 LEU cc_start: 0.8802 (tm) cc_final: 0.8321 (tm) REVERT: M 522 ASN cc_start: 0.8953 (t0) cc_final: 0.8638 (t0) REVERT: M 541 MET cc_start: 0.9094 (mmp) cc_final: 0.8357 (mmt) outliers start: 2 outliers final: 2 residues processed: 778 average time/residue: 0.1152 time to fit residues: 150.9791 Evaluate side-chains 551 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 549 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 191 HIS L 247 HIS L 252 ASN 2 44 HIS C 101 GLN C 176 ASN Q 44 HIS ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 HIS M 339 HIS M 446 HIS M 515 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090788 restraints weight = 64392.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092961 restraints weight = 29604.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094357 restraints weight = 17035.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095344 restraints weight = 11355.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095937 restraints weight = 8460.585| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.683 21001 Z= 0.229 Angle : 1.298 45.544 29503 Z= 0.500 Chirality : 0.047 0.618 3102 Planarity : 0.005 0.066 3485 Dihedral : 19.506 179.868 3688 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 0.50 % Allowed : 4.18 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.49 (0.18), residues: 2041 helix: 0.08 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -4.72 (0.17), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.028 0.002 TYR 4 34 PHE 0.026 0.002 PHE C 242 TRP 0.047 0.002 TRP 8 53 HIS 0.023 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (20936) covalent geometry : angle 1.29757 / 0.50 (29503) hydrogen bonds : bond 0.06716 / 4.75 ( 930) hydrogen bonds : angle 4.54444 / 3.36 ( 2751) Misc. bond : bond 0.09085 / 3.62 ( 65) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 641 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7803 (tm-30) REVERT: L 41 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8639 (mp0) REVERT: L 57 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7189 (p) REVERT: L 82 LEU cc_start: 0.9465 (tp) cc_final: 0.9222 (tp) REVERT: L 126 PHE cc_start: 0.9069 (t80) cc_final: 0.8817 (t80) REVERT: L 198 ASN cc_start: 0.9139 (m-40) cc_final: 0.8844 (t0) REVERT: L 281 CYS cc_start: 0.8863 (t) cc_final: 0.8546 (t) REVERT: C 183 GLU cc_start: 0.8983 (pm20) cc_final: 0.8761 (pm20) REVERT: C 199 LEU cc_start: 0.9150 (tp) cc_final: 0.8936 (tt) REVERT: C 205 TYR cc_start: 0.8500 (t80) cc_final: 0.7817 (t80) REVERT: G 31 LYS cc_start: 0.8644 (mttt) cc_final: 0.8131 (mptt) REVERT: J 33 SER cc_start: 0.8942 (t) cc_final: 0.8735 (t) REVERT: H 15 SER cc_start: 0.9235 (t) cc_final: 0.8821 (p) REVERT: H 38 TRP cc_start: 0.8724 (t60) cc_final: 0.8093 (t60) REVERT: 9 38 TRP cc_start: 0.8543 (p-90) cc_final: 0.8294 (p-90) REVERT: 7 33 SER cc_start: 0.8862 (t) cc_final: 0.8539 (m) REVERT: 1 20 LEU cc_start: 0.9016 (tp) cc_final: 0.8772 (tt) REVERT: 1 29 VAL cc_start: 0.9555 (t) cc_final: 0.9351 (p) REVERT: M 391 PHE cc_start: 0.9252 (t80) cc_final: 0.8974 (t80) REVERT: M 415 LEU cc_start: 0.9074 (tp) cc_final: 0.8501 (tp) REVERT: M 468 GLN cc_start: 0.8766 (mp10) cc_final: 0.8469 (mp10) REVERT: M 522 ASN cc_start: 0.8896 (t0) cc_final: 0.8686 (t0) REVERT: M 526 MET cc_start: 0.8467 (mtp) cc_final: 0.8220 (mtm) REVERT: M 528 SER cc_start: 0.9534 (m) cc_final: 0.9071 (t) REVERT: M 541 MET cc_start: 0.9172 (mmp) cc_final: 0.8565 (mmt) outliers start: 7 outliers final: 0 residues processed: 646 average time/residue: 0.1077 time to fit residues: 120.5412 Evaluate side-chains 513 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 58 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS L 279 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093958 restraints weight = 64245.