Starting phenix.real_space_refine on Mon Aug 25 11:35:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.map" model { file = "/net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z83_39837/08_2025/8z83_39837.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 58 5.49 5 Mg 46 5.21 5 S 100 5.16 5 C 19326 2.51 5 N 3784 2.21 5 O 4679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27998 Number of models: 1 Model: "" Number of chains: 74 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2618 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 314} Chain: "L" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2170 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "M" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2518 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain: "H" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2174 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 253} Chain: "A" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "F" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "I" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "K" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Q" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "T" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "U" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "W" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "4" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "5" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "6" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "7" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "8" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "9" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "0" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 362 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 283 Unusual residues: {' MG': 1, 'HEC': 4, 'LMT': 1, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 569 Unusual residues: {'BCL': 3, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UQ8:plan-6': 3, 'UQ8:plan-7': 3, 'UQ8:plan-8': 3, 'UQ8:plan-9': 2, 'PGV:plan-3': 1, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-4': 1} Unresolved non-hydrogen planarities: 74 Chain: "M" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 543 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 5, 'CRT': 1, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 186 Chain: "H" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 260 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "E" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 163 Unusual residues: {'BCL': 1, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "N" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 161 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "P" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 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: "T" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "V" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'PGV:plan-1': 1, 'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 9 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: "X" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-1': 2, 'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 10 Chain: "1" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-1': 1, 'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 6 Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "5" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "8" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 197 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 16 Chain: "9" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.47, per 1000 atoms: 0.23 Number of scatterers: 27998 At special positions: 0 Unit cell: (129.56, 132.84, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 100 16.00 P 58 15.00 Mg 46 11.99 O 4679 8.00 N 3784 7.00 C 19326 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=59, symmetry=0 Number of additional bonds: simple=59, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4942 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 11 sheets defined 64.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.550A pdb=" N ILE C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.395A pdb=" N THR C 109 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 152 through 158 removed outlier: 3.787A pdb=" N CYS C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.659A pdb=" N THR C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.114A pdb=" N CYS C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.960A pdb=" N LEU C 261 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 288 removed outlier: 4.103A pdb=" N GLU C 272 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 32 through 58 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.612A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 220 removed outlier: 3.540A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 250 removed outlier: 3.581A pdb=" N GLY L 228 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.664A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 269 through 273 removed outlier: 3.978A pdb=" N SER L 273 " --> pdb=" O PRO L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.880A pdb=" N ILE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.596A pdb=" N LYS M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.601A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 112 through 117 Processing helix chain 'H' and resid 118 through 122 Processing helix chain 'H' and