Starting phenix.real_space_refine on Wed Nov 19 05:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_6828.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_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 { model { file = "/net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_6828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_6828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_6828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yq7_6828/11_2025/5yq7_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 4.77, per 1000 atoms: 0.24 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: 2.33 Conformation dependent library (CDL) restraints added in 669.8 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: 0.46 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: 3.17 Time building geometry restraints manager: 2.97 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: 10233 35.99 - 71.98: 181 71.98 - 107.97: 38 107.97 - 143.96: 35 143.96 - 179.95: 3 Dihedral angle restraints: 10490 sinusoidal: 4298 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 10487 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.460 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 17.920 179.948 6464 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 covalent geometry : bond 0.01943 (20936) covalent geometry : angle 1.76313 (29503) hydrogen bonds : bond 0.11656 ( 930) hydrogen bonds : angle 5.60307 ( 2751) Misc. bond : bond 0.19475 ( 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 : 0.666 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: 0.9150 (t) cc_final: 0.8808 (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: 0.8356 (mmt) outliers start: 2 outliers final: 2 residues processed: 778 average time/residue: 0.1103 time to fit residues: 143.7280 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 : 0.938 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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** M 339 HIS M 446 HIS M 515 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090814 restraints weight = 64406.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093062 restraints weight = 29650.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094432 restraints weight = 16867.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095415 restraints weight = 11407.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095999 restraints weight = 8488.663| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.701 21001 Z= 0.228 Angle : 1.303 45.557 29503 Z= 0.502 Chirality : 0.047 0.626 3102 Planarity : 0.005 0.066 3485 Dihedral : 19.578 179.876 3898 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % 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 : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.18), residues: 2041 helix: 0.07 (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 0.029 0.002 TYR 4 34 PHE 0.025 0.002 PHE C 242 TRP 0.048 0.002 TRP 8 53 HIS 0.023 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00543 (20936) covalent geometry : angle 1.30295 (29503) hydrogen bonds : bond 0.06739 ( 930) hydrogen bonds : angle 4.55012 ( 2751) Misc. bond : bond 0.09334 ( 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 649 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 642 time to evaluate : 0.646 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: 0.8051 (tm-30) cc_final: 0.7803 (tm-30) REVERT: L 57 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7196 (p) REVERT: L 82 LEU cc_start: 0.9470 (tp) cc_final: 0.9233 (tp) REVERT: L 126 PHE cc_start: 0.9070 (t80) cc_final: 0.8811 (t80) REVERT: L 198 ASN cc_start: 0.9142 (m-40) cc_final: 0.8844 (t0) REVERT: L 281 CYS cc_start: 0.8869 (t) cc_final: 0.8554 (t) REVERT: 6 14 TRP cc_start: 0.6771 (t60) cc_final: 0.6561 (t60) REVERT: C 199 LEU cc_start: 0.9156 (tp) cc_final: 0.8941 (tt) REVERT: C 205 TYR cc_start: 0.8514 (t80) cc_final: 0.7869 (t80) REVERT: G 31 LYS cc_start: 0.8640 (mttt) cc_final: 0.8128 (mptt) REVERT: Q 47 CYS cc_start: 0.8789 (m) cc_final: 0.8494 (m) REVERT: J 33 SER cc_start: 0.8942 (t) cc_final: 0.8736 (t) REVERT: H 15 SER cc_start: 0.9236 (t) cc_final: 0.8853 (p) REVERT: H 38 TRP cc_start: 0.8716 (t60) cc_final: 0.8092 (t60) REVERT: 9 38 TRP cc_start: 0.8541 (p-90) cc_final: 0.8297 (p-90) REVERT: 7 33 SER cc_start: 0.8859 (t) cc_final: 0.8536 (m) REVERT: 1 20 LEU cc_start: 0.9022 (tp) cc_final: 0.8704 (tt) REVERT: 1 29 VAL cc_start: 0.9552 (t) cc_final: 0.9348 (p) REVERT: M 358 VAL cc_start: 0.8301 (m) cc_final: 0.8101 (t) REVERT: M 391 PHE cc_start: 0.9250 (t80) cc_final: 0.8981 (t80) REVERT: M 415 LEU cc_start: 0.9073 (tp) cc_final: 0.8491 (tp) REVERT: M 468 GLN cc_start: 0.8766 (mp10) cc_final: 0.8425 (mp10) REVERT: M 522 ASN cc_start: 0.8901 (t0) cc_final: 0.8690 (t0) REVERT: M 526 MET cc_start: 0.8469 (mtp) cc_final: 0.8225 (mtm) REVERT: M 528 SER cc_start: 0.9533 (m) cc_final: 0.9062 (t) REVERT: M 541 MET cc_start: 0.9187 (mmp) cc_final: 0.8556 (mmt) outliers start: 7 outliers final: 0 residues processed: 647 average time/residue: 0.1023 time to fit residues: 114.1814 Evaluate side-chains 518 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 4.9990 chunk 131 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3551 r_free = 0.3551 target = 0.105082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093057 restraints weight = 63841.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095400 restraints weight = 29270.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096877 restraints weight = 16659.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097810 restraints weight = 11016.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098391 restraints weight = 8286.526| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.649 21001 Z= 0.171 Angle : 1.210 45.380 29503 Z= 0.460 Chirality : 0.043 0.360 3102 Planarity : 0.004 0.080 3485 Dihedral : 18.745 179.797 3898 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.14 % Allowed : 3.33 % Favored : 96.53 % 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: -1.61 (0.19), residues: 2041 helix: 0.90 (0.14), residues: 1234 sheet: None (None), residues: 0 loop : -4.53 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 503 TYR 0.025 0.002 TYR 4 34 PHE 0.030 0.002 PHE T 28 TRP 0.036 0.002 TRP B 53 HIS 0.029 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00390 (20936) covalent geometry : angle 1.20965 (29503) hydrogen bonds : bond 0.05895 ( 930) hydrogen bonds : angle 4.12862 ( 2751) Misc. bond : bond 0.08570 ( 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 635 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 0.662 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 41 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8620 (mp0) REVERT: L 82 LEU cc_start: 0.9456 (tp) cc_final: 0.9011 (tp) REVERT: L 198 ASN cc_start: 0.9152 (m-40) cc_final: 0.8869 (m-40) REVERT: L 279 ASN cc_start: 0.8509 (m-40) cc_final: 0.8256 (m-40) REVERT: L 281 CYS cc_start: 0.8792 (t) cc_final: 0.8452 (t) REVERT: C 199 LEU cc_start: 0.9144 (tp) cc_final: 0.8934 (tt) REVERT: C 205 TYR cc_start: 0.8270 (t80) cc_final: 0.7578 (t80) REVERT: C 218 SER cc_start: 0.6815 (m) cc_final: 0.6291 (p) REVERT: C 232 MET cc_start: 0.9079 (tpp) cc_final: 0.8858 (mmt) REVERT: C 261 ILE cc_start: 0.8994 (pt) cc_final: 0.8657 (tt) REVERT: I 47 CYS cc_start: 0.8419 (t) cc_final: 0.8208 (t) REVERT: G 27 ASP cc_start: 0.8450 (t70) cc_final: 0.8181 (t0) REVERT: G 31 LYS cc_start: 0.8508 (mttt) cc_final: 0.7988 (mptt) REVERT: H 15 SER cc_start: 0.9259 (t) cc_final: 0.8878 (p) REVERT: 7 33 SER cc_start: 0.8858 (t) cc_final: 0.8492 (m) REVERT: 1 18 LEU cc_start: 0.9058 (tt) cc_final: 0.8325 (tp) REVERT: M 358 VAL cc_start: 0.8312 (m) cc_final: 0.8090 (t) REVERT: M 391 PHE cc_start: 0.9272 (t80) cc_final: 0.8892 (t80) REVERT: M 415 LEU cc_start: 0.9006 (tp) cc_final: 0.8501 (tp) REVERT: M 526 MET cc_start: 0.8419 (mtp) cc_final: 0.8215 (mtm) REVERT: M 528 SER cc_start: 0.9494 (m) cc_final: 0.8958 (t) REVERT: M 541 MET cc_start: 0.9112 (mmp) cc_final: 0.8424 (mmt) outliers start: 2 outliers final: 0 residues processed: 634 average time/residue: 0.0998 time to fit residues: 109.9262 Evaluate side-chains 514 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 170 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 HIS ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 500 HIS M 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091664 restraints weight = 64025.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093909 restraints weight = 30043.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095346 restraints weight = 17284.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096293 restraints weight = 11480.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096787 restraints weight = 8570.733| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.670 21001 Z= 0.188 Angle : 1.190 45.416 29503 Z= 0.455 Chirality : 0.045 0.677 3102 Planarity : 0.004 0.067 3485 Dihedral : 18.733 179.864 3898 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.75 % 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: -1.46 (0.19), residues: 2041 helix: 0.98 (0.15), residues: 1249 sheet: None (None), residues: 0 loop : -4.49 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 399 TYR 0.018 0.001 TYR M 480 PHE 0.018 0.002 PHE L 207 TRP 0.027 0.002 TRP 8 53 HIS 0.015 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00445 (20936) covalent geometry : angle 1.18951 (29503) hydrogen bonds : bond 0.05775 ( 930) hydrogen bonds : angle 4.05077 ( 2751) Misc. bond : bond 0.08665 ( 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 611 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 607 time to evaluate : 0.633 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 41 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8645 (mp0) REVERT: L 82 LEU cc_start: 0.9502 (tp) cc_final: 0.9064 (tp) REVERT: L 86 PHE cc_start: 0.9082 (m-80) cc_final: 0.8574 (m-80) REVERT: L 198 ASN cc_start: 0.9182 (m-40) cc_final: 0.8952 (m-40) REVERT: L 281 CYS cc_start: 0.8764 (t) cc_final: 0.8432 (t) REVERT: C 199 LEU cc_start: 0.9140 (tp) cc_final: 0.8922 (tt) REVERT: C 205 TYR cc_start: 0.8332 (t80) cc_final: 0.7822 (t80) REVERT: C 232 MET cc_start: 0.9029 (tpp) cc_final: 0.8415 (mmt) REVERT: C 235 SER cc_start: 0.9188 (p) cc_final: 0.8820 (p) REVERT: C 261 ILE cc_start: 0.9047 (pt) cc_final: 0.8740 (tt) REVERT: I 47 CYS cc_start: 0.8547 (t) cc_final: 0.8317 (t) REVERT: G 31 LYS cc_start: 0.8521 (mttt) cc_final: 0.8147 (mttp) REVERT: T 38 TRP cc_start: 0.6739 (m100) cc_final: 0.6538 (m100) REVERT: H 15 SER cc_start: 0.9244 (t) cc_final: 0.8869 (p) REVERT: 9 24 LEU cc_start: 0.9389 (tp) cc_final: 0.9013 (tp) REVERT: 7 33 SER cc_start: 0.8882 (t) cc_final: 0.8537 (m) REVERT: M 391 PHE cc_start: 0.9245 (t80) cc_final: 0.8759 (t80) REVERT: M 415 LEU cc_start: 0.8971 (tp) cc_final: 0.8534 (tp) REVERT: M 528 SER cc_start: 0.9515 (m) cc_final: 0.9015 (t) REVERT: M 541 MET cc_start: 0.9127 (mmp) cc_final: 0.8489 (mmt) REVERT: M 605 ILE cc_start: 0.9338 (tp) cc_final: 0.9131 (tp) outliers start: 4 outliers final: 1 residues processed: 609 average time/residue: 0.0996 time to fit residues: 105.2043 Evaluate side-chains 496 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 62 optimal weight: 0.0020 chunk 141 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS C 101 GLN C 219 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090678 restraints weight = 64350.