Starting phenix.real_space_refine on Sat Aug 8 14:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z82_39836/08_2026/8z82_39836.map" } resolution = 2.4 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 9 7.16 5 P 60 5.49 5 Mg 46 5.21 5 S 111 5.16 5 C 20019 2.51 5 N 3926 2.21 5 O 4847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29018 Number of models: 1 Model: "" Number of chains: 76 Chain: "C" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2642 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 317} 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: "a" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 248 Unusual residues: {' MG': 1, 'HEC': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 494 Unusual residues: {'BCL': 3, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 1, 'UQ8': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 99 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: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 578 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 5, 'CRT': 1, 'LMT': 1, 'MQ8': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 187 Chain: "H" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 198 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 75 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: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 195 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 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: 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: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 207 Unusual residues: {'BCL': 2, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 244 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "O" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 285 Unusual residues: {'BCL': 2, 'CDL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "P" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 183 Unusual residues: {'BCL': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "T" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" 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: 15 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: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 218 Unusual residues: {'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "2" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "8" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21923 SG CYS a 82 66.921 55.732 18.086 1.00 26.44 S ATOM 21942 SG CYS a 85 66.502 53.648 24.091 1.00 38.64 S ATOM 22064 SG CYS a 100 60.851 54.806 21.365 1.00 30.85 S ATOM 22194 SG CYS a 117 64.224 59.438 22.845 1.00 36.47 S Time building chain proxies: 5.49, per 1000 atoms: 0.19 Number of scatterers: 29018 At special positions: 0 Unit cell: (129.56, 133.66, 153.34, 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 9 26.01 S 111 16.00 P 60 15.00 Mg 46 11.99 O 4847 8.00 N 3926 7.00 C 20019 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: 3.29 Conformation dependent library (CDL) restraints added in 991.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 a 201 " pdb="FE2 SF4 a 201 " - pdb=" SG CYS a 85 " pdb="FE4 SF4 a 201 " - pdb=" SG CYS a 117 " pdb="FE3 SF4 a 201 " - pdb=" SG CYS a 100 " pdb="FE1 SF4 a 201 " - pdb=" SG CYS a 82 " Number of angles added : 12 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 13 sheets defined 63.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.547A pdb=" N ARG C 52 " --> pdb=" O PRO C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.530A pdb=" N CYS C 111 " --> pdb=" O CYS C 108 " (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: 3.811A 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: 3.528A pdb=" N THR C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.173A pdb=" N CYS C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 4.034A pdb=" N LEU C 261 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 268 through 288 removed outlier: 4.191A pdb=" N GLU C 272 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.041A pdb=" N ALA C 294 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'L' and resid 7 through 11 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: 3.732A 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 removed outlier: 3.519A pdb=" N ASP L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) 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 Processing helix chain 'L' and resid 224 through 250 removed outlier: 3.595A pdb=" N GLY L 228 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.606A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 3.983A 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 'M' and resid 37 through 44 removed outlier: 3.976A pdb=" N ILE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 removed outlier: 3.555A pdb=" N VAL M 79 " --> pdb=" O MET M 75 " (cutoff:3.500A) 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: 3.524A 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 261 through 287 removed outlier: 4.161A pdb=" N HIS M 266 " --> pdb=" O MET M 262 " (cutoff:3.500A) removed outlier: 3.587A 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 37 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 82 through 92 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: 3.583A pdb=" N GLY H 265 " --> pdb=" O TYR H 261 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 266 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 4.549A 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 6 through 10 removed outlier: 3.523A pdb=" N GLY B 9 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 10 " --> pdb=" O LEU B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 1 through 7 Processing helix chain 'D' and resid 9 through 35 Processing helix chain 'E' and resid 11 through 44 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 1 through 7 Processing helix chain 'I' and resid 9 through 34 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 1 through 7 Processing helix chain 'K' and resid 9 through 34 Processing helix chain 'N' and resid 11 through 44 Processing helix chain 'O' and resid 1 through 7 removed outlier: 3.648A pdb=" N MET O 4 " --> pdb=" O MET O 1 