resid 154 through 161 Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 235 through 241 Processing helix chain 'H' and resid 251 through 269 removed outlier: 3.574A pdb=" N GLY H 265 " --> pdb=" O TYR H 261 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL H 266 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU H 267 " --> pdb=" O GLY H 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 9 through 35 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.808A pdb=" N ILE D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 35 Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.529A pdb=" N ALA E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 9 through 35 Processing helix chain 'G' and resid 11 through 44 Processing helix chain 'I' and resid 3 through 8 removed outlier: 3.569A pdb=" N ILE I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.500A pdb=" N VAL I 15 " --> pdb=" O ARG I 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 9 through 35 Processing helix chain 'N' and resid 11 through 44 Processing helix chain 'O' and resid 1 through 7 removed outlier: 3.825A pdb=" N MET O 4 " --> pdb=" O MET O 1 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP O 5 " --> pdb=" O TRP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 34 removed outlier: 3.692A pdb=" N VAL O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 3 through 8 Processing helix chain 'Q' and resid 9 through 35 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 2 through 7 removed outlier: 3.510A pdb=" N TRP S 5 " --> pdb=" O TRP S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 34 removed outlier: 3.651A pdb=" N VAL S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'V' and resid 11 through 44 Processing helix chain 'W' and resid 1 through 7 removed outlier: 3.661A pdb=" N MET W 4 " --> pdb=" O MET W 1 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP W 5 " --> pdb=" O TRP W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 35 Processing helix chain 'X' and resid 11 through 44 Processing helix chain 'Y' and resid 3 through 8 Processing helix chain 'Y' and resid 9 through 35 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.682A pdb=" N LYS Z 16 " --> pdb=" O ASP Z 12 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 7 Processing helix chain '1' and resid 9 through 35 removed outlier: 3.565A pdb=" N VAL 1 15 " --> pdb=" O ARG 1 11 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 44 Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 9 through 35 Processing helix chain '4' and resid 11 through 44 Processing helix chain '5' and resid 3 through 8 removed outlier: 3.811A pdb=" N ILE 5 7 " --> pdb=" O ARG 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 35 Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 1 through 7 Processing helix chain '7' and resid 9 through 35 Processing helix chain '8' and resid 11 through 44 removed outlier: 3.537A pdb=" N MET 8 23 " --> pdb=" O HIS 8 19 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 8 removed outlier: 3.759A pdb=" N ILE 9 7 " --> pdb=" O ARG 9 3 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 35 Processing helix chain '0' and resid 11 through 44 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 167 Processing sheet with id=AA3, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA7, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AA8, first strand: chain 'H' and resid 68 through 71 Processing sheet with id=AA9, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AB1, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.470A pdb=" N ILE H 184 " --> pdb=" O MET H 201 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET H 201 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP H 186 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU H 199 " --> pdb=" O ASP H 186 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 188 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG H 195 " --> pdb=" O ASP H 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.759A pdb=" N GLY H 182 " --> pdb=" O VAL H 173 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3837 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: 5.76 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9667 1.38 - 1.56: 18901 1.56 - 1.74: 116 1.74 - 1.92: 189 1.92 - 2.11: 192 Bond restraints: 29065 Sorted by residual: bond pdb=" CA7 CDL M 402 " pdb=" OA8 CDL M 402 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CB7 CDL M 402 " pdb=" OB8 CDL M 402 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL M 410 " pdb=" OB8 CDL M 410 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL F 101 " pdb=" OB8 CDL F 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL U 101 " pdb=" OB8 CDL U 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 29060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 37982 4.91 - 9.82: 1709 9.82 - 14.73: 124 14.73 - 19.64: 36 19.64 - 24.56: 11 Bond angle restraints: 39862 Sorted by residual: angle pdb=" C2 CRT R 101 " pdb=" C1 CRT R 101 " pdb=" C4 CRT R 101 " ideal model delta sigma weight residual 110.24 85.68 24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C2 CRT Z 102 " pdb=" C1 CRT Z 102 " pdb=" C4 CRT Z 102 " ideal model delta sigma weight residual 110.24 85.69 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C2 CRT N 102 " pdb=" C1 CRT N 102 " pdb=" C4 CRT N 102 " ideal model delta sigma weight residual 110.24 85.94 24.30 3.00e+00 1.11e-01 6.56e+01 angle pdb=" C2 CRT 4 101 " pdb=" C1 CRT 4 101 " pdb=" C4 CRT 4 101 " ideal model delta sigma