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092849 restraints weight = 29616.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094200 restraints weight = 17149.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095169 restraints weight = 11604.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095704 restraints weight = 8692.208| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.691 21001 Z= 0.208 Angle : 1.187 45.423 29503 Z= 0.458 Chirality : 0.047 0.847 3102 Planarity : 0.004 0.063 3485 Dihedral : 18.475 179.821 3898 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.28 % Allowed : 2.97 % Favored : 96.74 % 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: -1.42 (0.19), residues: 2041 helix: 1.02 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : -4.46 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.018 0.002 TYR M 586 PHE 0.022 0.002 PHE L 207 TRP 0.053 0.002 TRP H 38 HIS 0.031 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00495 (20936) covalent geometry : angle 1.18663 (29503) hydrogen bonds : bond 0.05824 ( 930) hydrogen bonds : angle 4.10127 ( 2751) Misc. bond : bond 0.08960 ( 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 587 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 583 time to evaluate : 0.535 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: 0.8944 (mm-30) cc_final: 0.8614 (mp0) REVERT: L 82 LEU cc_start: 0.9509 (tp) cc_final: 0.9016 (tp) REVERT: L 86 PHE cc_start: 0.9015 (m-80) cc_final: 0.8403 (m-80) REVERT: L 87 TYR cc_start: 0.9256 (t80) cc_final: 0.8855 (t80) REVERT: L 198 ASN cc_start: 0.9229 (m-40) cc_final: 0.8528 (t0) REVERT: L 281 CYS cc_start: 0.8726 (t) cc_final: 0.8411 (t) REVERT: 2 42 ILE cc_start: 0.9243 (mm) cc_final: 0.8973 (tp) REVERT: C 147 LEU cc_start: 0.9328 (tt) cc_final: 0.9125 (tt) REVERT: C 199 LEU cc_start: 0.9171 (tp) cc_final: 0.8598 (tt) REVERT: C 205 TYR cc_start: 0.8460 (t80) cc_final: 0.7985 (t80) REVERT: C 261 ILE cc_start: 0.9036 (pt) cc_final: 0.8756 (tt) REVERT: I 47 CYS cc_start: 0.8621 (t) cc_final: 0.8390 (t) REVERT: G 31 LYS cc_start: 0.8469 (mttt) cc_final: 0.8135 (mttm) REVERT: T 22 MET cc_start: 0.8936 (tpp) cc_final: 0.8729 (tpp) REVERT: H 15 SER cc_start: 0.9189 (t) cc_final: 0.8889 (p) REVERT: 9 24 LEU cc_start: 0.9386 (tp) cc_final: 0.8972 (tp) REVERT: 7 33 SER cc_start: 0.8889 (t) cc_final: 0.8562 (m) REVERT: M 391 PHE cc_start: 0.9248 (t80) cc_final: 0.8748 (t80) REVERT: M 415 LEU cc_start: 0.8966 (tp) cc_final: 0.8532 (tp) REVERT: M 528 SER cc_start: 0.9499 (m) cc_final: 0.8941 (t) REVERT: M 541 MET cc_start: 0.9230 (mmp) cc_final: 0.8750 (mmt) outliers start: 4 outliers final: 1 residues processed: 585 average time/residue: 0.1000 time to fit residues: 101.6956 Evaluate side-chains 497 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 HIS ** C 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3454 r_free = 0.3454 target = 0.099316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087719 restraints weight = 65208.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089827 restraints weight = 30048.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091150 restraints weight = 17442.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092112 restraints weight = 11730.