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096271 restraints weight = 29694.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097736 restraints weight = 16999.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098724 restraints weight = 11288.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099298 restraints weight = 8386.542| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.623 21001 Z= 0.162 Angle : 1.210 45.333 29503 Z= 0.459 Chirality : 0.043 0.357 3102 Planarity : 0.004 0.071 3485 Dihedral : 18.753 179.796 3688 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.65 (0.19), residues: 2041 helix: 0.86 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -4.54 (0.18), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 143 TYR 0.025 0.002 TYR 4 34 PHE 0.035 0.002 PHE T 28 TRP 0.033 0.002 TRP B 53 HIS 0.028 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (20936) covalent geometry : angle 1.21014 / 0.46 (29503) hydrogen bonds : bond 0.05902 / 4.17 ( 930) hydrogen bonds : angle 4.11548 / 3.03 ( 2751) Misc. bond : bond 0.08230 / 3.23 ( 65) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 LEU cc_start: 0.9454 (tp) cc_final: 0.9166 (tp) REVERT: L 198 ASN cc_start: 0.9130 (m-40) cc_final: 0.8826 (m-40) REVERT: L 279 ASN cc_start: 0.8521 (m-40) cc_final: 0.8299 (m-40) REVERT: L 281 CYS cc_start: 0.8777 (t) cc_final: 0.8427 (t) REVERT: C 199 LEU cc_start: 0.9119 (tp) cc_final: 0.8904 (tt) REVERT: C 205 TYR cc_start: 0.8234 (t80) cc_final: 0.7752 (t80) REVERT: C 218 SER cc_start: 0.6734 (m) cc_final: 0.6381 (p) REVERT: C 232 MET cc_start: 0.9061 (tpp) cc_final: 0.8827 (mmt) REVERT: C 261 ILE cc_start: 0.8980 (pt) cc_final: 0.8652 (tt) REVERT: G 27 ASP cc_start: 0.8451 (t70) cc_final: 0.8186 (t0) REVERT: G 31 LYS cc_start: 0.8501 (mttt) cc_final: 0.7984 (mptt) REVERT: H 15 SER cc_start: 0.9253 (t) cc_final: 0.8866 (p) REVERT: D 25 LEU cc_start: 0.9710 (tp) cc_final: 0.9508 (tt) REVERT: 7 33 SER cc_start: 0.8833 (t) cc_final: 0.8469 (m) REVERT: 1 18 LEU cc_start: 0.9060 (tt) cc_final: 0.8294 (tt) REVERT: M 391 PHE cc_start: 0.9278 (t80) cc_final: 0.8881 (t80) REVERT: M 415 LEU cc_start: 0.8992 (tp) cc_final: 0.8497 (tp) REVERT: M 507 ASP cc_start: 0.8544 (t0) cc_final: 0.8120 (t0) REVERT: M 526 MET cc_start: 0.8411 (mtp) cc_final: 0.8197 (mtm) REVERT: M 528 SER cc_start: 0.9486 (m) cc_final: 0.8956 (t) REVERT: M 541 MET cc_start: 0.9091 (mmp) cc_final: 0.8429 (mmt) outliers start: 2 outliers final: 0 residues processed: 643 average time/residue: 0.1098 time to fit residues: 122.6948 Evaluate side-chains 525 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 143 GLN L 247 HIS ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 500 HIS M 518 ASN M 522 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.105746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094008 restraints weight = 63450.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096263 restraints weight = 28828.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097730 restraints weight = 16545.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098668 restraints weight = 10982.