weight residual 110.24 85.95 24.29 3.00e+00 1.11e-01 6.55e+01 angle pdb=" C2 CRT V 102 " pdb=" C1 CRT V 102 " pdb=" C4 CRT V 102 " ideal model delta sigma weight residual 110.24 86.48 23.76 3.00e+00 1.11e-01 6.27e+01 ... (remaining 39857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 15273 35.30 - 70.61: 1039 70.61 - 105.91: 159 105.91 - 141.21: 73 141.21 - 176.52: 13 Dihedral angle restraints: 16557 sinusoidal: 8890 harmonic: 7667 Sorted by residual: dihedral pdb=" C1 BCL Z 103 " pdb=" CGA BCL Z 103 " pdb=" O2A BCL Z 103 " pdb=" CBA BCL Z 103 " ideal model delta sinusoidal sigma weight residual -180.00 -40.89 -139.11 1 6.00e+00 2.78e-02 4.68e+02 dihedral pdb=" C1 BCL I 102 " pdb=" CGA BCL I 102 " pdb=" O2A BCL I 102 " pdb=" CBA BCL I 102 " ideal model delta sinusoidal sigma weight residual 180.00 94.24 85.76 1 6.00e+00 2.78e-02 2.47e+02 dihedral pdb=" C1 BCL 3 102 " pdb=" CGA BCL 3 102 " pdb=" O2A BCL 3 102 " pdb=" CBA BCL 3 102 " ideal model delta sinusoidal sigma weight residual -180.00 -108.62 -71.38 1 6.00e+00 2.78e-02 1.82e+02 ... (remaining 16554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3095 0.058 - 0.116: 530 0.116 - 0.174: 152 0.174 - 0.233: 38 0.233 - 0.291: 33 Chirality restraints: 3848 Sorted by residual: chirality pdb=" C05 PGV E 102 " pdb=" C04 PGV E 102 " pdb=" C06 PGV E 102 " pdb=" O05 PGV E 102 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C05 PGV 1 101 " pdb=" C04 PGV 1 101 " pdb=" C06 PGV 1 101 " pdb=" O05 PGV 1 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C05 PGV Z 101 " pdb=" C04 PGV Z 101 " pdb=" C06 PGV Z 101 " pdb=" O05 PGV Z 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3845 not shown) Planarity restraints: 4636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL I 102 " -0.371 3.00e-02 1.11e+03 3.08e-01 5.26e+02 pdb=" CBA BCL I 102 " -0.119 3.00e-02 1.11e+03 pdb=" CGA BCL I 102 " 0.076 3.00e-02 1.11e+03 pdb=" O1A BCL I 102 " -0.133 3.00e-02 1.11e+03 pdb=" O2A BCL I 102 " 0.547 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 3 102 " -0.377 3.00e-02 1.11e+03 3.06e-01 5.21e+02 pdb=" CBA BCL 3 102 " -0.177 3.00e-02 1.11e+03 pdb=" CGA BCL 3 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL 3 102 " -0.065 3.00e-02 1.11e+03 pdb=" O2A BCL 3 102 " 0.533 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 101 " -0.330 3.00e-02 1.11e+03 2.66e-01 3.92e+02 pdb=" CBA BCL T 101 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL T 101 " 0.078 3.00e-02 1.11e+03 pdb=" O1A BCL T 101 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL T 101 " 0.447 3.00e-02 1.11e+03 ... (remaining 4633 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 125 2.44 - 3.06: 16453 3.06 - 3.67: 44695 3.67 - 4.29: 75255 4.29 - 4.90: 119393 Nonbonded interactions: 255921 Sorted by model distance: nonbonded pdb="MG MG C 405 " pdb=" O HOH C 502 " model vdw 1.828 2.170 nonbonded pdb="MG MG C 405 " pdb=" O HOH M 501 " model vdw 1.981 2.170 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.000 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.057 2.260 nonbonded pdb="MG MG C 405 " pdb=" O HOH C 501 " model vdw 2.094 2.170 ... (remaining 255916 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 9 through 53) selection = (chain '2' and resid 9 through 53) selection = (chain '6' and resid 9 through 53) selection = (chain 'E' and resid 9 through 53) selection = (chain 'J' and resid 9 through 53) selection = (chain 'P' and resid 9 through 53) selection = (chain 'T' and resid 9 through 53) selection = (chain 'X' and resid 9 through 53) } ncs_group { reference = (chain '1' and (resid 1 through 46 or resid 102)) selection = (chain '5' and (resid 1 through 46 or resid 102)) selection = (chain '9' and (resid 1 through 46 or resid 102)) selection = (chain 'D' and (resid 1 through 46 or resid 102)) selection = (chain 'I' and (resid 1 through 46 or resid 102)) selection = (chain 'O' and (resid 1 through 46 or resid 102)) selection = (chain 'S' and (resid 1 through 46 or resid 102)) selection = (chain 'W' and (resid 1 through 46 or resid 102)) } ncs_group { reference = (chain '3' and resid 1 through 46) selection = (chain '7' and resid 1 through 46) selection = (chain 'A' and resid 1 through 46) selection = (chain 'F' and resid 1 through 46) selection = (chain 'K' and resid 1 through 46) selection = (chain 'Q' and resid 1 through 46) selection = (chain 'U' and resid 1 through 46) selection = (chain 'Y' and resid 1 through 46) } ncs_group { reference = (chain '4' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain '8' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'B' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C13 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C29 or name O0 \ 1 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or nam \ e O14 or name P )))) selection = (chain 'G' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'N' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'R' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C14 or name C2 or name C20 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )))) selection = (chain 'V' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) selection = (chain 'Z' and (resid 7 through 53 or (resid 104 and (name C01 or name C02 or na \ me C03 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 o \ r name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.850 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 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:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 0.571 29124 Z= 1.173 