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 34 removed outlier: 3.661A 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 1 through 7 Processing helix chain 'S' and resid 9 through 34 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 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 removed outlier: 3.543A pdb=" N LEU Y 7 " --> pdb=" O ARG Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.536A 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 Processing helix chain '2' and resid 11 through 44 Processing helix chain '3' and resid 3 through 8 removed outlier: 3.510A pdb=" N LEU 3 7 " --> pdb=" O ARG 3 3 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 35 Processing helix chain '4' and resid 11 through 44 Processing helix chain '5' and resid 1 through 7 Processing helix chain '5' and resid 9 through 35 Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 3 through 8 removed outlier: 3.552A pdb=" N LEU 7 7 " --> pdb=" O ARG 7 3 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 35 Processing helix chain '8' and resid 11 through 44 Processing helix chain '9' and resid 1 through 7 removed outlier: 3.585A pdb=" N ILE 9 7 " --> pdb=" O MET 9 4 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 35 removed outlier: 3.589A pdb=" N VAL 9 15 " --> pdb=" O ARG 9 11 " (cutoff:3.500A) Processing helix chain '0' and resid 11 through 44 Processing helix chain 'a' and resid 33 through 40 Processing helix chain 'a' and resid 102 through 104 No H-bonds generated for 'chain 'a' and resid 102 through 104' Processing helix chain 'a' and resid 135 through 140 removed outlier: 3.889A pdb=" N ARG a 140 " --> pdb=" O ALA a 136 " (cutoff:3.500A) 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 'L' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA8, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AA9, first strand: chain 'H' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 removed outlier: 5.844A pdb=" N ILE H 184 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP H 202 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP H 190 " --> pdb=" O PRO H 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.568A pdb=" N VAL H 173 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN H 172 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 88 through 90 1371 hydrogen bonds defined for protein. 3861 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: 5.00 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 11509 1.42 - 1.63: 18196 1.63 - 1.85: 195 1.85 - 2.06: 188 2.06 - 2.28: 20 Bond restraints: 30108 Sorted by residual: bond pdb=" CAC HEC C 402 " pdb=" CBC HEC C 402 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" CAC HEC C 401 " pdb=" CBC HEC C 401 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" CAC HEC C 403 " pdb=" CBC HEC C 403 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CAC HEC C 404 " pdb=" CBC HEC C 404 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CAB HEC C 404 " pdb=" CBB HEC C 404 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 30103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 39282 4.95 - 9.90: 1751 9.90 - 14.84: 130 14.84 - 19.79: 32 19.79 - 24.74: 12 Bond angle restraints: 41207 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 85.50 24.74 3.00e+00 1.11e-01 6.80e+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 86.20 24.04 3.00e+00 1.11e-01 6.42e+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 86.37 23.87 3.00e+00 1.11e-01 6.33e+01 angle pdb=" C2 CRT 8 101 " pdb=" C1 CRT 8 101 " pdb=" C4 CRT 8 101 " ideal model delta sigma weight residual 110.24 86.50 23.74 3.00e+00 1.11e-01 6.26e+01 angle pdb=" C1D BCL Y 401 " pdb=" C2D BCL Y 401 " pdb=" CMD BCL Y 401 " ideal model delta sigma weight residual 125.57 139.74 -14.17 1.83e+00 2.99e-01 6.01e+01 ... (remaining 41202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 15996 35.80 - 71.59: 1141 71.59 - 107.39: 169 107.39 - 143.19: 62 143.19 - 178.98: 20 Dihedral angle restraints: 17388 sinusoidal: 9445 harmonic: 7943 Sorted by residual: dihedral pdb=" C1 BCL Z 102 " pdb=" CGA BCL Z 102 " pdb=" O2A BCL Z 102 " pdb=" CBA BCL Z 102 " ideal model delta sinusoidal sigma weight residual -180.00 -87.64 -92.36 1 6.00e+00 2.78e-02 2.78e+02 dihedral pdb=" C1 BCL M 403 " pdb=" CGA BCL M 403 " pdb=" O2A BCL M 403 " pdb=" CBA BCL M 403 " ideal model delta sinusoidal sigma weight residual 180.00 91.16 88.84 1 6.00e+00 2.78e-02 2.61e+02 dihedral pdb=" CBD BCL Y 401 " pdb=" CGD BCL Y 401 " pdb=" O2D BCL Y 401 " pdb=" CED BCL Y 401 " ideal model delta sinusoidal sigma weight residual -180.00 -109.56 -70.44 1 5.00e+00 4.00e-02 2.55e+02 ... (remaining 17385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3254 0.061 - 0.122: 480 0.122 - 0.182: 154 0.182 - 0.243: 34 0.243 - 0.304: 33 Chirality restraints: 3955 Sorted by residual: chirality pdb=" C05 PGV V 104 " pdb=" C04 PGV V 104 " pdb=" C06 PGV V 104 " pdb=" O05 PGV V 104 " both_signs ideal model delta sigma weight residual False 2.29 2.60 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C05 PGV I 101 " pdb=" C04 PGV I 101 " pdb=" C06 PGV I 101 " pdb=" O05 PGV I 101 " both_signs ideal model delta sigma weight residual False 2.29 2.60 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C05 PGV G 101 " pdb=" C04 PGV G 101 " pdb=" C06 PGV G 101 " pdb=" O05 PGV G 101 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3952 not shown) Planarity restraints: 4804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 3 102 " -0.395 3.00e-02 1.11e+03 3.23e-01 5.80e+02 pdb=" CBA BCL 3 102 " -0.147 3.00e-02 1.11e+03 pdb=" CGA BCL 3 102 " 0.089 3.00e-02 1.11e+03 pdb=" O1A BCL 3 102 " -0.116 3.00e-02 1.11e+03 pdb=" O2A BCL 3 102 " 0.569 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 102 " -0.374 3.00e-02 1.11e+03 3.12e-01 5.40e+02 pdb=" CBA BCL Z 102 " -0.094 3.00e-02 1.11e+03 pdb=" CGA BCL Z 102 " 0.077 3.00e-02 1.11e+03 pdb=" O1A BCL Z 102 " -0.160 3.00e-02 1.11e+03 pdb=" O2A BCL Z 102 " 0.552 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 403 " -0.358 3.00e-02 1.11e+03 3.00e-01 4.99e+02 pdb=" CBA BCL M 403 " -0.107 3.00e-02 1.11e+03 pdb=" CGA BCL M 403 " 0.076 3.00e-02 1.11e+03 pdb=" O1A BCL M 403 " -0.142 3.00e-02 