Starting phenix.real_space_refine on Mon May 26 19:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z82_39836/05_2025/8z82_39836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z82_39836/05_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_39836/05_2025/8z82_39836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z82_39836/05_2025/8z82_39836.map" model { file = "/net/cci-nas-00/data/ceres_data/8z82_39836/05_2025/8z82_39836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z82_39836/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 18.98, per 1000 atoms: 0.65 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: 9.86 Conformation dependent library (CDL) restraints added in 2.7 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: 2.52 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: 7.91 Time building geometry restraints manager: 10.90 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: 3.180 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: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 70.110 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.400 ------------------------------------------------------------------------------- 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 : 2.573 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: 1.6421 time to fit residues: 748.1622 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 : 2.641 ------------------------------------------------------------------------------- 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 = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098178 restraints weight = 36805.019| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.19 r_work: 0.3123 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 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 7.55695 ( 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 : 2.887 Fit side-chains REVERT: M 14 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7270 (ttp80) REVERT: M 216 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8375 (t80) REVERT: H 92 THR cc_start: 0.6743 (m) cc_final: 0.6392 (m) REVERT: H 150 GLU cc_start: 0.7482 (pt0) cc_final: 0.6794 (pm20) REVERT: F 3 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.7117 (mtt180) REVERT: G 14 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: J 17 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6582 (mm-30) REVERT: K 1 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6713 (tpt) REVERT: N 23 MET cc_start: 0.8144 (tpt) cc_final: 0.7774 (tpp) REVERT: O 1 MET cc_start: 0.6415 (mmm) cc_final: 0.6195 (mmm) REVERT: R 23 MET cc_start: 0.8033 (mmm) cc_final: 0.7764 (mmp) REVERT: U 3 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7148 (mtp85) REVERT: V 13 GLU cc_start: 0.5930 (tm-30) cc_final: 0.5649 (tm-30) REVERT: W 9 ASP cc_start: 0.7928 (t0) cc_final: 0.7707 (t0) REVERT: W 42 GLN cc_start: 0.8205 (tp40) cc_final: 0.7883 (tp-100) REVERT: 1 11 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7529 (ttm170) REVERT: 1 36 GLU cc_start: 0.7923 (tt0) cc_final: 0.7607 (tt0) REVERT: 6 16 LYS cc_start: 0.7931 (mttp) cc_final: 0.7614 (mmmm) REVERT: 7 9 ASP cc_start: 0.7079 (t70) cc_final: 0.6573 (t0) REVERT: 7 12 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6478 (mtt-85) REVERT: 8 23 MET cc_start: 0.8095 (mmp) cc_final: 0.7710 (mmm) REVERT: 8 38 PHE cc_start: 0.7872 (m-80) cc_final: 0.7644 (m-80) REVERT: 8 51 GLU cc_start: 0.6860 (pm20) cc_final: 0.6400 (pm20) REVERT: 0 14 GLU cc_start: 0.6309 (pt0) cc_final: 0.6031 (pt0) REVERT: a 40 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.7108 (t0) outliers start: 69 outliers final: 36 residues processed: 376 average time/residue: 1.5992 time to fit residues: 693.3751 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 : 2.890 ------------------------------------------------------------------------------- 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: 10.0000 chunk 171 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.116734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094600 restraints weight = 36842.726| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.15 r_work: 0.3061 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 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 = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.515 30171 Z= 0.290 Angle : 1.004 20.837 41219 Z= 0.383 Chirality : 0.049 0.501 3955 Planarity : 0.006 0.065 4804 Dihedral : 24.531 170.226 7261 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.13 % Allowed : 10.50 % Favored : 85.37 % 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: 1.21 (0.16), residues: 2699 helix: 1.60 (0.12), residues: 1557 sheet: 0.02 (0.69), residues: 59 loop : -0.26 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 271 HIS 0.013 0.003 HIS M 182 PHE 0.029 0.003 PHE C 345 TYR 0.024 0.003 TYR L 164 ARG 0.007 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 1369) hydrogen bonds : angle 4.57191 ( 3861) metal coordination : bond 0.01304 ( 4) metal coordination : angle 7.10167 ( 12) covalent