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099364 restraints weight = 8181.453| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.614 21001 Z= 0.159 Angle : 1.172 45.337 29503 Z= 0.446 Chirality : 0.045 0.868 3102 Planarity : 0.004 0.068 3485 Dihedral : 18.380 179.840 3688 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 0.28 % Allowed : 3.33 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 2041 helix: 1.03 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -4.45 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 399 TYR 0.017 0.001 TYR M 480 PHE 0.017 0.001 PHE 7 36 TRP 0.026 0.002 TRP 8 53 HIS 0.013 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (20936) covalent geometry : angle 1.17175 / 0.45 (29503) hydrogen bonds : bond 0.05425 / 3.83 ( 930) hydrogen bonds : angle 3.96745 / 2.91 ( 2751) Misc. bond : bond 0.07859 / 3.12 ( 65) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 621 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.8845 (mp0) cc_final: 0.8637 (mp0) REVERT: L 129 MET cc_start: 0.8789 (mmm) cc_final: 0.8545 (mmm) REVERT: L 198 ASN cc_start: 0.9175 (m-40) cc_final: 0.8894 (m-40) REVERT: L 269 TRP cc_start: 0.8238 (m100) cc_final: 0.8007 (m-90) REVERT: L 281 CYS cc_start: 0.8711 (t) cc_final: 0.8366 (t) REVERT: 2 42 ILE cc_start: 0.9298 (mm) cc_final: 0.9043 (tp) REVERT: C 35 SER cc_start: 0.8789 (t) cc_final: 0.8476 (p) REVERT: C 199 LEU cc_start: 0.9071 (tp) cc_final: 0.8865 (tt) REVERT: C 205 TYR cc_start: 0.8133 (t80) cc_final: 0.7715 (t80) REVERT: C 232 MET cc_start: 0.9008 (tpp) cc_final: 0.8430 (mmt) REVERT: C 235 SER cc_start: 0.9067 (p) cc_final: 0.8737 (p) REVERT: C 261 ILE cc_start: 0.8949 (pt) cc_final: 0.8655 (tt) REVERT: I 47 CYS cc_start: 0.8484 (t) cc_final: 0.8283 (t) REVERT: G 31 LYS cc_start: 0.8499 (mttt) cc_final: 0.8132 (mttp) REVERT: Q 33 ILE cc_start: 0.9334 (tp) cc_final: 0.9037 (tp) REVERT: H 15 SER cc_start: 0.9191 (t) cc_final: 0.8838 (p) REVERT: 9 24 LEU cc_start: 0.9319 (tp) cc_final: 0.8965 (tp) REVERT: 7 33 SER cc_start: 0.8838 (t) cc_final: 0.8474 (m) REVERT: M 391 PHE cc_start: 0.9179 (t80) cc_final: 0.8740 (t80) REVERT: M 415 LEU cc_start: 0.8973 (tp) cc_final: 0.8559 (tp) REVERT: M 528 SER cc_start: 0.9474 (m) cc_final: 0.8962 (t) REVERT: M 539 LEU cc_start: 0.8626 (tp) cc_final: 0.8405 (tp) REVERT: M 541 MET cc_start: 0.9121 (mmp) cc_final: 0.8487 (mmt) REVERT: M 605 ILE cc_start: 0.9287 (tp) cc_final: 0.9079 (tp) outliers start: 4 outliers final: 0 residues processed: 623 average time/residue: 0.1068 time to fit residues: 116.3743 Evaluate side-chains 499 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 11 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 143 GLN ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS 4 44 HIS ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092777 restraints weight = 64507.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094990 restraints weight = 29790.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096396 restraints weight = 17249.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097383 restraints weight = 11521.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097944 restraints weight = 8526.442| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.660 21001 Z= 0.183 Angle : 1.166 45.373 29503 Z= 0.447 Chirality : 0.045 0.683 3102 Planarity : 0.004 0.062 3485 Dihedral : 17.943 179.836 3688 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 0.28 % Allowed : 3.18 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 2041 helix: 1.02 (0.15), residues: 1250 sheet: None (None), residues: 0 loop : -4.35 (0.18), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 399 TYR 0.016 0.001 TYR M 586 PHE 0.020 0.001 PHE L 207 TRP 0.047 