Starting phenix.real_space_refine on Tue Jun 24 16:45:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_39836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_39836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_39836.map" model { file = "/net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_39836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z82_39836/06_2025/8z82_39836.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PGV:plan-3': 1, 'UQ8:plan-4': 1, 'UQ8:plan-6': 3, 'UQ8:plan-7': 3, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-8': 3, 'UQ8:plan-9': 2} 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: 186 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: 74 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: 17.63, per 1000 atoms: 0.61 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: 8.91 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.32 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: 7.99 Time building geometry restraints manager: 10.09 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=" CA7 CDL S 101 " pdb=" OA8 CDL S 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL M 408 " pdb=" OB8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL M 402 " pdb=" OB8 CDL M 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL M 409 " pdb=" OB8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL S 101 " pdb=" OB8 CDL S 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 ... (remaining 30103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 39301 4.95 - 9.90: 1740 9.90 - 14.84: 122 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: 15833 35.80 - 71.59: 1156 71.59 - 107.39: 170 107.39 - 143.19: 65 143.19 - 178.98: 22 Dihedral angle restraints: 17246 sinusoidal: 9303 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 17243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3253 0.061 - 0.122: 482 0.122 - 0.182: 154 0.182 - 0.243: 33 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 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: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 66.990 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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= 1.157 Angle : 2.031 27.472 41219 Z= 0.859 Chirality : 0.058 0.304 3955 Planarity : 0.023 0.323 4804 Dihedral : 24.514 178.982 12126 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP F 5 HIS 0.007 0.002 HIS W 29 PHE 0.024 0.001 PHE C 345 TYR 0.017 0.001 TYR L 164 ARG 0.004 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.16693 ( 1369) hydrogen bonds : angle 5.69938 ( 3861) metal coordination : bond 0.25979 ( 4) metal coordination : angle 15.77302 ( 12) covalent geometry : bond 0.02067 (30108) covalent geometry : angle 2.01353 (41207) Misc. bond : bond 0.17976 ( 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 : 2.551 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: 0.8933 (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: 1.9094 time to fit residues: 872.5300 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 : 3.669 ------------------------------------------------------------------------------- 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 215 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN L 213 ASN L 239 ASN H 138 GLN R 24 GLN Z 24 GLN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 44 ASN 0 24 GLN a 40 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098216 restraints weight = 36805.109| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.18 r_work: 0.3123 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 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 = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.481 30171 Z= 0.144 Angle : 0.768 16.151 41219 Z= 0.292 Chirality : 0.041 0.331 3955 Planarity : 0.004 0.066 4804 Dihedral : 24.742 175.432 7274 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.03 % Allowed : 9.80 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2699 helix: 2.14 (0.12), residues: 1552 sheet: 0.34 (0.68), residues: 59 loop : -0.08 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 271 HIS 0.006 0.001 HIS W 29 PHE 0.022 0.001 PHE C 345 TYR 0.015 0.001 TYR M 134 ARG 0.004 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 1369) hydrogen bonds : angle 4.38242 ( 3861) metal coordination : bond 0.01353 ( 4) metal coordination : angle 7.55697 ( 12) covalent geometry : bond 0.00328 (30108) covalent geometry : angle 0.75730 (41207) Misc. bond : bond 0.08375 ( 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 403 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 2.636 Fit side-chains REVERT: M 14 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7267 (ttp80) REVERT: M 216 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8375 (t80) REVERT: H 92 THR cc_start: 0.6741 (m) cc_final: 0.6391 (m) REVERT: H 150 GLU cc_start: 0.7481 (pt0) cc_final: 0.6793 (pm20) REVERT: F 3 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7113 (mtt180) REVERT: G 14 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: J 17 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6576 (mm-30) REVERT: K 1 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6711 (tpt) REVERT: N 23 MET cc_start: 0.8143 (tpt) cc_final: 0.7772 (tpp) REVERT: O 1 MET cc_start: 0.6413 (mmm) cc_final: 0.6193 (mmm) REVERT: R 23 MET cc_start: 0.8030 (mmm) cc_final: 0.7761 (mmp) REVERT: U 3 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7143 (mtp85) REVERT: V 13 GLU cc_start: 0.5926 (tm-30) cc_final: 0.5644 (tm-30) REVERT: W 9 ASP cc_start: 0.7926 (t0) cc_final: 0.7705 (t0) REVERT: W 42 GLN cc_start: 0.8204 (tp40) cc_final: 0.7882 (tp-100) REVERT: 1 11 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7526 (ttm170) REVERT: 1 36 GLU cc_start: 0.7918 (tt0) cc_final: 0.7602 (tt0) REVERT: 6 16 LYS cc_start: 0.7929 (mttp) cc_final: 0.7612 (mmmm) REVERT: 7 9 ASP cc_start: 0.7077 (t70) cc_final: 0.6570 (t0) REVERT: 7 12 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6475 (mtt-85) REVERT: 8 23 MET cc_start: 0.8094 (mmp) cc_final: 0.7708 (mmm) REVERT: 8 38 PHE cc_start: 0.7870 (m-80) cc_final: 0.7641 (m-80) REVERT: 8 51 GLU cc_start: 0.6858 (pm20) cc_final: 0.6397 (pm20) REVERT: 0 14 GLU cc_start: 0.6303 (pt0) cc_final: 0.6026 (pt0) REVERT: a 40 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7105 (t0) outliers start: 69 outliers final: 36 residues processed: 376 average time/residue: 1.6311 time to fit residues: 707.3264 Evaluate side-chains 355 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 314 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 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 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 202 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 GLN R 24 GLN Z 24 GLN 0 24 GLN a 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095324 restraints weight = 36817.659| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.15 r_work: 0.3068 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.489 30171 Z= 0.239 Angle : 0.901 17.899 41219 Z= 0.346 Chirality : 0.045 0.489 3955 Planarity : 0.005 0.065 4804 Dihedral : 23.997 168.456 7261 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.91 % Allowed : 10.54 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.16), residues: 2699 helix: 1.82 (0.12), residues: 1553 sheet: 0.14 (0.68), residues: 59 loop : -0.18 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 271 HIS 0.011 0.003 HIS M 182 PHE 0.027 0.002 PHE C 345 TYR 0.022 0.002 TYR L 164 ARG 0.007 0.001 ARG a 109 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 1369) hydrogen bonds : angle 4.46127 ( 3861) metal coordination : bond 0.01174 ( 4) metal coordination : angle 6.50873 ( 12) covalent geometry : bond 0.00568 (30108) covalent geometry : angle 0.89376 (41207) Misc. bond : bond 0.08359 ( 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 415 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 326 time to evaluate : 2.606 Fit side-chains REVERT: C 84 ASP cc_start: 0.7029 (m-30) cc_final: 0.6800 (m-30) REVERT: M 216 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8310 (t80) REVERT: H 53 ARG cc_start: 0.6912 (mpp-170) cc_final: 0.6689 (mpp80) REVERT: H 92 THR cc_start: 0.6768 (m) cc_final: 0.6459 (m) REVERT: G 14 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: J 17 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6654 (mm-30) REVERT: K 1 MET cc_start: 0.7234 (tpp) cc_final: 0.6951 (tpt) REVERT: P 51 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: S 9 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7349 (t70) REVERT: T 51 GLU cc_start: 0.6992 (mp0) cc_final: 0.6709 (mp0) REVERT: U 3 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7084 (mtp85) REVERT: U 12 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6412 (mtp85) REVERT: V 13 GLU cc_start: 0.5906 (tm-30) cc_final: 0.5572 (tm-30) REVERT: W 1 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5405 (tpp) REVERT: W 9 ASP cc_start: 0.7865 (t70) cc_final: 0.7625 (t0) REVERT: W 42 GLN cc_start: 0.8104 (tp40) cc_final: 0.7763 (tp40) REVERT: 1 36 GLU cc_start: 0.7933 (tt0) cc_final: 0.7593 (tt0) REVERT: 7 9 ASP cc_start: 0.7160 (t70) cc_final: 0.6725 (t0) REVERT: 7 12 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7106 (mtt180) REVERT: 8 23 MET cc_start: 0.8205 (mmp) cc_final: 0.7798 (mmm) REVERT: 8 38 PHE cc_start: 0.7875 (m-80) cc_final: 0.7622 (m-80) REVERT: 8 51 GLU cc_start: 0.7034 (pm20) cc_final: 0.6567 (pm20) REVERT: 0 14 GLU cc_start: 0.6428 (pt0) cc_final: 0.6190 (pt0) REVERT: a 40 ASN cc_start: 0.7206 (t0) cc_final: 0.6633 (m-40) outliers start: 89 outliers final: 46 residues processed: 379 average time/residue: 1.5925 time to fit residues: 697.1725 Evaluate side-chains 362 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 2.867 ------------------------------------------------------------------------------- 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 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 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 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 B residue 20 SER 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 P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 20 SER 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 182 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 GLN I 18 HIS R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098458 restraints weight = 37177.728| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.19 r_work: 0.3128 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.405 30171 Z= 0.156 Angle : 0.700 12.503 41219 Z= 0.269 Chirality : 0.039 0.453 3955 Planarity : 0.004 0.065 4804 Dihedral : 22.191 154.992 7261 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 12.17 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2699 helix: 2.12 (0.12), residues: 1554 sheet: 0.22 (0.72), residues: 54 loop : -0.12 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 252 HIS 0.005 0.001 HIS X 37 PHE 0.021 0.001 PHE C 345 TYR 0.013 0.001 TYR L 164 ARG 0.007 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 1369) hydrogen bonds : angle 4.19481 ( 3861) metal coordination : bond 0.00674 ( 4) metal coordination : angle 5.35543 ( 12) covalent geometry : bond 0.00282 (30108) covalent geometry : angle 0.69381 (41207) Misc. bond : bond 0.07585 ( 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 399 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 3.031 Fit side-chains REVERT: C 72 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6223 (mmp80) REVERT: C 311 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: L 3 MET cc_start: 0.8111 (mtm) cc_final: 0.7892 (mtp) REVERT: M 18 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.6262 (t70) REVERT: M 216 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8113 (t80) REVERT: H 92 THR cc_start: 0.6774 (m) cc_final: 0.6425 (m) REVERT: H 150 GLU cc_start: 0.7549 (pt0) cc_final: 0.7239 (pm20) REVERT: J 17 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6657 (mm-30) REVERT: K 1 MET cc_start: 0.7194 (tpp) cc_final: 0.6928 (tpt) REVERT: U 3 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7140 (mtp85) REVERT: U 8 TYR cc_start: 0.8019 (m-80) cc_final: 0.7815 (m-80) REVERT: V 13 GLU cc_start: 0.5987 (tm-30) cc_final: 0.5669 (tm-30) REVERT: V 27 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7515 (mt) REVERT: W 1 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5392 (tpp) REVERT: W 9 ASP cc_start: 0.7915 (t70) cc_final: 0.7609 (t0) REVERT: W 11 ARG cc_start: 0.7152 (mtt90) cc_final: 0.6753 (mtm-85) REVERT: W 36 GLU cc_start: 0.8233 (tt0) cc_final: 0.8007 (tp30) REVERT: W 42 GLN cc_start: 0.8147 (tp40) cc_final: 0.7859 (tp40) REVERT: X 17 GLU cc_start: 0.6325 (tp30) cc_final: 0.6116 (tp30) REVERT: 1 36 GLU cc_start: 0.7924 (tt0) cc_final: 0.7710 (tp30) REVERT: 4 38 PHE cc_start: 0.7999 (m-80) cc_final: 0.7743 (m-10) REVERT: 7 9 ASP cc_start: 0.7179 (t70) cc_final: 0.6640 (t0) REVERT: 7 12 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6379 (mtt-85) REVERT: 8 23 MET cc_start: 0.8159 (mmp) cc_final: 0.7815 (mmm) REVERT: 8 38 PHE cc_start: 0.7878 (m-80) cc_final: 0.7587 (m-80) REVERT: 8 51 GLU cc_start: 0.6983 (pm20) cc_final: 0.6519 (pm20) REVERT: a 40 ASN cc_start: 0.7057 (t0) cc_final: 0.6832 (t0) REVERT: a 81 PHE cc_start: 0.7257 (m-80) cc_final: 0.6927 (m-80) REVERT: a 105 MET cc_start: 0.7571 (mmm) cc_final: 0.7363 (mmt) outliers start: 72 outliers final: 34 residues processed: 374 average time/residue: 1.6630 time to fit residues: 719.1970 Evaluate side-chains 347 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 2.746 ------------------------------------------------------------------------------- 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 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 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 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 I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain Q residue 36 ASP 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 Z residue 51 GLU Chi-restraints excluded: chain 1 residue 8 LEU 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 0 residue 10 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 GLN R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095791 restraints weight = 36845.964| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.15 r_work: 0.3082 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.462 30171 Z= 0.214 Angle : 0.850 16.429 41219 Z= 0.326 Chirality : 0.043 0.441 3955 Planarity : 0.005 0.065 4804 Dihedral : 22.498 174.759 7257 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.78 % Allowed : 12.