Angle : 2.019 24.556 39862 Z= 0.864 Chirality : 0.058 0.291 3848 Planarity : 0.022 0.308 4636 Dihedral : 23.546 176.516 11615 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.32 % Allowed : 5.41 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.75 (0.16), residues: 2605 helix: 1.98 (0.12), residues: 1471 sheet: 0.68 (0.70), residues: 54 loop : 0.11 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 136 TYR 0.021 0.001 TYR L 164 PHE 0.025 0.001 PHE C 345 TRP 0.015 0.001 TRP F 5 HIS 0.006 0.001 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.02098 (29065) covalent geometry : angle 2.01924 (39862) hydrogen bonds : bond 0.17718 ( 1338) hydrogen bonds : angle 5.97231 ( 3837) Misc. bond : bond 0.18183 ( 59) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 1.037 Fit side-chains REVERT: C 131 MET cc_start: 0.9111 (mmt) cc_final: 0.8385 (mmt) REVERT: C 328 MET cc_start: 0.7721 (ptt) cc_final: 0.7322 (ptm) REVERT: H 221 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7355 (ttp-110) REVERT: E 29 TYR cc_start: 0.8816 (t80) cc_final: 0.8475 (t80) REVERT: V 13 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6154 (mm-30) REVERT: V 23 MET cc_start: 0.8332 (mmm) cc_final: 0.8107 (mmm) REVERT: Z 27 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (tp) REVERT: 3 1 MET cc_start: 0.6725 (tpp) cc_final: 0.6348 (tpp) REVERT: 4 13 GLU cc_start: 0.6707 (pp20) cc_final: 0.6434 (pp20) REVERT: 5 12 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7074 (ttt-90) REVERT: 7 9 ASP cc_start: 0.7522 (t0) cc_final: 0.7205 (t0) outliers start: 51 outliers final: 27 residues processed: 403 average time/residue: 0.8401 time to fit residues: 386.5725 Evaluate side-chains 342 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 221 ARG Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain S residue 4 MET Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 HIS L 264 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN B 24 GLN G 24 GLN O 42 GLN 4 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103314 restraints weight = 36326.281| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.30 r_work: 0.3094 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.375 29124 Z= 0.200 Angle : 0.819 15.642 39862 Z= 0.318 Chirality : 0.043 0.306 3848 Planarity : 0.004 0.072 4636 Dihedral : 23.646 176.623 6951 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.50 % Allowed : 9.13 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.73 (0.16), residues: 2605 helix: 2.13 (0.12), residues: 1475 sheet: 0.52 (0.66), residues: 64 loop : -0.19 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 12 TYR 0.022 0.002 TYR L 164 PHE 0.024 0.002 PHE C 345 TRP 0.017 0.001 TRP M 271 HIS 0.008 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00480 (29065) covalent geometry : angle 0.81866 (39862) hydrogen bonds : bond 0.05366 ( 1338) hydrogen bonds : angle 4.50153 ( 3837) Misc. bond : bond 0.08297 ( 59) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 323 time to evaluate : 0.792 Fit side-chains REVERT: C 96 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: H 254 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: I 6 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8028 (mttt) REVERT: J 30 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8476 (mp) REVERT: N 51 GLU cc_start: 0.7472 (pm20) cc_final: 0.7228 (pm20) REVERT: R 51 GLU cc_start: 0.8296 (pm20) cc_final: 0.8042 (pm20) REVERT: T 14 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6772 (mt-10) REVERT: V 13 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6409 (mm-30) REVERT: V 23 MET cc_start: 0.8451 (mmm) cc_final: 0.8149 (mmm) REVERT: W 6 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8382 (mttm) REVERT: Z 11 SER cc_start: 0.7267 (p) cc_final: 0.6989 (p) REVERT: Z 17 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: Z 27 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8331 (tp) REVERT: 3 1 MET cc_start: 0.6795 (tpp) cc_final: 0.6360 (tpp) REVERT: 4 13 GLU cc_start: 0.6774 (pp20) cc_final: 0.6511 (pp20) REVERT: 5 12 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.6849 (ttm110) REVERT: 8 24 GLN cc_start: 0.7773 (mt0) cc_final: 0.7378 (mm-40) outliers start: 77 outliers final: 36 residues processed: 370 average time/residue: 0.6350 time to fit residues: 269.7444 Evaluate side-chains 345 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 301 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 164 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 264 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN B 24 GLN G 24 GLN 4 24 GLN 9 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103613 restraints weight = 36422.893| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.32 r_work: 0.3095 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.326 29124 Z= 0.179 Angle : 0.774 15.115 39862 Z= 0.299 Chirality : 0.042 0.391 3848 Planarity : 0.004 0.073 4636 Dihedral : 21.374 163.065 6936 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.68 % Allowed : 10.04 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.79 (0.16), residues: 2605 helix: 2.21 (0.12), residues: 1470 sheet: 0.85 (0.72), residues: 52 loop : -0.20 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 12 TYR 0.022 0.002 TYR L 164 PHE 0.022 0.002 PHE C 345 TRP 0.017 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00420 (29065) covalent geometry : angle 0.77358 (39862) hydrogen bonds : bond 0.05031 ( 1338) hydrogen bonds : angle 4.34449 ( 3837) Misc. bond : bond 0.06962 ( 59) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 0.679 Fit side-chains REVERT: C 95 MET cc_start: 0.8747 (mmt) cc_final: 0.7510 (mmt) REVERT: H 254 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: G 30 THR cc_start: 0.8770 (m) cc_final: 0.8526 (m) REVERT: J 9 ASN cc_start: 0.4740 (t0) cc_final: 0.4160 (t0) REVERT: J 17 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: N 51 GLU cc_start: 0.7471 (pm20) cc_final: 0.7210 (pm20) REVERT: P 17 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7440 (mt-10) REVERT: T 14 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6630 (mt-10) REVERT: U 11 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7202 (ttt180) REVERT: V 13 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: V 23 MET cc_start: 0.8437 (mmm) cc_final: 0.8132 (mmm) REVERT: W 6 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8104 (mttm) REVERT: Y 3 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7548 (mtt90) REVERT: Z 11 SER cc_start: 0.7034 (p) cc_final: 0.6755 (p) REVERT: Z 17 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: 4 13 GLU cc_start: 0.6780 (pp20) cc_final: 0.6474 (pp20) REVERT: 5 12 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.6904 (ttt-90) REVERT: 6 51 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: 7 9 ASP cc_start: 0.7418 (t0) cc_final: 0.7189 (t0) REVERT: 8 27 LEU cc_start: 0.8279 (tp) cc_final: 0.7851 (tt) REVERT: 8 51 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7342 (mm-30) outliers start: 81 outliers final: 34 residues processed: 369 average time/residue: 0.6652 time to fit residues: 283.0912 Evaluate side-chains 340 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 6 residue 51 GLU Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 114 optimal weight: 5.9990 chunk 230 optimal weight: 0.0470 chunk 154 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 264 ASN H 138 GLN H 172 GLN B 24 GLN D 18 HIS G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 ASN 4 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 42 GLN 8 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105298 restraints weight = 36255.156| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.35 r_work: 0.3123 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.292 29124 Z= 0.196 Angle : 0.718 14.431 39862 Z= 0.276 Chirality : 0.040 0.377 3848 Planarity : 0.004 0.070 4636 Dihedral : 20.216 152.399 6928 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.23 % Allowed : 10.95 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 2.00 (0.16), residues: 2605 helix: 2.41 (0.12), residues: 1470 sheet: 0.98 (0.76), residues: 42 loop : -0.17 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 12 TYR 0.018 0.001 TYR L 164 PHE 0.019 0.001 PHE C 345 TRP 0.015 0.001 TRP M 252 HIS 0.005 0.001 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00328 (29065) covalent geometry : angle 0.71774 (39862) hydrogen bonds : bond 0.04635 ( 1338) hydrogen bonds : angle 4.20188 ( 3837) Misc. bond : bond 0.06648 ( 59) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.692 Fit side-chains REVERT: C 95 MET cc_start: 0.8717 (mmt) cc_final: 0.7531 (mmt) REVERT: C 309 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: L 8 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8208 (tptt) REVERT: M 216 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8518 (t80) REVERT: G 30 THR cc_start: 0.8780 (m) cc_final: 0.8553 (m) REVERT: P 13 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7081 (mm-30) REVERT: P 17 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7399 (mt-10) REVERT: Q 6 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7844 (mmmm) REVERT: Q 41 VAL cc_start: 0.8858 (m) cc_final: 0.8536 (t) REVERT: R 51 GLU cc_start: 0.8241 (pm20) cc_final: 0.8033 (pm20) REVERT: T 14 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6624 (mt-10) REVERT: T 16 LYS cc_start: 0.8192 (mptt) cc_final: 0.7648 (mtpt) REVERT: V 13 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6295 (mm-30) REVERT: V 23 MET cc_start: 0.8437 (mmm) cc_final: 0.8138 (mmm) REVERT: W 12 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7618 (ttm-80) REVERT: Y 3 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7578 (mtt90) REVERT: Z 11 SER cc_start: 0.7109 (p) cc_final: 0.6810 (p) REVERT: Z 17 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: 4 13 GLU cc_start: 0.6839 (pp20) cc_final: 0.6526 (pp20) REVERT: 5 12 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.6962 (ttt-90) REVERT: 7 9 ASP cc_start: 0.7259 (t0) cc_final: 0.6994 (t0) REVERT: 8 27 LEU cc_start: 0.8265 (tp) cc_final: 0.7861 (tt) outliers start: 71 outliers final: 33 residues processed: 370 average time/residue: 0.6820 time to fit residues: 291.4025 Evaluate side-chains 344 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 4 residue 20 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 162 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101251 restraints weight = 36351.705| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.27 r_work: 0.3060 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.349 29124 Z= 0.280 Angle : 0.900 14.404 39862 Z= 0.350 Chirality : 0.046 0.381 3848 Planarity : 0.005 0.076 4636 Dihedral : 21.198 154.992 6923 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.68 % Allowed : 11.36 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.46 (0.16), residues: 2605 helix: 1.90 (0.12), residues: 1472 sheet: 0.50 (0.63), residues: 67 loop : -0.29 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 12 TYR 0.028 0.002 TYR L 164 PHE 0.029 