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092685 restraints weight = 8772.232| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.729 21001 Z= 0.272 Angle : 1.240 45.494 29503 Z= 0.484 Chirality : 0.049 0.951 3102 Planarity : 0.005 0.069 3485 Dihedral : 18.517 179.906 3898 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 0.21 % Allowed : 2.48 % Favored : 97.31 % 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: -1.50 (0.19), residues: 2041 helix: 0.96 (0.14), residues: 1237 sheet: None (None), residues: 0 loop : -4.44 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 174 TYR 0.050 0.002 TYR I 34 PHE 0.023 0.002 PHE L 207 TRP 0.039 0.002 TRP A 38 HIS 0.017 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00657 (20936) covalent geometry : angle 1.24029 (29503) hydrogen bonds : bond 0.06386 ( 930) hydrogen bonds : angle 4.28072 ( 2751) Misc. bond : bond 0.09711 ( 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 571 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 568 time to evaluate : 0.971 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 87 TYR cc_start: 0.9258 (t80) cc_final: 0.9009 (t80) REVERT: L 281 CYS cc_start: 0.8704 (t) cc_final: 0.8446 (t) REVERT: 2 42 ILE cc_start: 0.9285 (mm) cc_final: 0.8955 (tp) REVERT: C 199 LEU cc_start: 0.9239 (tp) cc_final: 0.8672 (tt) REVERT: C 205 TYR cc_start: 0.8633 (t80) cc_final: 0.8137 (t80) REVERT: C 232 MET cc_start: 0.9082 (tpp) cc_final: 0.8461 (mmt) REVERT: C 261 ILE cc_start: 0.9154 (pt) cc_final: 0.8907 (tt) REVERT: I 30 VAL cc_start: 0.8679 (p) cc_final: 0.8432 (m) REVERT: G 31 LYS cc_start: 0.8373 (mttt) cc_final: 0.7903 (mptt) REVERT: T 22 MET cc_start: 0.8924 (tpp) cc_final: 0.8624 (tpp) REVERT: H 15 SER cc_start: 0.9305 (t) cc_final: 0.8938 (p) REVERT: A 24 LEU cc_start: 0.9309 (tp) cc_final: 0.9055 (tp) REVERT: 7 33 SER cc_start: 0.8972 (t) cc_final: 0.8669 (m) REVERT: M 391 PHE cc_start: 0.9275 (t80) cc_final: 0.8976 (t80) REVERT: M 528 SER cc_start: 0.9584 (m) cc_final: 0.9147 (t) REVERT: M 541 MET cc_start: 0.9328 (mmp) cc_final: 0.8748 (mmt) outliers start: 3 outliers final: 1 residues processed: 569 average time/residue: 0.0995 time to fit residues: 98.7702 Evaluate side-chains 477 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 0.9990 chunk 116 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092122 restraints weight = 63825.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094335 restraints weight = 29449.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095767 restraints weight = 17007.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096723 restraints weight = 11338.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097347 restraints weight = 8441.078| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.585 21001 Z= 0.157 Angle : 1.134 45.173 29503 Z= 0.436 Chirality : 0.044 0.656 3102 Planarity : 0.004 0.067 3485 Dihedral : 17.940 179.801 3898 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.05 % 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: -1.25 (0.19), residues: 2041 helix: 1.15 (0.15), residues: 1247 sheet: None (None), residues: 0 loop : -4.38 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.020 0.001 TYR M 586 PHE 0.034 0.002 PHE L 207 TRP 0.060 0.002 TRP H 38 HIS 0.013 0.001 HIS H 27 Details of bonding type rmsd covalent geometry : bond 0.00365 (20936) covalent geometry : angle 1.13440 (29503) hydrogen bonds : bond 0.05503 ( 930) hydrogen bonds : angle 3.94753 ( 2751) Misc. bond : bond 0.07572 ( 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 607 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.633 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: L 86 PHE cc_start: 0.9086 (m-80) cc_final: 0.8505 (m-80) REVERT: L 87 TYR cc_start: 0.9269 (t80) cc_final: 0.9045 (t80) REVERT: L 126 PHE cc_start: 0.9080 (t80) cc_final: 0.8505 (t80) REVERT: L 129 MET cc_start: 0.8713 (mmm) cc_final: 0.8433 (mmm) REVERT: L 281 CYS cc_start: 0.8578 (t) cc_final: 0.8330 (t) REVERT: 6 38 ILE cc_start: 0.8771 (mm) cc_final: 0.8527 (mm) REVERT: 2 42 ILE cc_start: 0.9256 (mm) cc_final: 0.8944 (tp) REVERT: C 147 LEU cc_start: 0.9359 (tt) cc_final: 0.9125 (tt) REVERT: C 199 LEU cc_start: 0.9181 (tp) cc_final: 0.8897 (tt) REVERT: C 205 TYR cc_start: 0.8466 (t80) cc_final: 0.8105 (t80) REVERT: C 261 ILE cc_start: 0.9002 (pt) cc_final: 0.8726 (tt) REVERT: G 31 LYS cc_start: 0.8316 (mttt) cc_final: 0.7842 (mptt) REVERT: H 15 SER cc_start: 0.9183 (t) cc_final: 0.8878 (p) REVERT: H 39 LEU cc_start: 0.8640 (mt) cc_final: 0.8351 (mt) REVERT: 7 33 SER cc_start: 0.8926 (t) cc_final: 0.8617 (m) REVERT: M 391 PHE cc_start: 0.9226 (t80) cc_final: 0.8764 (t80) REVERT: M 415 LEU cc_start: 0.8885 (tp) cc_final: 0.8571 (tp) REVERT: M 528 SER cc_start: 0.9480 (m) cc_final: 0.9018 (t) REVERT: M 541 MET cc_start: 0.9258 (mmp) cc_final: 0.8745 (mtt) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.1013 time to fit residues: 106.3025 Evaluate side-chains 501 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 52 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN L 192 HIS L 247 HIS ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 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** ** 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 = 0.3472 r_free = 0.3472 target = 0.100409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088670 restraints weight = 65154.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090803 restraints weight = 30297.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092180 restraints weight = 17516.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093136 restraints weight = 11776.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093758 restraints weight = 8817.452| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.668 21001 Z= 0.247 Angle : 1.204 45.482 29503 Z= 0.471 Chirality : 0.047 0.769 3102 Planarity : 0.005 0.070 3485 Dihedral : 17.940 179.916 3898 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.19), residues: 2041 helix: 0.97 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -4.41 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.035 0.002 TYR I 34 PHE 0.033 0.002 PHE C 242 TRP 0.036 0.002 TRP 3 38 HIS 0.041 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00599 (20936) covalent geometry : angle 1.20425 (29503) hydrogen bonds : bond 0.06030 ( 930) hydrogen bonds : angle 4.20977 ( 2751) Misc. bond : bond 0.08994 ( 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 581 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 0.624 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 87 TYR cc_start: 0.9311 (t80) cc_final: 0.9107 (t80) REVERT: L 129 MET cc_start: 0.8704 (mmm) cc_final: 0.8455 (mmm) REVERT: L 228 MET cc_start: 0.8804 (tpp) cc_final: 0.8552 (mmm) REVERT: L 281 CYS cc_start: 0.8654 (t) cc_final: 0.8412 (t) REVERT: 2 42 ILE cc_start: 0.9283 (mm) cc_final: 0.9020 (tp) REVERT: C 199 LEU cc_start: 0.9222 (tp) cc_final: 0.8623 (tt) REVERT: C 261 ILE cc_start: 0.9131 (pt) cc_final: 0.8880 (tt) REVERT: G 31 LYS cc_start: 0.8336 (mttt) cc_final: 0.7822 (mptt) REVERT: T 22 MET cc_start: 0.8860 (tpp) cc_final: 0.8620 (tpp) REVERT: H 15 SER cc_start: 0.9240 (t) cc_final: 0.8927 (p) REVERT: F 20 LEU cc_start: 0.9281 (tp) cc_final: 0.9017 (tt) REVERT: A 24 LEU cc_start: 0.9271 (tp) cc_final: 0.9021 (tp) REVERT: 9 24 LEU