geometry : bond 0.00700 (30108) covalent geometry : angle 0.99709 (41207) Misc. bond : bond 0.08715 ( 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 420 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 326 time to evaluate : 3.007 Fit side-chains REVERT: C 72 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6619 (mmp80) REVERT: C 84 ASP cc_start: 0.7031 (m-30) cc_final: 0.6770 (m-30) REVERT: C 177 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: M 124 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (mp) REVERT: M 216 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8408 (t80) REVERT: H 53 ARG cc_start: 0.6878 (mpp-170) cc_final: 0.6651 (mpp80) REVERT: H 92 THR cc_start: 0.6714 (m) cc_final: 0.6407 (m) REVERT: H 127 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7057 (mm-30) REVERT: G 14 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: J 17 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6676 (mm-30) REVERT: K 1 MET cc_start: 0.7233 (tpp) cc_final: 0.6908 (tpt) REVERT: N 10 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6053 (tp) REVERT: P 51 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: R 7 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4609 (pp) REVERT: S 1 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.3933 (mmp) REVERT: S 9 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7348 (t70) REVERT: T 51 GLU cc_start: 0.6997 (mp0) cc_final: 0.6784 (mp0) REVERT: U 3 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7072 (mtp85) REVERT: U 12 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6433 (mtp85) REVERT: V 13 GLU cc_start: 0.5887 (tm-30) cc_final: 0.5584 (tm-30) REVERT: W 1 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5462 (tpp) REVERT: W 9 ASP cc_start: 0.7868 (t70) cc_final: 0.7633 (t0) REVERT: W 42 GLN cc_start: 0.8121 (tp40) cc_final: 0.7791 (tp40) REVERT: 1 36 GLU cc_start: 0.7880 (tt0) cc_final: 0.7548 (tt0) REVERT: 7 9 ASP cc_start: 0.7165 (t70) cc_final: 0.6773 (t0) REVERT: 8 23 MET cc_start: 0.8230 (mmp) cc_final: 0.7930 (mmm) REVERT: 8 38 PHE cc_start: 0.7871 (m-80) cc_final: 0.7663 (m-80) REVERT: 8 51 GLU cc_start: 0.7094 (pm20) cc_final: 0.6621 (pm20) REVERT: 9 11 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6758 (mtp180) REVERT: a 40 ASN cc_start: 0.7138 (t0) cc_final: 0.6583 (m-40) REVERT: a 122 ASP cc_start: 0.7795 (t0) cc_final: 0.7593 (t70) outliers start: 94 outliers final: 50 residues processed: 387 average time/residue: 1.5624 time to fit residues: 697.0969 Evaluate side-chains 373 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 310 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain P residue 51 GLU Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 11 SER 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 9 residue 11 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 182 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3611 r_free = 0.3611 target = 0.120397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098306 restraints weight = 37134.108| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.19 r_work: 0.3128 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.416 30171 Z= 0.160 Angle : 0.708 12.306 41219 Z= 0.271 Chirality : 0.039 0.449 3955 Planarity : 0.004 0.066 4804 Dihedral : 22.511 163.808 7261 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.30 % Allowed : 11.99 % Favored : 84.71 % 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: 1.69 (0.16), residues: 2699 helix: 2.04 (0.12), residues: 1554 sheet: 0.18 (0.73), residues: 54 loop : -0.14 (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 0.020 0.001 PHE C 345 TYR 0.014 0.001 TYR Y 8 ARG 0.005 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 1369) hydrogen bonds : angle 4.22105 ( 3861) metal coordination : bond 0.00702 ( 4) metal coordination : angle 5.40256 ( 12) covalent geometry : bond 0.00279 (30108) covalent geometry : angle 0.70184 (41207) Misc. bond : bond 0.07795 ( 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 404 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 2.685 Fit side-chains REVERT: C 241 MET cc_start: 0.8969 (mmt) cc_final: 0.8727 (mmt) REVERT: M 216 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8125 (t80) REVERT: H 82 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6945 (mtt180) REVERT: H 92 THR cc_start: 0.6775 (m) cc_final: 0.6447 (m) REVERT: H 150 GLU cc_start: 0.7520 (pt0) cc_final: 0.7213 (pm20) REVERT: F 3 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7187 (mtt180) REVERT: J 17 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6648 (mm-30) REVERT: K 1 MET cc_start: 0.7189 (tpp) cc_final: 0.6846 (tpt) REVERT: T 51 GLU cc_start: 0.6994 (mp0) cc_final: 0.6683 (mp0) REVERT: U 3 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7113 (mtp85) REVERT: V 13 GLU cc_start: 0.5985 (tm-30) cc_final: 0.5607 (tm-30) REVERT: V 27 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7496 (mt) REVERT: W 1 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5428 (tpp) REVERT: W 9 ASP cc_start: 0.7859 (t70) cc_final: 0.7545 (t0) REVERT: W 11 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6693 (mtm-85) REVERT: W 42 GLN cc_start: 0.8127 (tp40) cc_final: 0.7843 (tp40) REVERT: X 17 GLU cc_start: 0.6367 (tp30) cc_final: 0.6139 (tp30) REVERT: 1 36 GLU cc_start: 0.7910 (tt0) cc_final: 0.7706 (tp30) REVERT: 4 38 PHE cc_start: 0.7990 (m-80) cc_final: 0.7751 (m-10) REVERT: 6 16 LYS cc_start: 0.7895 (mttp) cc_final: 0.7564 (mmmm) REVERT: 7 9 ASP cc_start: 0.7207 (t70) cc_final: 0.6646 (t0) REVERT: 7 12 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6617 (mtt-85) REVERT: 8 23 MET cc_start: 0.8147 (mmp) cc_final: 0.7792 (mmm) REVERT: 8 38 PHE cc_start: 0.7857 (m-80) cc_final: 0.7566 (m-80) REVERT: 8 51 GLU cc_start: 0.7002 (pm20) cc_final: 0.6521 (pm20) REVERT: a 40 ASN cc_start: 0.7062 (t0) cc_final: 0.6839 (t0) REVERT: a 81 PHE cc_start: 0.7297 (m-80) cc_final: 0.6979 (m-80) outliers start: 75 outliers final: 36 residues processed: 382 average time/residue: 1.6078 time to fit residues: 709.0989 Evaluate side-chains 349 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 9 residue 8 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 236 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 117 optimal weight: 0.0010 chunk 139 optimal weight: 8.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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** 0 24 GLN a 39 ASN ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097535 restraints weight = 36925.449| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.19 r_work: 0.3115 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.402 30171 Z= 0.143 Angle : 0.727 14.058 41219 Z= 0.279 Chirality : 0.040 0.427 3955 Planarity : 0.004 0.063 4804 Dihedral : 21.826 177.950 7258 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.99 % Allowed : 13.05 % 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: 1.76 (0.16), residues: 2699 helix: 2.10 (0.12), residues: 1554 sheet: 0.13 (0.72), residues: 54 loop : -0.10 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.007 0.002 HIS W 29 PHE 0.022 0.001 PHE C 345 TYR 0.017 0.001 TYR L 164 ARG 0.004 0.000 ARG H 155 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 1369) hydrogen bonds : angle 4.18113 ( 3861) metal coordination : bond 0.00802 ( 4) metal coordination : angle 5.26566 ( 12) covalent geometry : bond 0.00327 (30108) covalent geometry : angle 0.72106 (41207) Misc. bond : bond 0.07174 ( 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 380 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 2.632 Fit side-chains REVERT: C 241 MET cc_start: 0.9052 (mmt) cc_final: 0.8707 (mmt) REVERT: C 311 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: M 216 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8150 (t80) REVERT: H 53 ARG cc_start: 0.6924 (mpp-170) cc_final: 0.6706 (mpp80) REVERT: H 82 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6872 (mtt180) REVERT: H 92 THR cc_start: 0.6763 (m) cc_final: 0.6440 (m) REVERT: H 127 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: H 150 GLU cc_start: 0.7489 (pt0) cc_final: 0.7260 (pm20) REVERT: F 3 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7182 (mtt180) REVERT: J 17 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6582 (mm-30) REVERT: K 1 MET cc_start: 0.7196 (tpp) cc_final: 0.6914 (tpt) REVERT: P 51 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: S 9 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7111 (t70) REVERT: U 3 ARG cc_start: 0.7619 (mtp85) cc_final: 0.7132 (mtp85) REVERT: V 13 GLU cc_start: 0.5975 (tm-30) cc_final: 0.5653 (tm-30) REVERT: V 27 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7493 (mt) REVERT: W 1 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5425 (tpp) REVERT: W 9 ASP cc_start: 0.7806 (t70) cc_final: 0.7519 (t0) REVERT: W 11 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6423 (mtp180) REVERT: W 36 GLU cc_start: 0.8055 (tt0) cc_final: 0.7713 (tp30) REVERT: W 42 GLN cc_start: 0.8135 (tp40) cc_final: 0.7843 (tp40) REVERT: 1 36 GLU cc_start: 0.7926 (tt0) cc_final: 0.7573 (tt0) REVERT: 7 12 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6690 (mtt-85) REVERT: 8 23 MET cc_start: 0.8185 (mmp) cc_final: 0.7691 (mmm) REVERT: 8 38 PHE cc_start: 0.7888 (m-80) cc_final: 0.7610 (m-80) REVERT: 8 51 GLU cc_start: 0.7025 (pm20) cc_final: 0.6548 (pm20) REVERT: 0 17 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: a 40 ASN cc_start: 0.7074 (t0) cc_final: 0.6794 (t0) REVERT: a 81 PHE cc_start: 0.7286 (m-80) cc_final: 0.6697 (m-80) outliers start: 68 outliers final: 37 residues processed: 353 average time/residue: 1.5825 time to fit residues: 642.1428 Evaluate side-chains 357 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 210 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 a 39 ASN ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096451 restraints weight = 36909.353| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.15 r_work: 0.3091 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.437 30171 Z= 0.180 Angle : 0.795 15.169 