0.002 PHE C 345 TRP 0.015 0.002 TRP M 252 HIS 0.011 0.003 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00676 (29065) covalent geometry : angle 0.90026 (39862) hydrogen bonds : bond 0.05430 ( 1338) hydrogen bonds : angle 4.46790 ( 3837) Misc. bond : bond 0.07202 ( 59) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 311 time to evaluate : 0.996 Fit side-chains REVERT: C 75 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6124 (mt-10) REVERT: C 78 GLN cc_start: 0.7252 (mt0) cc_final: 0.7035 (pt0) REVERT: C 96 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: L 39 THR cc_start: 0.8717 (t) cc_final: 0.8464 (m) REVERT: L 185 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8311 (tp) REVERT: M 216 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8581 (t80) REVERT: H 76 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7554 (mtp180) REVERT: G 30 THR cc_start: 0.8754 (m) cc_final: 0.8527 (m) REVERT: J 9 ASN cc_start: 0.4905 (t0) cc_final: 0.4327 (t0) REVERT: J 17 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: P 17 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7493 (mt-10) REVERT: V 13 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: Y 3 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7598 (mtt90) REVERT: Z 11 SER cc_start: 0.7177 (p) cc_final: 0.6867 (p) REVERT: Z 14 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7218 (mt-10) REVERT: Z 17 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: Z 51 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: 4 13 GLU cc_start: 0.6940 (pp20) cc_final: 0.6656 (pp20) REVERT: 5 36 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: 7 36 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: 8 27 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (tt) outliers start: 81 outliers final: 45 residues processed: 362 average time/residue: 0.6497 time to fit residues: 271.2399 Evaluate side-chains 360 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 17 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 118 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 24 GLN ** 5 18 HIS ** 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 = 0.3561 r_free = 0.3561 target = 0.122743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104233 restraints weight = 36194.101| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.33 r_work: 0.3105 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 29124 Z= 0.154 Angle : 0.745 13.422 39862 Z= 0.285 Chirality : 0.040 0.364 3848 Planarity : 0.004 0.072 4636 Dihedral : 20.246 155.850 6923 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.18 % Allowed : 12.04 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.83 (0.16), residues: 2605 helix: 2.26 (0.12), residues: 1470 sheet: 0.47 (0.66), residues: 57 loop : -0.21 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 12 TYR 0.019 0.001 TYR L 164 PHE 0.019 0.002 PHE H 21 TRP 0.014 0.001 TRP M 252 HIS 0.006 0.001 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00360 (29065) covalent geometry : angle 0.74451 (39862) hydrogen bonds : bond 0.04738 ( 1338) hydrogen bonds : angle 4.25092 ( 3837) Misc. bond : bond 0.06763 ( 59) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.675 Fit side-chains REVERT: C 75 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6004 (mt-10) REVERT: C 95 MET cc_start: 0.8787 (mmt) cc_final: 0.7441 (mmt) REVERT: G 30 THR cc_start: 0.8776 (m) cc_final: 0.8558 (m) REVERT: J 9 ASN cc_start: 0.4942 (t0) cc_final: 0.4385 (t0) REVERT: J 17 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: P 17 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7448 (mt-10) REVERT: Q 41 VAL cc_start: 0.8853 (m) cc_final: 0.8525 (t) REVERT: T 14 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6714 (mt-10) REVERT: V 13 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6244 (mm-30) REVERT: V 23 MET cc_start: 0.8411 (mmm) cc_final: 0.8105 (mmm) REVERT: Y 3 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7600 (mtt90) REVERT: Z 11 SER cc_start: 0.7227 (p) cc_final: 0.6969 (p) REVERT: Z 17 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: 4 10 LEU cc_start: 0.7230 (mt) cc_final: 0.7011 (mp) REVERT: 4 13 GLU cc_start: 0.6856 (pp20) cc_final: 0.6575 (pp20) REVERT: 5 36 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: 7 9 ASP cc_start: 0.7227 (t0) cc_final: 0.6972 (t0) REVERT: 7 36 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: 8 27 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7934 (tt) outliers start: 70 outliers final: 40 residues processed: 363 average time/residue: 0.6802 time to fit residues: 285.4940 Evaluate side-chains 349 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 202 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100645 restraints weight = 36155.276| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.28 r_work: 0.3044 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.394 29124 Z= 0.303 Angle : 0.932 19.449 39862 Z= 0.361 Chirality : 0.048 0.423 3848 Planarity : 0.005 0.076 4636 Dihedral : 21.186 164.047 6922 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.41 % Allowed : 12.36 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.35 (0.15), residues: 2605 helix: 1.80 (0.12), residues: 1468 sheet: 0.44 (0.66), residues: 57 loop : -0.32 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 12 TYR 0.028 0.002 TYR L 164 PHE 0.030 0.002 PHE C 345 TRP 0.015 0.002 TRP M 252 HIS 0.011 0.003 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00729 (29065) covalent geometry : angle 0.93242 (39862) hydrogen bonds : bond 0.05505 ( 1338) hydrogen bonds : angle 4.50011 ( 3837) Misc. bond : bond 0.08044 ( 59) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 309 time to evaluate : 0.948 Fit side-chains REVERT: C 75 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6289 (mt-10) REVERT: L 39 THR cc_start: 0.8717 (t) cc_final: 0.8482 (m) REVERT: L 185 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8300 (tp) REVERT: M 216 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8570 (t80) REVERT: G 30 THR cc_start: 0.8748 (m) cc_final: 0.8539 (m) REVERT: J 9 ASN cc_start: 0.4985 (t0) cc_final: 0.4411 (t0) REVERT: J 17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: J 30 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8528 (mp) REVERT: O 39 ASN cc_start: 0.9120 (t160) cc_final: 0.8886 (t0) REVERT: P 17 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7560 (mt-10) REVERT: V 13 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: Y 3 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7654 (mtt90) REVERT: Z 11 SER cc_start: 0.7290 (p) cc_final: 0.7011 (p) REVERT: Z 17 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: 4 13 GLU cc_start: 0.7026 (pp20) cc_final: 0.6731 (pp20) REVERT: 5 36 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: 7 36 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: 8 27 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8102 (tp) outliers start: 75 outliers final: 45 residues processed: 356 average time/residue: 0.7265 time to fit residues: 298.0570 Evaluate side-chains 358 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102910 restraints weight = 36238.065| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.33 r_work: 0.3100 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 29124 Z= 0.161 Angle : 0.760 13.305 39862 Z= 0.292 Chirality : 0.040 0.341 3848 Planarity : 0.004 0.073 4636 Dihedral : 20.194 161.426 6922 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.59 % Allowed : 13.54 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.73 (0.16), residues: 2605 helix: 2.18 (0.12), residues: 1470 sheet: 0.35 (0.65), residues: 57 loop : -0.25 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 12 TYR 0.020 0.001 TYR L 164 PHE 0.019 0.002 PHE H 21 TRP 0.015 0.001 TRP M 252 HIS 0.006 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00377 (29065) covalent geometry : angle 0.75969 (39862) hydrogen bonds : bond 0.04784 ( 1338) hydrogen bonds : angle 4.27837 ( 3837) Misc. bond : bond 0.07200 ( 59) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.705 Fit side-chains REVERT: C 95 MET cc_start: 0.8789 (mmt) cc_final: 0.7541 (mmt) REVERT: C 96 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: L 39 THR cc_start: 0.8640 (t) cc_final: 0.8409 (m) REVERT: L 204 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7539 (mt-10) REVERT: G 30 THR cc_start: 0.8778 (m) cc_final: 0.8570 (m) REVERT: J 9 ASN cc_start: 0.4917 (t0) cc_final: 0.4379 (t0) REVERT: J 17 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: P 17 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7474 (mt-10) REVERT: Q 41 VAL cc_start: 0.8829 (m) cc_final: 0.8527 (t) REVERT: U 12 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: V 13 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6340 (mm-30) REVERT: Y 3 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7592 (mtt90) REVERT: Z 11 SER cc_start: 0.7310 (p) cc_final: 0.7030 (p) REVERT: Z 17 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: 4 10 LEU cc_start: 0.7176 (mt) cc_final: 0.6949 (mp) REVERT: 4 13 GLU cc_start: 0.6929 (pp20) cc_final: 0.6542 (pp20) REVERT: 5 36 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: 7 9 ASP cc_start: 0.7322 (t0) cc_final: 0.7083 (t0) REVERT: 7 36 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: 8 27 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8030 (tp) outliers start: 57 outliers final: 40 residues processed: 354 average time/residue: 0.6739 time to fit residues: 276.2873 Evaluate side-chains 349 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 264 ASN H 172 GLN B 24 GLN G 24 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101644 restraints weight = 36137.923| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.28 r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.387 29124 Z= 0.253 Angle : 0.871 14.376 39862 Z= 0.338 Chirality : 0.045 0.384 3848 Planarity : 0.005 0.074 4636 Dihedral : 20.608 164.631 6919 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.09 % Allowed : 13.54 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.50 (0.16), residues: 2605 helix: 1.97 (0.12), residues: 1461 sheet: 0.40 (0.65), residues: 57 loop : -0.30 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 12 TYR 0.027 0.002 TYR L 164 PHE 0.026 0.002 PHE H 21 TRP 0.016 0.002 TRP M 252 HIS 0.010 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00607 (29065) covalent geometry : angle 0.87097 (39862) hydrogen bonds : bond 0.05248 ( 1338) hydrogen bonds : angle 4.41586 ( 3837) Misc. bond : bond 0.07865 ( 59) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 1.096 Fit side-chains REVERT: C 96 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: L 39 THR cc_start: 0.8690 (t) cc_final: 0.8440 (m) REVERT: L 204 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7598 (mt-10) REVERT: J 9 ASN cc_start: 0.4924 (t0) cc_final: 0.4394 (t0) REVERT: J 17 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: O 42 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: P 17 