0.002 TRP H 38 HIS 0.031 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (20936) covalent geometry : angle 1.16551 / 0.45 (29503) hydrogen bonds : bond 0.05442 / 3.84 ( 930) hydrogen bonds : angle 3.98554 / 2.92 ( 2751) Misc. bond : bond 0.08448 / 3.37 ( 65) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 603 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.8947 (mp0) cc_final: 0.8668 (mp0) REVERT: L 87 TYR cc_start: 0.9249 (t80) cc_final: 0.8823 (t80) REVERT: L 129 MET cc_start: 0.8681 (mmm) cc_final: 0.8443 (mmm) REVERT: L 198 ASN cc_start: 0.9183 (m-40) cc_final: 0.8970 (m-40) REVERT: L 281 CYS cc_start: 0.8691 (t) cc_final: 0.8356 (t) REVERT: 2 42 ILE cc_start: 0.9236 (mm) cc_final: 0.8953 (tp) REVERT: C 199 LEU cc_start: 0.9122 (tp) cc_final: 0.8893 (tt) REVERT: C 205 TYR cc_start: 0.8178 (t80) cc_final: 0.7765 (t80) REVERT: C 261 ILE cc_start: 0.8954 (pt) cc_final: 0.8666 (tt) REVERT: I 47 CYS cc_start: 0.8624 (t) cc_final: 0.8350 (t) REVERT: G 31 LYS cc_start: 0.8466 (mttt) cc_final: 0.7991 (mmtm) REVERT: T 22 MET cc_start: 0.8973 (tpp) cc_final: 0.8743 (tpp) REVERT: H 15 SER cc_start: 0.9173 (t) cc_final: 0.8871 (p) REVERT: A 31 LEU cc_start: 0.8608 (tt) cc_final: 0.7904 (mp) REVERT: 9 24 LEU cc_start: 0.9303 (tp) cc_final: 0.8963 (tp) REVERT: 7 33 SER cc_start: 0.8868 (t) cc_final: 0.8525 (m) REVERT: M 391 PHE cc_start: 0.9213 (t80) cc_final: 0.8709 (t80) REVERT: M 415 LEU cc_start: 0.8949 (tp) cc_final: 0.8551 (tp) REVERT: M 507 ASP cc_start: 0.8806 (t0) cc_final: 0.8467 (t0) REVERT: M 522 ASN cc_start: 0.8224 (t0) cc_final: 0.8021 (t0) REVERT: M 528 SER cc_start: 0.9464 (m) cc_final: 0.8855 (t) REVERT: M 541 MET cc_start: 0.9208 (mmp) cc_final: 0.8687 (mmt) REVERT: M 605 ILE cc_start: 0.9337 (tp) cc_final: 0.9124 (tp) outliers start: 4 outliers final: 1 residues processed: 606 average time/residue: 0.1079 time to fit residues: 114.1265 Evaluate side-chains 505 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 192 HIS L 247 HIS C 101 GLN C 219 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.091055 restraints weight = 63938.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093282 restraints weight = 29802.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094696 restraints weight = 17042.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095613 restraints weight = 11389.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096259 restraints weight = 8575.817| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.664 21001 Z= 0.194 Angle : 1.165 45.390 29503 Z= 0.450 Chirality : 0.045 0.674 3102 Planarity : 0.004 0.068 3485 Dihedral : 17.697 179.836 3688 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.21 % Allowed : 2.41 % Favored : 97.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2041 helix: 1.11 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -4.32 (0.18), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.050 0.002 TYR I 34 PHE 0.020 0.002 PHE L 207 TRP 0.034 0.002 TRP 3 38 HIS 0.018 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (20936) covalent geometry : angle 1.16475 / 0.45 (29503) hydrogen bonds : bond 0.05560 / 3.94 ( 930) hydrogen bonds : angle 4.03982 / 2.96 ( 2751) Misc. bond : bond 0.08538 / 3.41 ( 65) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 596 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.8965 (mp0) cc_final: 0.8738 (mp0) REVERT: L 82 LEU cc_start: 0.9462 (tp) cc_final: 0.9047 (tp) REVERT: L 86 PHE cc_start: 0.8797 (m-80) cc_final: 0.8205 (m-80) REVERT: L 87 TYR cc_start: 0.9288 (t80) cc_final: 0.8857 (t80) REVERT: L 129 MET cc_start: 0.8720 (mmm) cc_final: 0.8460 (mmm) REVERT: L 198 ASN cc_start: 0.9229 (m-40) cc_final: 0.9020 (m-40) REVERT: L 281 CYS cc_start: 0.8680 (t) cc_final: 0.8396 (t) REVERT: 2 42 ILE cc_start: 0.9233 (mm) cc_final: 0.9006 (tp) REVERT: C 35 SER cc_start: 0.8787 (t) cc_final: 0.8476 (p) REVERT: C 199 LEU cc_start: 0.9191 (tp) cc_final: 0.8618 (tt) REVERT: C 205 TYR cc_start: 0.8214 (t80) cc_final: 0.7772 (t80) REVERT: C 261 ILE cc_start: 0.9008 (pt) cc_final: 0.8744 (tt) REVERT: I 30 VAL cc_start: 0.8584 (p) cc_final: 0.8354 (m) REVERT: G 31 LYS cc_start: 0.8367 (mttt) cc_final: 0.7891 (mptt) REVERT: T 22 MET cc_start: 0.8926 (tpp) cc_final: 0.8712 (tpp) REVERT: H 15 SER cc_start: 0.9186 (t) cc_final: 0.8880 (p) REVERT: F 37 ASN cc_start: 0.8541 (t0) cc_final: 0.8326 (t0) REVERT: A 31 LEU cc_start: 0.8706 (tt) cc_final: 0.8041 (mp) REVERT: 7 33 SER cc_start: 0.8906 (t) cc_final: 0.8578 (m) REVERT: M 391 PHE cc_start: 0.9227 (t80) cc_final: 0.8952 (t80) REVERT: M 415 LEU cc_start: 0.8956 (tp) cc_final: 0.8555 (tp) REVERT: M 507 ASP cc_start: 0.8859 (t0) cc_final: 0.8430 (t0) REVERT: M 522 ASN cc_start: 0.8465 (t0) cc_final: 0.8080 (t0) REVERT: M 528 SER cc_start: 0.9529 (m) cc_final: 0.8981 (t) REVERT: M 541 MET cc_start: 0.9301 (mmp) cc_final: 0.8718 (mmt) REVERT: M 605 ILE cc_start: 0.9299 (tp) cc_final: 0.9084 (tp) outliers start: 3 outliers final: 1 residues processed: 597 average time/residue: 0.1071 time to fit residues: 112.0792 Evaluate side-chains 501 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 30.0000 chunk 75 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 192 HIS L 247 HIS C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091285 restraints weight = 64377.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093465 restraints weight = 29841.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094872 restraints weight = 17266.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095816 restraints weight = 11647.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096375 restraints weight = 8676.580| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.627 21001 Z= 0.182 Angle : 1.146 45.320 29503 Z= 0.441 Chirality : 0.045 0.803 3102 Planarity : 0.004 0.065 3485 Dihedral : 17.549 179.838 3688 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2041 helix: 1.13 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -4.30 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 399 TYR 0.017 0.002 TYR M 586 PHE 0.020 0.002 PHE 5 8 TRP 0.064 0.002 TRP H 38 HIS 0.024 0.002 HIS R 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (20936) covalent geometry : angle 1.14557 / 0.44 (29503) hydrogen bonds : bond 0.05456 / 3.87 ( 930) hydrogen bonds : angle 3.98422 / 2.92 ( 2751) Misc. bond : bond 0.08076 / 3.23 ( 65) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.9012 (mp0) cc_final: 0.8765 (mp0) REVERT: L 86 PHE cc_start: 0.8844 (m-80) cc_final: 0.8208 (m-80) REVERT: L 87 TYR cc_start: 0.9289 (t80) cc_final: 0.9038 (t80) REVERT: L 126 PHE cc_start: 0.9191 (t80) cc_final: 0.8640 (t80) REVERT: L 198 ASN cc_start: 0.9234 (m-40) cc_final: 0.9017 (m-40) REVERT: L 228 MET cc_start: 0.8869 (tpp) cc_final: 0.8636 (tpp) REVERT: L 269 TRP cc_start: 0.8624 (m100) cc_final: 0.8327 (m-90) REVERT: L 281 CYS cc_start: 0.8653 (t) cc_final: 0.8381 (t) REVERT: 6 38 ILE cc_start: 0.8824 (mm) cc_final: 0.8574 (mm) REVERT: 4 42 ILE cc_start: 0.9441 (tp) cc_final: 0.9240 (tp) REVERT: 2 42 ILE cc_start: 0.9235 (mm) cc_final: 0.9008 (tp) REVERT: C 199 LEU cc_start: 0.9190 (tp) cc_final: 0.8606 (tt) REVERT: C 205 TYR cc_start: 0.8268 (t80) cc_final: 0.7875 (t80) REVERT: C 261 ILE cc_start: 0.8996 (pt) cc_final: 0.8719 (tt) REVERT: G 31 LYS cc_start: 0.8366 (mttt) cc_final: 0.7866 (mptt) REVERT: T 22 MET cc_start: 0.9119 (tpp) cc_final: 0.8910 (tpp) REVERT: H 15 SER cc_start: 0.9178 (t) cc_final: 0.8878 (p) REVERT: H 38 TRP cc_start: 0.8168 (t60) cc_final: 0.7752 (t60) REVERT: H 39 LEU cc_start: 0.8548 (mt) cc_final: 0.8308 (mt) REVERT: A 31 LEU cc_start: 0.8788 (tt) cc_final: 0.8115 (mp) REVERT: 9 24 LEU cc_start: 0.9239 (tp) cc_final: 0.8963 (tp) REVERT: 7 33 SER cc_start: 0.8929 (t) cc_final: 0.8625 (m) REVERT: M 391 PHE cc_start: 0.9158 (t80) cc_final: 0.8724 (t80) REVERT: M 415 LEU cc_start: 0.8940 (tp) cc_final: 0.8576 (tp) REVERT: M 507 ASP cc_start: 0.8842 (t0) cc_final: 0.8377 (t0) REVERT: M 522 ASN cc_start: 0.8579 (t0) cc_final: 0.8169 (t0) REVERT: M 526 MET cc_start: 0.8525 (mtm) cc_final: 0.8200 (mtm) REVERT: M 528 SER cc_start: 0.9525 (m) cc_final: 0.8976 (t) REVERT: M 541 MET cc_start: 0.9296 (mmp) cc_final: 0.8731 (mmt) REVERT: M 605 ILE cc_start: 0.9295 (tp) cc_final: 0.9093 (tp) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.1085 time to fit residues: 114.1138 Evaluate side-chains 505 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 166 optimal weight: 50.0000 chunk 52 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088193 restraints weight = 65583.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090317 restraints weight = 30719.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091674 restraints weight = 17765.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092555 restraints weight = 11937.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093186 restraints weight = 9068.473| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.670 21001 Z= 0.258 Angle : 1.212 45.476 29503 Z= 0.474 Chirality : 0.048 0.836 3102 Planarity : 0.005 0.071 3485 Dihedral : 17.562 179.918 3688 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.26 % Favored : 85.74 % Rotamer: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 2041 helix: 0.99 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -4.33 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.038 0.002 TYR I 34 PHE 0.031 0.002 PHE M 531 TRP 0.053 0.002 TRP H 38 HIS 0.047 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.26 (20936) covalent geometry : angle 1.21217 / 0.47 (29503) hydrogen bonds : bond 0.06099 / 4.35 ( 930) hydrogen bonds : angle 4.19667 / 3.08 ( 2751) Misc. bond : bond 0.08962 / 3.62 ( 65) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.9314 (t80) cc_final: 0.9080 (t80) REVERT: L 228 MET cc_start: 0.8744 (tpp) cc_final: 0.8451 (tpp) REVERT: L 281 CYS cc_start: 0.8661 (t) cc_final: 0.8435 (t) REVERT: C 199 LEU cc_start: 0.9222 (tp) cc_final: 0.8683 (tt) REVERT: C 205 TYR cc_start: 0.8372 (t80) cc_final: 0.7860 (t80) REVERT: C 232 MET cc_start: 0.9237 (tpp) cc_final: 0.8516 (mmt) REVERT: C 261 ILE cc_start: 0.9109 (pt) cc_final: 0.8858 (tt) REVERT: G 31 LYS cc_start: 0.8397 (mttt) cc_final: 0.7870 (mptt) REVERT: N 22 MET cc_start: 0.9033 (mtp) cc_final: 0.8724 (mmm) REVERT: H 15 SER cc_start: 0.9229 (t) cc_final: 0.8932 (p) REVERT: F 37 ASN cc_start: 0.8509 (t0) cc_final: 0.8260 (t0) REVERT: 7 33 SER cc_start: 0.9018 (t) cc_final: 0.8735 (m) REVERT: M 391 PHE cc_start: 0.9294 (t80) cc_final: 0.8851 (t80) REVERT: M 511 TYR cc_start: 0.9204 (m-10) cc_final: 0.8240 (m-80) REVERT: M 522 ASN cc_start: 0.8678 (t0) cc_final: 0.8180 (t0) REVERT: M 526 MET cc_start: 0.8601 (mtm) cc_final: 0.8295 (mtm) REVERT: M 528 SER cc_start: 0.9567 (m) cc_final: 0.9080 (t) REVERT: M 541 MET cc_start: 0.9287 (mmp) cc_final: 0.8760 (mmt) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.0999 time to fit residues: 103.6608 Evaluate side-chains 488 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 145 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 192 HIS L 247 HIS 4 44 HIS C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091556 restraints weight = 63952.