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2699 helix: 1.89 (0.12), residues: 1553 sheet: 0.08 (0.68), residues: 59 loop : -0.17 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 271 HIS 0.011 0.002 HIS M 182 PHE 0.026 0.002 PHE C 345 TYR 0.021 0.002 TYR L 164 ARG 0.005 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 1369) hydrogen bonds : angle 4.35433 ( 3861) metal coordination : bond 0.01046 ( 4) metal coordination : angle 6.03525 ( 12) covalent geometry : bond 0.00505 (30108) covalent geometry : angle 0.84416 (41207) Misc. bond : bond 0.08148 ( 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 402 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 316 time to evaluate : 2.874 Fit side-chains REVERT: C 72 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6626 (mmp80) REVERT: M 216 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8226 (t80) REVERT: H 53 ARG cc_start: 0.6872 (mpp-170) cc_final: 0.6658 (mpp80) REVERT: H 82 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6875 (mtt180) REVERT: H 92 THR cc_start: 0.6772 (m) cc_final: 0.6461 (m) REVERT: H 127 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: J 17 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6646 (mm-30) REVERT: K 1 MET cc_start: 0.7218 (tpp) cc_final: 0.6952 (tpt) REVERT: N 10 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6044 (tp) REVERT: P 51 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: S 1 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.3804 (mmp) REVERT: S 9 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7187 (t70) REVERT: T 51 GLU cc_start: 0.7053 (mp0) cc_final: 0.6772 (mp0) REVERT: U 3 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7114 (mtp85) REVERT: V 13 GLU cc_start: 0.5944 (tm-30) cc_final: 0.5600 (tm-30) REVERT: V 27 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7506 (mt) REVERT: W 1 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5429 (tpp) REVERT: W 9 ASP cc_start: 0.7849 (t70) cc_final: 0.7556 (t0) REVERT: W 11 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6866 (mtm-85) REVERT: W 42 GLN cc_start: 0.8131 (tp40) cc_final: 0.7842 (tp40) REVERT: 1 36 GLU cc_start: 0.7881 (tt0) cc_final: 0.7534 (tt0) REVERT: 7 12 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6929 (mtt180) REVERT: 8 23 MET cc_start: 0.8177 (mmp) cc_final: 0.7891 (mmm) REVERT: 8 38 PHE cc_start: 0.7872 (m-80) cc_final: 0.7643 (m-80) REVERT: 8 51 GLU cc_start: 0.7100 (pm20) cc_final: 0.6596 (pm20) REVERT: 9 11 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6669 (mtp180) REVERT: a 40 ASN cc_start: 0.7067 (t0) cc_final: 0.6770 (t0) outliers start: 86 outliers final: 45 residues processed: 370 average time/residue: 1.5795 time to fit residues: 674.8095 Evaluate side-chains 361 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 2.662 ------------------------------------------------------------------------------- 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 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 17 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU 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 82 ARG Chi-restraints excluded: chain H residue 127 GLU 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 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 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain Q residue 36 ASP 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 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 11 ARG 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 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 210 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN a 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096747 restraints weight = 36986.991| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.19 r_work: 0.3102 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.431 30171 Z= 0.159 Angle : 0.751 14.063 41219 Z= 0.288 Chirality : 0.040 0.420 3955 Planarity : 0.004 0.066 4804 Dihedral : 21.879 172.521 7257 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.43 % Allowed : 13.05 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2699 helix: 2.00 (0.12), residues: 1548 sheet: 0.08 (0.69), residues: 59 loop : -0.14 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 PHE 0.023 0.002 PHE C 345 TYR 0.017 0.001 TYR L 164 ARG 0.004 0.000 ARG a 109 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 1369) hydrogen bonds : angle 4.24835 ( 3861) metal coordination : bond 0.00836 ( 4) metal coordination : angle 5.47951 ( 12) covalent geometry : bond 0.00367 (30108) covalent geometry : angle 0.74573 (41207) Misc. bond : bond 0.07548 ( 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 389 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 2.919 Fit side-chains REVERT: C 72 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6440 (mmp80) REVERT: C 311 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: M 216 