1.11e+03 pdb=" O2A BCL M 403 " 0.532 3.00e-02 1.11e+03 ... (remaining 4801 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 156 2.45 - 3.06: 17470 3.06 - 3.68: 46580 3.68 - 4.29: 77836 4.29 - 4.90: 123162 Nonbonded interactions: 265204 Sorted by model distance: nonbonded pdb="MG MG C 405 " pdb=" O HOH C 504 " model vdw 1.839 2.170 nonbonded pdb="MG MG C 405 " pdb=" O HOH C 503 " model vdw 1.990 2.170 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 401 " model vdw 1.996 2.340 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 1.998 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.074 2.260 ... (remaining 265199 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) selection = (chain '5' and resid 1 through 46) selection = (chain '9' and resid 1 through 46) selection = (chain 'D' and resid 1 through 46) selection = (chain 'I' and resid 1 through 46) selection = (chain 'O' and resid 1 through 46) selection = (chain 'S' and resid 1 through 46) selection = (chain 'W' and resid 1 through 46) } 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) selection = (chain '8' and resid 7 through 53) selection = (chain 'B' and resid 7 through 53) selection = (chain 'G' and resid 7 through 53) selection = (chain 'N' and resid 7 through 53) selection = (chain 'R' and resid 7 through 53) selection = (chain 'V' and resid 7 through 53) selection = (chain 'Z' and resid 7 through 53) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.180 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.538 30171 Z= 1.126 Angle : 2.039 27.472 41219 Z= 0.832 Chirality : 0.058 0.304 3955 Planarity : 0.023 0.323 4804 Dihedral : 24.188 178.982 12268 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.42 % Allowed : 7.21 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.15), residues: 2699 helix: 2.09 (0.12), residues: 1536 sheet: 0.33 (0.67), residues: 59 loop : 0.05 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 11 TYR 0.017 0.001 TYR L 164 PHE 0.024 0.001 PHE C 345 TRP 0.016 0.001 TRP F 5 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd/Z covalent geometry : bond 0.02066 / 0.91 (30108) covalent geometry : angle 2.02114 / 0.83 (41207) hydrogen bonds : bond 0.16693 / 11.14 ( 1369) hydrogen bonds : angle 5.69938 / 3.95 ( 3861) metal coordination : bond 0.25979 / 13.05 ( 4) metal coordination : angle 15.77302 / 8.50 ( 12) Misc. bond : bond 0.17976 / 12.68 ( 59) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: L 57 ASP cc_start: 0.6714 (p0) cc_final: 0.6486 (t0) REVERT: M 218 MET cc_start: 0.9165 (mtp) cc_final: 0.8903 (mtp) REVERT: H 92 THR cc_start: 0.6936 (m) cc_final: 0.6667 (m) REVERT: F 3 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.7147 (mtt180) REVERT: G 7 LEU cc_start: 0.3165 (OUTLIER) cc_final: 0.2921 (tp) REVERT: J 17 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6444 (mm-30) REVERT: O 4 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7234 (tpt) REVERT: P 17 GLU cc_start: 0.7207 (pt0) cc_final: 0.6951 (pt0) REVERT: R 23 MET cc_start: 0.7872 (mmm) cc_final: 0.7672 (mmp) REVERT: T 51 GLU cc_start: 0.6741 (mp0) cc_final: 0.6479 (mp0) REVERT: U 11 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6966 (ttp-170) REVERT: V 13 GLU cc_start: 0.5992 (tm-30) cc_final: 0.5609 (tm-30) REVERT: V 14 GLU cc_start: 0.7182 (tp30) cc_final: 0.6797 (tp30) REVERT: W 11 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6623 (mtm-85) REVERT: 1 36 GLU cc_start: 0.7453 (tt0) cc_final: 0.7237 (tt0) REVERT: 3 7 LEU cc_start: 0.7794 (mt) cc_final: 0.7439 (mm) REVERT: 4 24 GLN cc_start: 0.6806 (mt0) cc_final: 0.6514 (mt0) REVERT: 7 9 ASP cc_start: 0.7037 (t70) cc_final: 0.6702 (t70) REVERT: 8 38 PHE cc_start: 0.7909 (m-80) cc_final: 0.7702 (m-80) REVERT: 8 51 GLU cc_start: 0.6819 (pm20) cc_final: 0.6462 (pm20) REVERT: 0 14 GLU cc_start: 0.6432 (pt0) cc_final: 0.6206 (pt0) outliers start: 55 outliers final: 27 residues processed: 397 average time/residue: 0.7328 time to fit residues: 335.7899 Evaluate side-chains 344 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 53 LEU 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 12 ASN Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 96 GLN L 213 ASN L 239 ASN H 138 GLN R 24 GLN Z 24 GLN 0 24 GLN a 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097720 restraints weight = 36985.046| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.19 r_work: 0.3118 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.485 30171 Z= 0.148 Angle : 0.768 16.065 41219 Z= 0.293 Chirality : 0.041 0.323 3955 Planarity : 0.004 0.066 4804 Dihedral : 24.494 176.236 7416 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 9.84 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 2699 helix: 2.12 (0.12), residues: 1554 sheet: 0.34 (0.68), residues: 59 loop : -0.08 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.015 0.001 TYR L 164 PHE 0.022 0.001 PHE C 345 TRP 0.017 0.001 TRP M 271 HIS 0.006 0.002 HIS W 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (30108) covalent geometry : angle 0.75597 / 0.29 (41207) hydrogen bonds : bond 0.05170 / 3.47 ( 1369) hydrogen bonds : angle 4.41155 / 3.09 ( 3861) metal coordination : bond 0.01381 / 0.68 ( 4) metal coordination : angle 7.97423 / 4.07 ( 12) Misc. bond : bond 0.07939 / 4.86 ( 59) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.776 Fit side-chains REVERT: M 14 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7241 (ttp80) REVERT: M 216 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8357 (t80) REVERT: M 218 MET cc_start: 0.9073 (mtp) cc_final: 0.8654 (mtp) REVERT: H 92 THR cc_start: 0.6747 (m) cc_final: 0.6400 (m) REVERT: H 138 GLN cc_start: 0.8063 (tt0) cc_final: 0.7862 (tt0) REVERT: H 150 GLU cc_start: 0.7494 (pt0) cc_final: 0.6788 (pm20) REVERT: F 3 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7144 (mtt180) REVERT: G 14 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: J 17 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6585 (mm-30) REVERT: K 1 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6702 (tpt) REVERT: O 1 MET cc_start: 0.6431 (mmm) cc_final: 0.6230 (mmm) REVERT: O 4 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7435 (tpt) REVERT: R 23 MET