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093762 restraints weight = 30089.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095163 restraints weight = 17396.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096153 restraints weight = 11740.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096740 restraints weight = 8765.768| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.584 21001 Z= 0.172 Angle : 1.142 45.262 29503 Z= 0.442 Chirality : 0.047 1.082 3102 Planarity : 0.004 0.071 3485 Dihedral : 17.180 179.917 3688 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.19), residues: 2041 helix: 1.08 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -4.25 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.019 0.002 TYR M 586 PHE 0.031 0.002 PHE L 207 TRP 0.048 0.002 TRP H 38 HIS 0.029 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (20936) covalent geometry : angle 1.14221 / 0.44 (29503) hydrogen bonds : bond 0.05586 / 3.96 ( 930) hydrogen bonds : angle 4.03796 / 2.95 ( 2751) Misc. bond : bond 0.07619 / 3.07 ( 65) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.8876 (mp0) cc_final: 0.8638 (mp0) REVERT: L 82 LEU cc_start: 0.9376 (tp) cc_final: 0.9068 (tp) REVERT: L 86 PHE cc_start: 0.8994 (m-80) cc_final: 0.8535 (m-80) REVERT: L 228 MET cc_start: 0.8820 (tpp) cc_final: 0.8542 (mmm) REVERT: L 269 TRP cc_start: 0.8527 (m100) cc_final: 0.8270 (m-90) REVERT: 6 38 ILE cc_start: 0.8820 (mm) cc_final: 0.8569 (mm) REVERT: C 199 LEU cc_start: 0.9167 (tp) cc_final: 0.8602 (tt) REVERT: C 218 SER cc_start: 0.6466 (t) cc_final: 0.6064 (t) REVERT: C 235 SER cc_start: 0.9377 (t) cc_final: 0.9113 (p) REVERT: C 261 ILE cc_start: 0.9021 (pt) cc_final: 0.8742 (tt) REVERT: G 31 LYS cc_start: 0.8359 (mttt) cc_final: 0.7809 (mptt) REVERT: T 22 MET cc_start: 0.9087 (tpp) cc_final: 0.8885 (tpp) REVERT: R 31 LEU cc_start: 0.9629 (tp) cc_final: 0.9371 (tt) REVERT: H 15 SER cc_start: 0.9166 (t) cc_final: 0.8894 (p) REVERT: 7 33 SER cc_start: 0.8868 (t) cc_final: 0.8625 (m) REVERT: 1 31 LEU cc_start: 0.9350 (tt) cc_final: 0.8827 (pp) REVERT: M 391 PHE cc_start: 0.9168 (t80) cc_final: 0.8884 (t80) REVERT: M 507 ASP cc_start: 0.8850 (t0) cc_final: 0.8632 (t0) REVERT: M 526 MET cc_start: 0.8484 (mtm) cc_final: 0.8143 (mtm) REVERT: M 528 SER cc_start: 0.9499 (m) cc_final: 0.8948 (t) REVERT: M 541 MET cc_start: 0.9240 (mmp) cc_final: 0.8715 (mmt) REVERT: M 605 ILE cc_start: 0.9275 (tp) cc_final: 0.9060 (tp) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.1016 time to fit residues: 107.6657 Evaluate side-chains 504 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 192 HIS L 247 HIS C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088199 restraints weight = 65603.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090349 restraints weight = 30352.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091680 restraints weight = 17478.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092629 restraints weight = 11854.