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8194 (t80) REVERT: H 53 ARG cc_start: 0.6895 (mpp-170) cc_final: 0.6674 (mpp80) REVERT: H 82 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6814 (mtt180) REVERT: H 92 THR cc_start: 0.6759 (m) cc_final: 0.6437 (m) REVERT: B 28 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8156 (mp) REVERT: J 17 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6608 (mm-30) REVERT: K 1 MET cc_start: 0.7221 (tpp) cc_final: 0.6980 (tpt) REVERT: N 10 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6058 (tp) REVERT: P 51 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: S 1 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.3914 (mmp) REVERT: S 9 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7105 (t70) REVERT: T 51 GLU cc_start: 0.7049 (mp0) cc_final: 0.6740 (mp0) REVERT: U 3 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7113 (mtp85) REVERT: V 13 GLU cc_start: 0.5969 (tm-30) cc_final: 0.5648 (tm-30) REVERT: V 27 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7505 (mt) REVERT: W 1 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5434 (tpp) REVERT: W 9 ASP cc_start: 0.7817 (t70) cc_final: 0.7495 (t0) REVERT: W 11 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6827 (mtm-85) REVERT: W 42 GLN cc_start: 0.8146 (tp40) cc_final: 0.7841 (tp40) REVERT: 1 36 GLU cc_start: 0.7948 (tt0) cc_final: 0.7583 (tt0) REVERT: 7 12 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6491 (mtt-85) REVERT: 8 23 MET cc_start: 0.8173 (mmp) cc_final: 0.7678 (mmm) REVERT: 8 38 PHE cc_start: 0.7874 (m-80) cc_final: 0.7596 (m-80) REVERT: 8 51 GLU cc_start: 0.7069 (pm20) cc_final: 0.6569 (pm20) REVERT: 9 21 MET cc_start: 0.8231 (mmm) cc_final: 0.7908 (mmp) REVERT: 0 17 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: a 40 ASN cc_start: 0.7056 (t0) cc_final: 0.6516 (m-40) REVERT: a 81 PHE cc_start: 0.7339 (m-80) cc_final: 0.6800 (m-80) outliers start: 78 outliers final: 40 residues processed: 363 average time/residue: 1.7214 time to fit residues: 728.6962 Evaluate side-chains 361 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 3.026 ------------------------------------------------------------------------------- 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 M residue 17 THR Chi-restraints excluded: chain M residue 53 LEU 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 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 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 50 ASP Chi-restraints excluded: chain P residue 51 GLU 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 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 7 residue 12 ARG 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 142 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 GLN R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096203 restraints weight = 36751.053| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.15 r_work: 0.3088 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- 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 = 0.59 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 = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.446 30171 Z= 0.193 Angle : 0.818 15.752 41219 Z= 0.313 Chirality : 0.042 0.412 3955 Planarity : 0.004 0.065 4804 Dihedral : 21.939 170.853 7257 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.30 % Allowed : 13.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.16), residues: 2699 helix: 1.88 (0.12), residues: 1553 sheet: 0.09 (0.69), residues: 59 loop : -0.17 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 7 2 HIS 0.010 0.002 HIS M 182 PHE 0.024 0.002 PHE C 345 TYR 0.020 0.002 TYR L 164 ARG 0.005 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 1369) hydrogen bonds : angle 4.31982 ( 3861) metal coordination : bond 0.00941 ( 4) metal coordination : angle 5.71154 ( 12) covalent geometry : bond 0.00453 (30108) covalent geometry : angle 0.81226 (41207) Misc. bond : bond 0.07850 ( 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 391 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 2.693 Fit side-chains REVERT: C 72 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6686 (mmp80) REVERT: C 311 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: M 216 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8220 (t80) REVERT: H 53 ARG cc_start: 0.6911 (mpp-170) cc_final: 0.6693 (mpp80) REVERT: H 82 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6823 (mtt180) REVERT: H 92 THR cc_start: 0.6767 (m) cc_final: 0.6453 (m) REVERT: B 28 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (mp) REVERT: G 14 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: I 8 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7721 (mp) REVERT: J 17 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6625 (mm-30) REVERT: N 10 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5981 (tp) REVERT: P 51 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: S 1 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4353 (tpt) REVERT: S 9 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7140 (t70) REVERT: T 51 GLU cc_start: 0.7030 (mp0) cc_final: 0.6750 (mp0) REVERT: U 3 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7109 (mtp85) REVERT: V 13 GLU cc_start: 0.5986 (tm-30) cc_final: 0.5627 (tm-30) REVERT: V 27 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7518 (mt) REVERT: W 1 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5475 (tpp) REVERT: W 9 ASP cc_start: 0.7792 (t70) cc_final: 0.7484 (t0) REVERT: W 42 GLN cc_start: 0.8139 (tp40) cc_final: 0.7831 (tp40) REVERT: 1 36 GLU cc_start: 0.7881 (tt0) cc_final: 0.7538 (tt0) REVERT: 7 12 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6667 (mtt-85) REVERT: 8 23 MET cc_start: 0.8168 (mmp) cc_final: 0.7861 (mmm) REVERT: 8 38 PHE cc_start: 0.7882 (m-80) cc_final: 0.7618 (m-80) REVERT: 8 51 GLU cc_start: 0.7093 (pm20) cc_final: 0.6572 (pm20) REVERT: 9 11 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6632 (mtp180) REVERT: a 40 ASN cc_start: 0.7114 (t0) cc_final: 0.6600 (m-40) REVERT: a 105 MET cc_start: 0.7504 (mmt) cc_final: 0.7268 (mmt) outliers start: 75 outliers final: 44 residues processed: 369 average time/residue: 1.7062 time to fit residues: 727.1207 Evaluate side-chains 363 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 time to evaluate : 2.843 ------------------------------------------------------------------------------- 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 M residue 17 THR Chi-restraints excluded: chain M residue 53 LEU 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 B residue 28 ILE 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 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 51 GLU 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 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 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 142 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** 9 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096442 restraints weight = 36839.101| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.19 r_work: 0.3097 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.436 30171 Z= 0.174 Angle : 0.777 14.912 41219 Z= 0.298 Chirality : 0.041 0.399 3955 Planarity : 0.004 0.066 4804 Dihedral : 21.672 177.391 7257 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.94 % Allowed : 13.75 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2699 helix: 1.95 (0.12), residues: 1547 sheet: 0.09 (0.69), residues: 59 loop : -0.18 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 7 2 HIS 0.008 0.002 HIS M 182 PHE 0.024 0.002 PHE C 345 TYR 0.019 0.002 TYR L 164 ARG 0.004 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1369) hydrogen bonds : angle 4.28357 ( 3861) metal coordination : bond 0.00830 ( 4) metal coordination : angle 5.49916 ( 12) covalent geometry : bond 0.00409 (30108) covalent geometry : angle 0.77153 (41207) Misc. bond : bond 0.07588 ( 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 374 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 2.978 Fit side-chains REVERT: C 72 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6539 (mmp80) REVERT: C 311 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: L 202 LYS cc_start: 0.6166 (mppt) cc_final: 0.5665 (tttt) REVERT: M 216 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8208 (t80) REVERT: H 53 ARG cc_start: 0.6911 (mpp-170) cc_final: 0.6689 (mpp80) REVERT: H 82 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6810 (mtt180) REVERT: H 92 THR cc_start: 0.6732 (m) cc_final: 0.6425 (m) REVERT: H 194 LEU cc_start: 0.7628 (mm) cc_final: 0.7366 (mt) REVERT: B 28 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8108 (mp) REVERT: J 17 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6631 (mm-30) REVERT: N 10 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6051 (tp) REVERT: P 51 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: S 1 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.4367 (tpt) REVERT: S 9 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7124 (t70) REVERT: T 51 GLU cc_start: 0.7023 (mp0) cc_final: 0.6729 (mp0) REVERT: U 3 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7084 (mtp85) REVERT: V 13 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5695 (tm-30) REVERT: W 1 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5520 (tpp) REVERT: W 9 ASP cc_start: 0.7745 (t70) cc_final: 0.7390 (t0) REVERT: W 42 GLN cc_start: 0.8177 (tp40) cc_final: 0.7870 (tp40) REVERT: 1 36 GLU cc_start: 0.7929 (tt0) cc_final: 0.7568 (tt0) REVERT: 7 12 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6542 (mtt-85) REVERT: 8 23 MET cc_start: 0.8184 (mmp) cc_final: 0.7898 (mmm) REVERT: 8 38 PHE cc_start: 0.7865 (m-80) cc_final: 0.7591 (m-80) REVERT: 8 51 GLU cc_start: 0.7095 (pm20) cc_final: 0.6591 (pm20) REVERT: 9 11 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6539 (mtp180) REVERT: 0 24 GLN cc_start: 0.7566 (tt0) cc_final: 0.7225 (tt0) REVERT: a 81 PHE cc_start: 0.7315 (m-80) cc_final: 0.6781 (m-80) REVERT: a 105 MET cc_start: 0.7427 (mmt) cc_final: 0.7216 (mmt) outliers start: 67 outliers final: 41 residues processed: 354 average time/residue: 1.8124 time to fit residues: 737.6896 Evaluate side-chains 359 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 M residue 17 THR Chi-restraints excluded: chain M residue 53 LEU 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 28 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU 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 50 ASP Chi-restraints excluded: chain P residue 51 GLU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN 0 24 GLN a 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095881 restraints weight = 36658.655| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.15 r_work: 0.3085 rms_B_bonded: 2.12 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: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.464 30171 Z= 0.220 Angle : 0.868 17.630 41219 Z= 0.330 Chirality : 0.043 0.403 3955 Planarity : 0.005 0.065 4804 Dihedral : 21.975 176.628 7255 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.90 % Allowed : 14.06 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 2699 helix: 1.76 (0.12), residues: 1553 sheet: 0.12 (0.69), residues: 59 loop : -0.23 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 7 2 HIS 0.010 0.002 HIS M 182 PHE 0.025 0.002 PHE C 345 TYR 0.022 0.002 TYR L 164 ARG 0.004 0.001 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 1369) hydrogen bonds : angle 4.38402 ( 3861) metal coordination : bond 0.00924 ( 4) metal coordination : angle 5.96860 ( 12) covalent geometry : bond 0.00523 (30108) covalent geometry : angle 0.86186 (41207) Misc. bond : bond 0.08167 ( 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 376 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 310 time to evaluate : 2.749 Fit side-chains REVERT: C 311 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: L 202 LYS cc_start: 0.6305 (mppt) cc_final: 0.5789 (tttt) REVERT: M 75 MET cc_start: 0.9148 (mtt) cc_final: 0.8945 (mtt) REVERT: M 216 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8320 (t80) REVERT: H 53 ARG cc_start: 0.6948 (mpp-170) cc_final: 0.6705 (mpp80) REVERT: H 82 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6862 (mtt180) REVERT: H 92 THR cc_start: 0.6735 (m) cc_final: 0.6430 (m) REVERT: B 28 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (mp) REVERT: G 14 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: J 17 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6665 (mm-30) REVERT: N 10 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5954 (tp) REVERT: P 51 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: S 1 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.4542 (tpt) REVERT: S 9 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7243 (t70) REVERT: T 51 GLU cc_start: 0.6976 (mp0) cc_final: 0.6706 (mp0) REVERT: U 3 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7095 (mtp85) REVERT: V 13 GLU cc_start: 0.5989 (tm-30) cc_final: 0.5648 (tm-30) REVERT: W 1 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5432 (tpp) REVERT: W 9 ASP cc_start: 0.7744 (t70) cc_final: 0.7438 (t0) REVERT: W 42 GLN cc_start: 0.8188 (tp40) cc_final: 0.7894 (tp40) REVERT: 1 36 GLU cc_start: 0.7870 (tt0) cc_final: 0.7532 (tt0) REVERT: 7 12 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7075 (mtt180) REVERT: 8 23 MET cc_start: 0.8177 (mmp) cc_final: 0.7851 (mmm) REVERT: 8 38 PHE cc_start: 0.7864 (m-80) cc_final: 0.7626 (m-80) REVERT: 8 51 GLU cc_start: 0.7108 (pm20) cc_final: 0.6587 (pm20) REVERT: 9 11 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6682 (mtp180) REVERT: a 105 MET cc_start: 0.7454 (mmt) cc_final: 0.7252 (mmt) outliers start: 66 outliers final: 47 residues processed: 360 average time/residue: 1.6532 time to fit residues: 684.5084 Evaluate side-chains 362 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 303 time to evaluate : 2.893 ------------------------------------------------------------------------------- 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 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 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 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 B residue 28 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 1 MET 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 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 50 ASP Chi-restraints excluded: chain P residue 51 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN a 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097805 restraints weight = 36629.611| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.18 r_work: 0.3121 