cc_start: 0.9406 (tp) cc_final: 0.9172 (tt) REVERT: 7 33 SER cc_start: 0.9025 (t) cc_final: 0.8724 (m) REVERT: M 528 SER cc_start: 0.9551 (m) cc_final: 0.9083 (t) REVERT: M 541 MET cc_start: 0.9294 (mmp) cc_final: 0.8821 (mtt) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.0969 time to fit residues: 98.5791 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 : 0.419 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 GLN L 192 HIS L 247 HIS K 44 HIS C 101 GLN C 219 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092852 restraints weight = 63242.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095142 restraints weight = 29710.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096536 restraints weight = 16899.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097523 restraints weight = 11435.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098111 restraints weight = 8492.839| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.544 21001 Z= 0.155 Angle : 1.123 45.206 29503 Z= 0.435 Chirality : 0.046 1.100 3102 Planarity : 0.004 0.072 3485 Dihedral : 17.432 179.823 3898 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.22 (0.19), residues: 2041 helix: 1.16 (0.15), residues: 1247 sheet: None (None), residues: 0 loop : -4.34 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 399 TYR 0.018 0.001 TYR M 586 PHE 0.037 0.002 PHE 5 28 TRP 0.031 0.002 TRP 3 38 HIS 0.029 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00351 (20936) covalent geometry : angle 1.12314 (29503) hydrogen bonds : bond 0.05308 ( 930) hydrogen bonds : angle 3.93311 ( 2751) Misc. bond : bond 0.07029 ( 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 603 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 0.461 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: 0 27 ASP cc_start: 0.8332 (t70) cc_final: 0.8100 (t0) REVERT: L 86 PHE cc_start: 0.9043 (m-80) cc_final: 0.8541 (m-80) REVERT: L 198 ASN cc_start: 0.9071 (m-40) cc_final: 0.8382 (t0) REVERT: L 228 MET cc_start: 0.8735 (tpp) cc_final: 0.8386 (tpp) REVERT: L 269 TRP cc_start: 0.8539 (m100) cc_final: 0.8245 (m-90) REVERT: 2 42 ILE cc_start: 0.9240 (mm) cc_final: 0.8984 (tp) REVERT: C 199 LEU cc_start: 0.9200 (tp) cc_final: 0.8911 (tt) REVERT: C 261 ILE cc_start: 0.8947 (pt) cc_final: 0.8672 (tt) REVERT: G 31 LYS cc_start: 0.8417 (mttt) cc_final: 0.7852 (mptt) REVERT: T 22 MET cc_start: 0.8802 (tpp) cc_final: 0.8566 (tpp) REVERT: R 31 LEU cc_start: 0.9609 (tp) cc_final: 0.9330 (tt) REVERT: H 15 SER cc_start: 0.9190 (t) cc_final: 0.8892 (p) REVERT: 7 33 SER cc_start: 0.8897 (t) cc_final: 0.8597 (m) REVERT: M 511 TYR cc_start: 0.8971 (m-10) cc_final: 0.8117 (m-80) REVERT: M 528 SER cc_start: 0.9441 (m) cc_final: 0.8939 (t) REVERT: M 539 LEU cc_start: 0.8587 (tp) cc_final: 0.8383 (tp) REVERT: M 541 MET cc_start: 0.9236 (mmp) cc_final: 0.8791 (mtt) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.0985 time to fit residues: 103.0615 Evaluate side-chains 502 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 247 HIS ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 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** ** 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 = 0.3493 r_free = 0.3493 target = 0.101801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090005 restraints weight = 64904.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092200 restraints weight = 30107.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093562 restraints weight = 17480.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094577 restraints weight = 11791.