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7505 (mt-10) REVERT: V 13 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6569 (mm-30) REVERT: Y 3 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7610 (mtt90) REVERT: Z 11 SER cc_start: 0.7313 (p) cc_final: 0.7069 (p) REVERT: Z 14 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7266 (mt-10) REVERT: Z 17 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: 4 10 LEU cc_start: 0.7210 (mt) cc_final: 0.6986 (mp) REVERT: 4 13 GLU cc_start: 0.6935 (pp20) cc_final: 0.6642 (pp20) REVERT: 5 36 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: 7 36 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: 8 27 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8062 (tp) outliers start: 68 outliers final: 45 residues processed: 346 average time/residue: 0.6990 time to fit residues: 279.9215 Evaluate side-chains 353 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 51 GLU Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 0 residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 109 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 GLN B 24 GLN G 24 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 24 GLN ** 5 18 HIS ** 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 = 0.3551 r_free = 0.3551 target = 0.121996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103978 restraints weight = 35944.569| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.31 r_work: 0.3101 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.353 29124 Z= 0.172 Angle : 0.772 12.478 39862 Z= 0.299 Chirality : 0.040 0.327 3848 Planarity : 0.004 0.074 4636 Dihedral : 19.979 162.636 6919 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.64 % Allowed : 14.08 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.72 (0.16), residues: 2605 helix: 2.18 (0.12), residues: 1469 sheet: 0.35 (0.65), residues: 57 loop : -0.26 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 12 TYR 0.021 0.002 TYR L 164 PHE 0.021 0.002 PHE H 21 TRP 0.015 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00403 (29065) covalent geometry : angle 0.77153 (39862) hydrogen bonds : bond 0.04825 ( 1338) hydrogen bonds : angle 4.28786 ( 3837) Misc. bond : bond 0.07113 ( 59) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 308 time to evaluate : 0.990 Fit side-chains REVERT: C 95 MET cc_start: 0.8792 (mmt) cc_final: 0.7611 (mmt) REVERT: C 96 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: L 39 THR cc_start: 0.8645 (t) cc_final: 0.8414 (m) REVERT: L 204 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 87 ASP cc_start: 0.7681 (m-30) cc_final: 0.7435 (m-30) REVERT: J 9 ASN cc_start: 0.4859 (t0) cc_final: 0.4346 (t0) REVERT: J 17 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: O 42 GLN cc_start: 0.8471 (tp40) cc_final: 0.8201 (mt0) REVERT: P 17 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7465 (mt-10) REVERT: Q 41 VAL cc_start: 0.8782 (m) cc_final: 0.8490 (t) REVERT: R 27 LEU cc_start: 0.7601 (mt) cc_final: 0.7311 (tp) REVERT: V 13 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: Y 3 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7613 (mtt90) REVERT: Z 11 SER cc_start: 0.7334 (p) cc_final: 0.7099 (p) REVERT: Z 17 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: Z 51 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6447 (pp20) REVERT: 4 10 LEU cc_start: 0.7170 (mt) cc_final: 0.6948 (mp) REVERT: 4 13 GLU cc_start: 0.6910 (pp20) cc_final: 0.6618 (pp20) REVERT: 5 36 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: 7 36 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: 8 27 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8033 (tp) outliers start: 58 outliers final: 40 residues processed: 345 average time/residue: 0.7842 time to fit residues: 311.9384 Evaluate side-chains 352 residues out of total 2201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 2 residue 30 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 36 GLU Chi-restraints excluded: chain 6 residue 51 GLU Chi-restraints excluded: chain 7 residue 36 ASP Chi-restraints excluded: chain 7 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 LEU Chi-restraints excluded: chain 8 residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 187 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 165 optimal weight: 0.0040 chunk 117 optimal weight: 7.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 ASN L 264 ASN H 172 GLN B 24 GLN G 24 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103306 restraints weight = 35916.154| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.34 r_work: 0.3091 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.360 29124 Z= 0.183 Angle : 0.790 13.009 39862 Z= 0.307 Chirality : 0.041 0.324 3848 Planarity : 0.004 0.073 4636 Dihedral : 19.858 162.774 6919 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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 aren not related in a simple way. whole: 1.71 (0.16), residues: 2605 helix: 2.17 (0.12), residues: 1469 sheet: 0.40 (0.66), residues: 57 loop : -0.25 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 12 TYR 0.022 0.002 TYR L 164 PHE 0.022 0.002 PHE H 21 TRP 0.017 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd covalent geometry : bond 0.00432 (29065) covalent geometry : angle 0.79001 (39862) hydrogen bonds : bond 0.04886 ( 1338) hydrogen bonds : angle 4.29557 ( 3837) Misc. bond : bond 0.07362 ( 59) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10071.08 seconds wall clock time: 172 minutes 18.98 seconds (10338.98 seconds total)