cc_start: 0.8027 (mmm) cc_final: 0.7760 (mmp) REVERT: U 3 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7143 (mtp85) REVERT: V 13 GLU cc_start: 0.5925 (tm-30) cc_final: 0.5627 (tm-30) REVERT: W 9 ASP cc_start: 0.7930 (t0) cc_final: 0.7706 (t0) REVERT: W 42 GLN cc_start: 0.8235 (tp40) cc_final: 0.7919 (tp-100) REVERT: 1 11 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7559 (ttm170) REVERT: 1 36 GLU cc_start: 0.7926 (tt0) cc_final: 0.7612 (tt0) REVERT: 7 9 ASP cc_start: 0.7057 (t70) cc_final: 0.6552 (t0) REVERT: 7 12 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6691 (mtt180) REVERT: 8 23 MET cc_start: 0.8098 (mmp) cc_final: 0.7714 (mmm) REVERT: 8 38 PHE cc_start: 0.7879 (m-80) cc_final: 0.7648 (m-80) REVERT: 8 51 GLU cc_start: 0.6893 (pm20) cc_final: 0.6429 (pm20) REVERT: 9 21 MET cc_start: 0.8142 (mmm) cc_final: 0.7880 (mmp) REVERT: 0 14 GLU cc_start: 0.6307 (pt0) cc_final: 0.6031 (pt0) REVERT: a 40 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7170 (t0) outliers start: 69 outliers final: 37 residues processed: 379 average time/residue: 0.6946 time to fit residues: 303.6173 Evaluate side-chains 361 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 53 LEU 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 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 8 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 43 ASN Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 4 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 GLN C 135 ASN R 24 GLN Z 24 GLN 0 24 GLN a 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094248 restraints weight = 37054.326| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.16 r_work: 0.3047 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.523 30171 Z= 0.329 Angle : 1.056 23.567 41219 Z= 0.402 Chirality : 0.051 0.506 3955 Planarity : 0.006 0.066 4804 Dihedral : 24.828 175.302 7406 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 10.68 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 2699 helix: 1.50 (0.12), residues: 1557 sheet: -0.01 (0.69), residues: 59 loop : -0.30 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.025 0.003 TYR L 164 PHE 0.029 0.003 PHE C 345 TRP 0.023 0.003 TRP M 271 HIS 0.014 0.003 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.33 (30108) covalent geometry : angle 1.04846 / 0.40 (41207) hydrogen bonds : bond 0.05888 / 3.92 ( 1369) hydrogen bonds : angle 4.62632 / 3.24 ( 3861) metal coordination : bond 0.01353 / 0.66 ( 4) metal coordination : angle 7.41113 / 4.04 ( 12) Misc. bond : bond 0.08758 / 5.71 ( 59) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 331 time to evaluate : 0.644 Fit side-chains REVERT: C 84 ASP cc_start: 0.7043 (m-30) cc_final: 0.6777 (m-30) REVERT: C 177 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: L 202 LYS cc_start: 0.6162 (mppt) cc_final: 0.5659 (tttt) REVERT: M 216 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8426 (t80) REVERT: H 53 ARG cc_start: 0.6927 (mpp-170) cc_final: 0.6697 (mpp80) REVERT: H 92 THR cc_start: 0.6721 (m) cc_final: 0.6416 (m) REVERT: G 14 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: J 17 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6691 (mm-30) REVERT: K 1 MET cc_start: 0.7235 (tpp) cc_final: 0.6898 (tpt) REVERT: O 4 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7055 (mmp) REVERT: S 1 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.3952 (mmp) REVERT: S 9 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7371 (t70) REVERT: U 3 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7086 (mtp85) REVERT: U 12 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6433 (mtp85) REVERT: V 13 GLU cc_start: 0.5869 (tm-30) cc_final: 0.5570 (tm-30) REVERT: V 14 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: W 1 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5468 (tpp) REVERT: W 9 ASP cc_start: 0.7889 (t70) cc_final: 0.7659 (t0) REVERT: W 42 GLN cc_start: 0.8148 (tp40) cc_final: 0.7827 (tp40) REVERT: 1 36 GLU cc_start: 0.7892 (tt0) cc_final: 0.7563 (tt0) REVERT: 7 9 ASP cc_start: 0.7149 (t70) cc_final: 0.6814 (t0) REVERT: 8 23 MET cc_start: 0.8217 (mmp) cc_final: 0.7895 (mmm) REVERT: 8 38 PHE cc_start: 0.7868 (m-80) cc_final: 0.7658 (m-80) REVERT: 8 51 GLU cc_start: 0.7086 (pm20) cc_final: 0.6651 (pm20) REVERT: 9 11 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: 9 21 MET cc_start: 0.8203 (mmm) cc_final: 0.7936 (mmp) REVERT: a 122 ASP cc_start: 0.7805 (t0) cc_final: 0.7603 (t0) outliers start: 95 outliers final: 51 residues processed: 391 average time/residue: 0.6372 time to fit residues: 287.9792 Evaluate side-chains 373 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU 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 276 CYS Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 11 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 127 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 135 ASN I 18 HIS R 24 GLN 0 24 GLN a 39 ASN a 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096533 restraints weight = 36884.024| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.18 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.471 30171 Z= 0.181 Angle : 0.770 16.016 41219 Z= 0.295 Chirality : 0.041 0.463 3955 Planarity : 0.004 0.067 4804 Dihedral : 23.158 177.506 7405 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.78 % Allowed : 11.86 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2699 helix: 1.84 (0.12), residues: 1554 sheet: 0.10 (0.70), residues: 59 loop : -0.21 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 93 TYR 0.017 0.002 TYR L 164 PHE 0.022 0.002 PHE C 345 TRP 0.017 0.001 TRP M 271 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (30108) covalent geometry : angle 0.76392 / 0.30 (41207) hydrogen bonds : bond 0.04871 / 3.26 ( 1369) hydrogen bonds : angle 4.33548 / 3.04 ( 3861) metal coordination : bond 0.00928 / 0.46 ( 4) metal coordination : angle 5.77222 / 3.12 ( 12) Misc. bond : bond 0.07864 / 5.08 ( 59) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 324 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 ASP cc_start: 0.7089 (m-30) cc_final: 0.6873 (m-30) REVERT: M 18 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.6075 (t70) REVERT: M 75 MET cc_start: 0.9136 (mtt) cc_final: 0.8934 (mtt) REVERT: M 216 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8286 (t80) REVERT: H 53 ARG cc_start: 0.6903 (mpp-170) cc_final: 0.6683 (mpp80) REVERT: H 82 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6850 (mtt180) REVERT: H 92 THR cc_start: 0.6763 (m) cc_final: 0.6449 (m) REVERT: H 150 GLU cc_start: 0.7568 (pt0) cc_final: 0.7275 (pm20) REVERT: G 14 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6795 (mt-10) REVERT: J 17 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6678 (mm-30) REVERT: K 1 MET cc_start: 0.7217 (tpp) cc_final: 0.6893 (tpt) REVERT: U 3 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7102 (mtp85) REVERT: U 8 TYR cc_start: 0.8046 (m-80) cc_final: 0.7828 (m-80) REVERT: U 12 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6436 (mtp85) REVERT: V 13 GLU cc_start: 0.5985 (tm-30) cc_final: 0.5689 (tm-30) REVERT: V 27 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7519 (mt) REVERT: W 1 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5414 (tpp) REVERT: W 9 ASP cc_start: 0.7857 (t70) cc_final: 0.7554 (t0) REVERT: W 11 ARG cc_start: 0.7155 (mtt90) cc_final: 0.6743 (mtm-85) REVERT: W 42 GLN cc_start: 0.8166 (tp40) cc_final: 0.7826 (tp40) REVERT: 1 36 GLU cc_start: 0.7959 (tt0) cc_final: 0.7604 (tt0) REVERT: 7 9 ASP cc_start: 0.7121 (t70) cc_final: 0.6584 (t0) REVERT: 7 12 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6753 (mtt180) REVERT: 8 23 MET cc_start: 0.8159 (mmp) cc_final: 0.7745 (mmm) REVERT: 8 38 PHE cc_start: 0.7857 (m-80) cc_final: 0.7580 (m-80) REVERT: 8 51 GLU cc_start: 0.7085 (pm20) cc_final: 0.6586 (pm20) REVERT: 9 21 MET cc_start: 0.8211 (mmm) cc_final: 0.7941 (mmp) REVERT: a 122 ASP cc_start: 0.7842 (t0) cc_final: 0.7629 (t70) outliers start: 86 outliers final: 45 residues processed: 378 average time/residue: 0.6612 time to fit residues: 288.9358 Evaluate side-chains 370 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 53 LEU 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 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 8 LEU Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 238 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN a 39 ASN a 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096905 restraints weight = 36917.839| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.19 r_work: 0.3101 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.426 30171 Z= 0.156 Angle : 0.759 15.435 41219 Z= 0.289 Chirality : 0.040 0.438 3955 Planarity : 0.004 0.064 4804 Dihedral : 22.029 173.818 7405 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.60 % Allowed : 12.43 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 2699 helix: 2.00 (0.12), residues: 1548 sheet: 0.07 (0.70), residues: 59 loop : -0.14 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 109 TYR 0.017 0.001 TYR L 164 PHE 0.021 0.002 PHE C 345 TRP 0.015 0.001 TRP M 271 HIS 0.007 0.002 HIS W 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (30108) covalent geometry : angle 0.75342 / 0.29 (41207) hydrogen bonds : bond 0.04734 / 3.17 ( 1369) hydrogen bonds : angle 4.24309 / 2.98 ( 3861) metal coordination : bond 0.01000 / 0.49 ( 4) metal coordination : angle 5.48916 / 2.94 ( 12) Misc. bond : bond 0.07275 / 4.70 ( 59) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 0.938 Fit side-chains REVERT: C 72 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7206 (mmp-170) REVERT: C 84 ASP cc_start: 0.7086 (m-30) cc_final: 0.6875 (m-30) REVERT: C 241 MET cc_start: 0.9036 (mmt) cc_final: 0.8561 (mmt) REVERT: M 216 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8202 (t80) REVERT: H 53 ARG cc_start: 0.6895 (mpp-170) cc_final: 0.6668 (mpp80) REVERT: H 82 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6785 (mtt180) REVERT: H 92 THR cc_start: 0.6769 (m) cc_final: 0.6446 (m) REVERT: H 150 GLU cc_start: 0.7517 (pt0) cc_final: 0.7306 (pm20) REVERT: J 17 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6669 (mm-30) REVERT: N 10 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6108 (tp) REVERT: O 4 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7284 (tpt) REVERT: S 1 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.3903 (mmp) REVERT: S 9 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7096 (t70) REVERT: U 3 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7141 (mtp85) REVERT: U 8 TYR cc_start: 0.8084 (m-80) cc_final: 0.7845 (m-80) REVERT: U 12 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6430 (mtp85) REVERT: V 13 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5708 (tm-30) REVERT: V 27 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7491 (mt) REVERT: W 1 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5427 (tpp) REVERT: W 9 ASP cc_start: 0.7846 (t70) cc_final: 0.7533 (t0) REVERT: W 11 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6802 (mtm-85) REVERT: W 42 GLN cc_start: 0.8136 (tp40) cc_final: 0.7812 (tp40) REVERT: 1 36 GLU cc_start: 0.7975 (tt0) cc_final: 0.7618 (tt0) REVERT: 7 12 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6452 (mtt-85) REVERT: 8 23 MET cc_start: 0.8197 (mmp) cc_final: 0.7935 (mmm) REVERT: 8 38 PHE cc_start: 0.7875 (m-80) cc_final: 0.7598 (m-80) REVERT: 8 51 GLU cc_start: 0.7074 (pm20) cc_final: 0.6577 (pm20) REVERT: 9 21 MET cc_start: 0.8197 (mmm) cc_final: 0.7943 (mmp) REVERT: 0 17 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: a 81 PHE cc_start: 0.7315 (m-80) cc_final: 0.6800 (m-80) REVERT: a 105 MET cc_start: 0.7573 (mmt) cc_final: 0.7341 (tpp) REVERT: a 122 ASP cc_start: 0.7882 (t0) cc_final: 0.7551 (t70) outliers start: 82 outliers final: 47 residues processed: 375 average time/residue: 0.6587 time to fit residues: 285.5385 Evaluate side-chains 368 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU 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 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 3 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 GLN R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096294 restraints weight = 36702.900| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.15 r_work: 0.3095 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.443 