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095168 restraints weight = 8787.370| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.580 21001 Z= 0.213 Angle : 1.163 45.441 29503 Z= 0.456 Chirality : 0.047 0.897 3102 Planarity : 0.004 0.070 3485 Dihedral : 17.565 179.942 3898 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.39 (0.19), residues: 2041 helix: 1.01 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -4.38 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 399 TYR 0.031 0.002 TYR I 34 PHE 0.033 0.002 PHE T 28 TRP 0.032 0.002 TRP C 294 HIS 0.033 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00516 (20936) covalent geometry : angle 1.16319 (29503) hydrogen bonds : bond 0.05616 ( 930) hydrogen bonds : angle 4.10059 ( 2751) Misc. bond : bond 0.07711 ( 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 580 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.607 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 19 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7631 (tm-30) REVERT: L 205 ASN cc_start: 0.8513 (p0) cc_final: 0.8210 (p0) REVERT: L 226 LEU cc_start: 0.9212 (tp) cc_final: 0.9002 (tp) REVERT: L 228 MET cc_start: 0.8784 (tpp) cc_final: 0.8479 (tpp) REVERT: L 269 TRP cc_start: 0.8505 (m100) cc_final: 0.8216 (m-90) REVERT: L 281 CYS cc_start: 0.8656 (t) cc_final: 0.8347 (t) REVERT: C 199 LEU cc_start: 0.9233 (tp) cc_final: 0.8676 (tt) REVERT: C 235 SER cc_start: 0.9411 (t) cc_final: 0.9106 (p) REVERT: C 261 ILE cc_start: 0.9021 (pt) cc_final: 0.8778 (tt) REVERT: G 31 LYS cc_start: 0.8375 (mttt) cc_final: 0.7836 (mptt) REVERT: T 22 MET cc_start: 0.8875 (tpp) cc_final: 0.8624 (tpp) REVERT: H 15 SER cc_start: 0.9198 (t) cc_final: 0.8933 (p) REVERT: H 22 MET cc_start: 0.8902 (ttt) cc_final: 0.8690 (ttm) REVERT: F 20 LEU cc_start: 0.9270 (tp) cc_final: 0.9015 (tt) REVERT: 7 33 SER cc_start: 0.8956 (t) cc_final: 0.8679 (m) REVERT: M 528 SER cc_start: 0.9514 (m) cc_final: 0.8986 (t) REVERT: M 541 MET cc_start: 0.9280 (mmp) cc_final: 0.8808 (mtt) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.0971 time to fit residues: 98.1304 Evaluate side-chains 490 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 183 optimal weight: 0.1980 chunk 167 optimal weight: 50.0000 chunk 81 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 192 HIS L 247 HIS ** K 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 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** ** 7 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 = 0.3559 r_free = 0.3559 target = 0.106106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094399 restraints weight = 63864.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096661 restraints weight = 29912.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098162 restraints weight = 17232.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099141 restraints weight = 11352.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099811 restraints weight = 8389.090| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.454 21001 Z= 0.148 Angle : 1.106 45.163 29503 Z= 0.429 Chirality : 0.047 1.157 3102 Planarity : 0.004 0.075 3485 Dihedral : 17.053 179.845 3898 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.23 (0.19), residues: 2041 helix: 1.13 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -4.31 (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 0.029 0.002 PHE L 207 TRP 0.065 0.002 TRP H 38 HIS 0.023 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00332 (20936) covalent geometry : angle 1.10636 (29503) hydrogen bonds : bond 0.04912 ( 930) hydrogen bonds : angle 3.89501 ( 2751) Misc. bond : bond 0.05797 ( 65) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3169.89 seconds wall clock time: 55 minutes 22.81 seconds (3322.81 seconds total)