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093202 restraints weight = 8900.098| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.637 21001 Z= 0.250 Angle : 1.207 45.483 29503 Z= 0.474 Chirality : 0.051 1.285 3102 Planarity : 0.005 0.071 3485 Dihedral : 17.221 179.997 3688 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 2041 helix: 0.95 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -4.33 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 399 TYR 0.029 0.002 TYR I 34 PHE 0.035 0.002 PHE C 242 TRP 0.047 0.002 TRP H 38 HIS 0.031 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 (20936) covalent geometry : angle 1.20723 / 0.47 (29503) hydrogen bonds : bond 0.06090 / 4.34 ( 930) hydrogen bonds : angle 4.23476 / 3.09 ( 2751) Misc. bond : bond 0.08687 / 3.53 ( 65) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4082 Ramachandran restraints generated. 2041 Oldfield, 0 Emsley, 2041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 575 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 GLU cc_start: 0.8932 (mp0) cc_final: 0.8673 (mp0) REVERT: L 269 TRP cc_start: 0.8530 (m100) cc_final: 0.8293 (m-90) REVERT: L 281 CYS cc_start: 0.8716 (t) cc_final: 0.8376 (t) REVERT: C 199 LEU cc_start: 0.9224 (tp) cc_final: 0.8644 (tt) REVERT: C 232 MET cc_start: 0.9249 (tpp) cc_final: 0.8577 (mmt) REVERT: C 261 ILE cc_start: 0.9127 (pt) cc_final: 0.8854 (tt) REVERT: G 31 LYS cc_start: 0.8422 (mttt) cc_final: 0.7849 (mptt) REVERT: R 31 LEU cc_start: 0.9651 (tp) cc_final: 0.9395 (tt) REVERT: N 22 MET cc_start: 0.8998 (mtp) cc_final: 0.8756 (mmm) REVERT: H 15 SER cc_start: 0.9205 (t) cc_final: 0.8933 (p) REVERT: F 20 LEU cc_start: 0.9240 (tp) cc_final: 0.8985 (tt) REVERT: 9 24 LEU cc_start: 0.9259 (tt) cc_final: 0.8915 (tt) REVERT: 7 33 SER cc_start: 0.8955 (t) cc_final: 0.8699 (m) REVERT: M 511 TYR cc_start: 0.9208 (m-10) cc_final: 0.8148 (m-80) REVERT: M 526 MET cc_start: 0.8560 (mtm) cc_final: 0.8293 (mtm) REVERT: M 528 SER cc_start: 0.9568 (m) cc_final: 0.9107 (t) REVERT: M 541 MET cc_start: 0.9289 (mmp) cc_final: 0.8771 (mmt) outliers start: 1 outliers final: 0 residues processed: 575 average time/residue: 0.0991 time to fit residues: 99.6482 Evaluate side-chains 486 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 183 optimal weight: 0.0670 chunk 167 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS C 101 GLN C 219 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093284 restraints weight = 64187.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095541 restraints weight = 30230.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096923 restraints weight = 17417.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097915 restraints weight = 11781.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098487 restraints weight = 8787.281| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.476 21001 Z= 0.150 Angle : 1.109 45.134 29503 Z= 0.431 Chirality : 0.046 0.991 3102 Planarity : 0.004 0.075 3485 Dihedral : 16.695 179.936 3688 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 2041 helix: 1.11 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -4.24 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.017 0.001 TYR M 586 PHE 0.037 0.002 PHE 5 28 TRP 0.044 0.002 TRP H 38 HIS 0.022 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (20936) covalent geometry : angle 1.10928 / 0.43 (29503) hydrogen bonds : bond 0.05080 / 3.60 ( 930) hydrogen bonds : angle 3.96992 / 2.89 ( 2751) Misc. bond : bond 0.06130 / 2.47 ( 65) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3422.97 seconds wall clock time: 60 minutes 18.62 seconds (3618.62 seconds total)