30171 Z= 0.181 Angle : 0.806 15.200 41219 Z= 0.307 Chirality : 0.041 0.421 3955 Planarity : 0.004 0.067 4804 Dihedral : 21.829 174.546 7404 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.82 % Allowed : 12.79 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2699 helix: 1.89 (0.12), residues: 1553 sheet: 0.08 (0.69), residues: 59 loop : -0.16 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 11 TYR 0.020 0.002 TYR L 164 PHE 0.023 0.002 PHE C 345 TRP 0.017 0.002 TRP M 271 HIS 0.009 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (30108) covalent geometry : angle 0.80019 / 0.31 (41207) hydrogen bonds : bond 0.04924 / 3.29 ( 1369) hydrogen bonds : angle 4.29745 / 3.01 ( 3861) metal coordination : bond 0.00976 / 0.48 ( 4) metal coordination : angle 5.74584 / 3.10 ( 12) Misc. bond : bond 0.07691 / 4.96 ( 59) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 315 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: C 84 ASP cc_start: 0.7032 (m-30) cc_final: 0.6828 (m-30) REVERT: M 216 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8305 (t80) REVERT: H 53 ARG cc_start: 0.6918 (mpp-170) cc_final: 0.6694 (mpp80) REVERT: H 82 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6823 (mtt180) REVERT: H 92 THR cc_start: 0.6776 (m) cc_final: 0.6465 (m) REVERT: H 93 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: J 17 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6687 (mm-30) REVERT: N 10 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6067 (tp) REVERT: S 1 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.5059 (mmp) REVERT: S 9 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7132 (t70) REVERT: U 3 ARG cc_start: 0.7652 (mtp85) cc_final: 0.7165 (mtp85) REVERT: U 12 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6386 (mtp85) REVERT: V 13 GLU cc_start: 0.6000 (tm-30) cc_final: 0.5678 (tm-30) REVERT: V 27 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7534 (mt) REVERT: W 1 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5553 (tpp) REVERT: W 9 ASP cc_start: 0.7800 (t70) cc_final: 0.7475 (t0) REVERT: W 42 GLN cc_start: 0.8137 (tp40) cc_final: 0.7813 (tp40) REVERT: 1 36 GLU cc_start: 0.7928 (tt0) cc_final: 0.7585 (tt0) REVERT: 7 12 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6660 (mtt-85) REVERT: 8 23 MET cc_start: 0.8204 (mmp) cc_final: 0.7902 (mmm) REVERT: 8 38 PHE cc_start: 0.7880 (m-80) cc_final: 0.7619 (m-80) REVERT: 8 51 GLU cc_start: 0.7132 (pm20) cc_final: 0.6632 (pm20) REVERT: 9 21 MET cc_start: 0.8229 (mmm) cc_final: 0.7984 (mmp) REVERT: a 122 ASP cc_start: 0.7855 (t0) cc_final: 0.7522 (t70) outliers start: 87 outliers final: 52 residues processed: 376 average time/residue: 0.6539 time to fit residues: 284.9347 Evaluate side-chains 365 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU 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 276 CYS Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN a 39 ASN a 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095709 restraints weight = 36668.993| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.15 r_work: 0.3082 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.481 30171 Z= 0.226 Angle : 0.890 18.573 41219 Z= 0.337 Chirality : 0.044 0.414 3955 Planarity : 0.005 0.066 4804 Dihedral : 22.033 175.407 7401 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.78 % Allowed : 13.22 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2699 helix: 1.72 (0.12), residues: 1553 sheet: 0.13 (0.70), residues: 59 loop : -0.23 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 11 TYR 0.022 0.002 TYR L 164 PHE 0.026 0.002 PHE C 345 TRP 0.018 0.002 TRP M 271 HIS 0.011 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (30108) covalent geometry : angle 0.88405 / 0.34 (41207) hydrogen bonds : bond 0.05175 / 3.45 ( 1369) hydrogen bonds : angle 4.41187 / 3.09 ( 3861) metal coordination : bond 0.01073 / 0.53 ( 4) metal coordination : angle 6.15631 / 3.39 ( 12) Misc. bond : bond 0.08248 / 5.29 ( 59) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 310 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: C 84 ASP cc_start: 0.6962 (m-30) cc_final: 0.6734 (m-30) REVERT: C 241 MET cc_start: 0.9090 (mmt) cc_final: 0.8667 (mmt) REVERT: L 202 LYS cc_start: 0.6296 (mppt) cc_final: 0.5747 (tttt) REVERT: M 18 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.6107 (t70) REVERT: M 216 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8318 (t80) REVERT: H 53 ARG cc_start: 0.6967 (mpp-170) cc_final: 0.6722 (mpp80) REVERT: H 82 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6767 (mtt180) REVERT: H 92 THR cc_start: 0.6732 (m) cc_final: 0.6423 (m) REVERT: H 93 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.5955 (tt0) REVERT: B 28 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8172 (mp) REVERT: J 17 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6713 (mm-30) REVERT: N 10 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6020 (tp) REVERT: S 1 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.4006 (mmp) REVERT: S 9 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7332 (t70) REVERT: U 3 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7111 (mtp85) REVERT: U 12 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6408 (mtp85) REVERT: V 13 GLU cc_start: 0.6022 (tm-30) cc_final: 0.5708 (tm-30) REVERT: W 1 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5479 (tpp) REVERT: W 9 ASP cc_start: 0.7802 (t70) cc_final: 0.7477 (t0) REVERT: W 11 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6863 (mtt-85) REVERT: W 42 GLN cc_start: 0.8141 (tp40) cc_final: 0.7814 (tp40) REVERT: 1 36 GLU cc_start: 0.7905 (tt0) cc_final: 0.7575 (tt0) REVERT: 7 12 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7124 (mtt180) REVERT: 8 23 MET cc_start: 0.8184 (mmp) cc_final: 0.7841 (mmm) REVERT: 8 38 PHE cc_start: 0.7859 (m-80) cc_final: 0.7621 (m-80) REVERT: 8 51 GLU cc_start: 0.7119 (pm20) cc_final: 0.6596 (pm20) REVERT: 9 11 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6717 (mtp180) REVERT: 9 21 MET cc_start: 0.8245 (mmm) cc_final: 0.8001 (mmp) REVERT: a 105 MET cc_start: 0.7510 (mmt) cc_final: 0.7242 (mmt) REVERT: a 122 ASP cc_start: 0.7776 (t0) cc_final: 0.7565 (t70) outliers start: 86 outliers final: 53 residues processed: 371 average time/residue: 0.7133 time to fit residues: 306.0835 Evaluate side-chains 369 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU 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 276 CYS Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 11 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 108 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 44 ASN ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098483 restraints weight = 36790.287| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.18 r_work: 0.3132 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.398 30171 Z= 0.130 Angle : 0.710 15.916 41219 Z= 0.273 Chirality : 0.038 0.389 3955 Planarity : 0.004 0.066 4804 Dihedral : 20.890 174.074 7399 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 14.19 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.16), residues: 2699 helix: 2.07 (0.12), residues: 1547 sheet: 0.12 (0.74), residues: 54 loop : -0.15 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 11 TYR 0.014 0.001 TYR L 164 PHE 0.024 0.001 PHE G 26 TRP 0.025 0.001 TRP 7 2 HIS 0.005 0.001 HIS M 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (30108) covalent geometry : angle 0.70456 / 0.27 (41207) hydrogen bonds : bond 0.04509 / 3.03 ( 1369) hydrogen bonds : angle 4.19505 / 2.94 ( 3861) metal coordination : bond 0.00749 / 0.37 ( 4) metal coordination : angle 5.11532 / 2.71 ( 12) Misc. bond : bond 0.06608 / 4.17 ( 59) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 313 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: C 72 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7147 (mmp-170) REVERT: C 84 ASP cc_start: 0.7102 (m-30) cc_final: 0.6844 (m-30) REVERT: C 177 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7135 (mmm) REVERT: C 311 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: M 18 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6083 (t70) REVERT: M 216 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8152 (t80) REVERT: M 218 MET cc_start: 0.8976 (mtp) cc_final: 0.8543 (mtm) REVERT: H 53 ARG cc_start: 0.6941 (mpp-170) cc_final: 0.6695 (mpp80) REVERT: H 82 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6750 (mtt180) REVERT: H 92 THR cc_start: 0.6766 (m) cc_final: 0.6446 (m) REVERT: H 194 LEU cc_start: 0.7597 (mm) cc_final: 0.7314 (mt) REVERT: J 17 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6658 (mm-30) REVERT: S 1 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4259 (tpt) REVERT: U 3 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7128 (mtp85) REVERT: V 13 GLU cc_start: 0.5982 (tm-30) cc_final: 0.5638 (tm-30) REVERT: V 14 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: V 27 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7290 (mm) REVERT: W 1 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5409 (tpp) REVERT: W 9 ASP cc_start: 0.7687 (t70) cc_final: 0.7322 (t0) REVERT: W 11 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6436 (mtp180) REVERT: W 42 GLN cc_start: 0.8143 (tp40) cc_final: 0.7815 (tp40) REVERT: 1 36 GLU cc_start: 0.7936 (tt0) cc_final: 0.7712 (tp30) REVERT: 4 38 PHE cc_start: 0.7977 (m-80) cc_final: 0.7740 (m-10) REVERT: 7 12 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6464 (mtt-85) REVERT: 8 38 PHE cc_start: 0.7859 (m-80) cc_final: 0.7577 (m-80) REVERT: 8 51 GLU cc_start: 0.7090 (pm20) cc_final: 0.6653 (pm20) REVERT: 9 21 MET cc_start: 0.8249 (mmm) cc_final: 0.7985 (mmp) REVERT: 0 17 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: a 40 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6471 (m-40) REVERT: a 70 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5732 (p0) REVERT: a 81 PHE cc_start: 0.7322 (m-80) cc_final: 0.6762 (m-80) REVERT: a 105 MET cc_start: 0.7471 (mmt) cc_final: 0.7190 (mmt) REVERT: a 122 ASP cc_start: 0.7774 (t0) cc_final: 0.7433 (t70) outliers start: 66 outliers final: 34 residues processed: 360 average time/residue: 0.6516 time to fit residues: 270.9567 Evaluate side-chains 340 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 53 LEU 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 H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 142 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096035 restraints weight = 36581.307| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.14 r_work: 0.3086 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.450 30171 Z= 0.215 Angle : 0.870 16.677 41219 Z= 0.330 Chirality : 0.043 0.394 3955 Planarity : 0.005 0.064 4804 Dihedral : 21.373 179.269 7396 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.81 % Allowed : 14.89 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2699 helix: 1.85 (0.12), residues: 1547 sheet: 0.12 (0.69), residues: 59 loop : -0.21 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 11 TYR 0.022 0.002 TYR L 164 PHE 0.025 0.002 PHE C 345 TRP 0.027 0.002 TRP 7 2 HIS 0.011 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (30108) covalent geometry : angle 0.86370 / 0.33 (41207) hydrogen bonds : bond 0.05074 / 3.38 ( 1369) hydrogen bonds : angle 4.34327 / 3.04 ( 3861) metal coordination : bond 0.00932 / 0.46 ( 4) metal coordination : angle 6.17052 / 3.37 ( 12) Misc. bond : bond 0.08199 / 5.33 ( 59) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: C 84 ASP cc_start: 0.6944 (m-30) cc_final: 0.6718 (m-30) REVERT: C 311 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: L 202 LYS cc_start: 0.6291 (mppt) cc_final: 0.5732 (tttt) REVERT: M 216 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8315 (t80) REVERT: H 53 ARG cc_start: 0.6958 (mpp-170) cc_final: 0.6716 (mpp80) REVERT: H 82 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6776 (mtt180) REVERT: H 92 THR cc_start: 0.6737 (m) cc_final: 0.6433 (m) REVERT: B 28 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (mp) REVERT: J 17 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6694 (mm-30) REVERT: N 10 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6074 (tp) REVERT: S 1 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4275 (mmp) REVERT: S 8 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.6924 (pp) REVERT: U 