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 30171 Z= 0.139 Angle : 0.729 15.104 41219 Z= 0.280 Chirality : 0.039 0.381 3955 Planarity : 0.004 0.066 4804 Dihedral : 21.128 159.270 7253 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 14.85 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2699 helix: 2.04 (0.12), residues: 1547 sheet: 0.10 (0.74), residues: 54 loop : -0.18 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 7 2 HIS 0.006 0.001 HIS W 29 PHE 0.023 0.001 PHE G 26 TYR 0.015 0.001 TYR L 164 ARG 0.005 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1369) hydrogen bonds : angle 4.22124 ( 3861) metal coordination : bond 0.00655 ( 4) metal coordination : angle 5.17623 ( 12) covalent geometry : bond 0.00321 (30108) covalent geometry : angle 0.72421 (41207) Misc. bond : bond 0.07229 ( 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 366 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 2.991 Fit side-chains REVERT: C 72 ARG cc_start: 0.7343 (mmp-170) cc_final: 0.7059 (mmp80) REVERT: C 311 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: L 202 LYS cc_start: 0.6212 (mppt) cc_final: 0.5673 (tttt) REVERT: M 75 MET cc_start: 0.9128 (mtt) cc_final: 0.8923 (mtt) REVERT: M 216 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8161 (t80) REVERT: H 53 ARG cc_start: 0.6920 (mpp-170) cc_final: 0.6674 (mpp80) REVERT: H 92 THR cc_start: 0.6740 (m) cc_final: 0.6427 (m) REVERT: H 194 LEU cc_start: 0.7623 (mm) cc_final: 0.7373 (mt) REVERT: B 28 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8119 (mp) REVERT: G 14 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: J 17 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6643 (mm-30) REVERT: N 10 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6066 (tp) REVERT: S 1 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4260 (tpt) REVERT: T 51 GLU cc_start: 0.7020 (mp0) cc_final: 0.6728 (mp0) REVERT: U 3 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7150 (mtp85) REVERT: V 13 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5691 (tm-30) REVERT: W 1 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5460 (tpp) REVERT: W 9 ASP cc_start: 0.7696 (t70) cc_final: 0.7327 (t0) REVERT: W 11 ARG cc_start: 0.7120 (mtt90) cc_final: 0.6447 (mtp180) REVERT: W 42 GLN cc_start: 0.8189 (tp40) cc_final: 0.7894 (tp40) REVERT: 1 36 GLU cc_start: 0.7932 (tt0) cc_final: 0.7567 (tt0) REVERT: 4 38 PHE cc_start: 0.7956 (m-80) cc_final: 0.7716 (m-10) REVERT: 7 12 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6548 (mtt-85) REVERT: 8 38 PHE cc_start: 0.7871 (m-80) cc_final: 0.7597 (m-80) REVERT: 8 51 GLU cc_start: 0.7107 (pm20) cc_final: 0.6651 (pm20) REVERT: 0 17 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: a 70 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5758 (p0) REVERT: a 81 PHE cc_start: 0.7337 (m-80) cc_final: 0.6733 (m-80) REVERT: a 105 MET cc_start: 0.7457 (mmt) cc_final: 0.7225 (mmt) outliers start: 52 outliers final: 34 residues processed: 351 average time/residue: 1.6880 time to fit residues: 681.4784 Evaluate side-chains 352 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 H residue 8 THR Chi-restraints excluded: chain H residue 77 SER 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 G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU 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 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 36 GLU 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 7 residue 12 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 6 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN ** W 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN a 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095568 restraints weight = 36759.189| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.15 r_work: 0.3077 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- 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 = 0.62 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 = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.470 30171 Z= 0.246 Angle : 0.907 18.788 41219 Z= 0.346 Chirality : 0.045 0.397 3955 Planarity : 0.005 0.065 4804 Dihedral : 21.798 159.200 7252 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2699 helix: 1.73 (0.12), residues: 1548 sheet: 0.09 (0.70), residues: 59 loop : -0.21 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 7 2 HIS 0.012 0.003 HIS M 182 PHE 0.027 0.002 PHE C 345 TYR 0.023 0.002 TYR L 164 ARG 0.005 0.001 ARG 7 11 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 1369) hydrogen bonds : angle 4.40653 ( 3861) metal coordination : bond 0.01022 ( 4) metal coordination : angle 6.17905 ( 12) covalent geometry : bond 0.00589 (30108) covalent geometry : angle 0.90138 (41207) Misc. bond : bond 0.08285 ( 59) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26011.00 seconds wall clock time: 445 minutes 39.78 seconds (26739.78 seconds total)