3 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7114 (mtp85) REVERT: U 12 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6443 (mtp85) REVERT: V 13 GLU cc_start: 0.5970 (tm-30) cc_final: 0.5655 (tm-30) REVERT: V 27 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7351 (mm) REVERT: W 1 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5540 (tpp) REVERT: W 9 ASP cc_start: 0.7677 (t70) cc_final: 0.7382 (t0) REVERT: W 42 GLN cc_start: 0.8158 (tp40) cc_final: 0.7833 (tp40) REVERT: X 21 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7625 (mtm) REVERT: 1 36 GLU cc_start: 0.7910 (tt0) cc_final: 0.7575 (tt0) REVERT: 7 12 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7034 (mtt180) REVERT: 8 23 MET cc_start: 0.8253 (mmp) cc_final: 0.7774 (mmm) REVERT: 8 38 PHE cc_start: 0.7877 (m-80) cc_final: 0.7640 (m-80) REVERT: 8 51 GLU cc_start: 0.7160 (pm20) cc_final: 0.6634 (pm20) REVERT: 9 21 MET cc_start: 0.8239 (mmm) cc_final: 0.7995 (mmp) REVERT: a 40 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6453 (m-40) REVERT: a 105 MET cc_start: 0.7473 (mmt) cc_final: 0.7224 (mmt) outliers start: 64 outliers final: 43 residues processed: 347 average time/residue: 0.6954 time to fit residues: 277.7081 Evaluate side-chains 352 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 21 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 13 optimal weight: 30.0000 chunk 237 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098204 restraints weight = 36753.255| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.19 r_work: 0.3126 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.400 30171 Z= 0.132 Angle : 0.723 16.504 41219 Z= 0.279 Chirality : 0.038 0.376 3955 Planarity : 0.004 0.067 4804 Dihedral : 20.665 176.886 7396 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 15.47 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.16), residues: 2699 helix: 2.08 (0.12), residues: 1544 sheet: 0.11 (0.74), residues: 54 loop : -0.16 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 109 TYR 0.015 0.001 TYR L 164 PHE 0.024 0.001 PHE G 26 TRP 0.034 0.001 TRP 7 2 HIS 0.005 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (30108) covalent geometry : angle 0.71769 / 0.28 (41207) hydrogen bonds : bond 0.04553 / 3.05 ( 1369) hydrogen bonds : angle 4.19447 / 2.94 ( 3861) metal coordination : bond 0.00603 / 0.30 ( 4) metal coordination : angle 5.38049 / 2.88 ( 12) Misc. bond : bond 0.06957 / 4.49 ( 59) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: C 72 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7165 (mmp-170) REVERT: C 84 ASP cc_start: 0.7136 (m-30) cc_final: 0.6859 (m-30) REVERT: C 311 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: M 216 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8173 (t80) REVERT: M 218 MET cc_start: 0.8981 (mtp) cc_final: 0.8551 (mtm) REVERT: H 53 ARG cc_start: 0.6926 (mpp-170) cc_final: 0.6685 (mpp80) REVERT: H 82 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6781 (mtt180) REVERT: H 92 THR cc_start: 0.6763 (m) cc_final: 0.6445 (m) REVERT: H 194 LEU cc_start: 0.7617 (mm) cc_final: 0.7374 (mt) REVERT: J 17 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6662 (mm-30) REVERT: S 1 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.4259 (tpt) REVERT: S 8 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6902 (pp) REVERT: U 3 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7088 (mtp85) REVERT: V 13 GLU cc_start: 0.6009 (tm-30) cc_final: 0.5682 (tm-30) REVERT: V 27 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7252 (mm) REVERT: W 1 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5468 (tpp) REVERT: W 9 ASP cc_start: 0.7645 (t70) cc_final: 0.7299 (t0) REVERT: W 42 GLN cc_start: 0.8135 (tp40) cc_final: 0.7809 (tp40) REVERT: X 21 MET cc_start: 0.8237 (ptm) cc_final: 0.7792 (mtm) REVERT: 1 36 GLU cc_start: 0.7954 (tt0) cc_final: 0.7595 (tt0) REVERT: 4 38 PHE cc_start: 0.7956 (m-80) cc_final: 0.7738 (m-10) REVERT: 7 12 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6497 (mtt-85) REVERT: 8 23 MET cc_start: 0.8213 (mmp) cc_final: 0.7725 (mmm) REVERT: 8 38 PHE cc_start: 0.7866 (m-80) cc_final: 0.7623 (m-80) REVERT: 8 51 GLU cc_start: 0.7142 (pm20) cc_final: 0.6704 (pm20) REVERT: 9 21 MET cc_start: 0.8249 (mmm) cc_final: 0.7986 (mmp) REVERT: 0 17 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: a 40 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6431 (m-40) REVERT: a 70 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5811 (p0) REVERT: a 81 PHE cc_start: 0.7310 (m-80) cc_final: 0.6629 (m-80) REVERT: a 105 MET cc_start: 0.7518 (mmt) cc_final: 0.7228 (mmt) outliers start: 49 outliers final: 31 residues processed: 340 average time/residue: 0.7113 time to fit residues: 278.2341 Evaluate side-chains 341 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 53 LEU 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 H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 240 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN a 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095287 restraints weight = 36823.816| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.15 r_work: 0.3071 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.473 30171 Z= 0.263 Angle : 0.956 19.607 41219 Z= 0.362 Chirality : 0.046 0.394 3955 Planarity : 0.005 0.064 4804 Dihedral : 21.518 177.619 7395 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.72 % Allowed : 15.16 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2699 helix: 1.67 (0.12), residues: 1548 sheet: 0.11 (0.70), residues: 59 loop : -0.24 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 109 TYR 0.024 0.002 TYR L 164 PHE 0.027 0.003 PHE C 345 TRP 0.032 0.002 TRP 7 2 HIS 0.014 0.003 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (30108) covalent geometry : angle 0.94954 / 0.36 (41207) hydrogen bonds : bond 0.05340 / 3.55 ( 1369) hydrogen bonds : angle 4.44416 / 3.11 ( 3861) metal coordination : bond 0.01110 / 0.55 ( 4) metal coordination : angle 6.71600 / 3.71 ( 12) Misc. bond : bond 0.08522 / 5.54 ( 59) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10671.61 seconds wall clock time: 182 minutes 1.84 seconds (10921.84 seconds total)