41219 Z= 0.305 Chirality : 0.041 0.416 3955 Planarity : 0.004 0.067 4804 Dihedral : 21.817 171.485 7255 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.47 % Allowed : 13.14 % 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: 1.60 (0.16), residues: 2699 helix: 1.94 (0.12), residues: 1559 sheet: 0.07 (0.68), residues: 59 loop : -0.15 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 271 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 0.003 0.000 ARG H 155 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 1369) hydrogen bonds : angle 4.28646 ( 3861) metal coordination : bond 0.00890 ( 4) metal coordination : angle 5.51348 ( 12) covalent geometry : bond 0.00420 (30108) covalent geometry : angle 0.78980 (41207) Misc. bond : bond 0.07872 ( 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 391 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 312 time to evaluate : 2.861 Fit side-chains revert: symmetry clash REVERT: C 311 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8009 (pt0) REVERT: M 216 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8219 (t80) REVERT: H 53 ARG cc_start: 0.6898 (mpp-170) cc_final: 0.6675 (mpp80) REVERT: H 82 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6868 (mtt180) REVERT: H 92 THR cc_start: 0.6767 (m) cc_final: 0.6454 (m) REVERT: H 127 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: J 17 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6669 (mm-30) REVERT: N 10 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6031 (tp) REVERT: P 51 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: S 1 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.3871 (mmp) REVERT: S 9 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7117 (t70) REVERT: T 51 GLU cc_start: 0.7044 (mp0) cc_final: 0.6749 (mp0) REVERT: U 3 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7158 (mtp85) REVERT: V 13 GLU cc_start: 0.5966 (tm-30) cc_final: 0.5608 (tm-30) REVERT: V 27 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7503 (mt) REVERT: W 1 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5540 (tpp) REVERT: W 9 ASP cc_start: 0.7743 (t70) cc_final: 0.7459 (t0) REVERT: W 11 ARG cc_start: 0.7181 (mtt90) cc_final: 0.6862 (mtm-85) REVERT: W 42 GLN cc_start: 0.8138 (tp40) cc_final: 0.7832 (tp40) REVERT: 1 36 GLU cc_start: 0.7915 (tt0) cc_final: 0.7561 (tt0) REVERT: 6 16 LYS cc_start: 0.7889 (mttp) cc_final: 0.7612 (mmmm) REVERT: 7 12 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6708 (mtt-85) REVERT: 8 23 MET cc_start: 0.8186 (mmp) cc_final: 0.7892 (mmm) REVERT: 8 38 PHE cc_start: 0.7884 (m-80) cc_final: 0.7656 (m-80) REVERT: 8 51 GLU cc_start: 0.7113 (pm20) cc_final: 0.6623 (pm20) REVERT: a 40 ASN cc_start: 0.7087 (t0) cc_final: 0.6578 (m-40) REVERT: a 105 MET cc_start: 0.7458 (mmt) cc_final: 0.7232 (mmt) outliers start: 79 outliers final: 45 residues processed: 363 average time/residue: 1.6859 time to fit residues: 717.1438 Evaluate side-chains 356 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 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 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 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 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 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 4 LEU Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 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: 1.9990 chunk 155 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095332 restraints weight = 36795.676| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.15 r_work: 0.3071 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.493 30171 Z= 0.249 Angle : 0.924 19.813 41219 Z= 0.350 Chirality : 0.045 0.417 3955 Planarity : 0.005 0.067 4804 Dihedral : 22.438 171.376 7255 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.47 % Allowed : 13.14 % 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: 1.26 (0.16), residues: 2699 helix: 1.65 (0.12), residues: 1559 sheet: 0.07 (0.70), residues: 59 loop : -0.26 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 271 HIS 0.013 0.003 HIS M 182 PHE 0.027 0.002 PHE C 345 TYR 0.023 0.002 TYR L 164 ARG 0.004 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.05319 ( 1369) hydrogen bonds : angle 4.45142 ( 3861) metal coordination : bond 0.01065 ( 4) metal coordination : angle 6.36909 ( 12) covalent geometry : bond 0.00593 (30108) covalent geometry : angle 0.91784 (41207) Misc. bond : bond 0.08710 ( 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 384 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 305 time to evaluate : 2.595 Fit side-chains revert: symmetry clash REVERT: C 72 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6623 (mmp80) REVERT: L 202 LYS cc_start: 0.6255 (mppt) cc_final: 0.5806 (tttt) REVERT: M 216 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8313 (t80) REVERT: H 53 ARG cc_start: 0.6937 (mpp-170) cc_final: 0.6710 (mpp80) REVERT: H 82 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6830 (mtt180) REVERT: H 92 THR cc_start: 0.6728 (m) cc_final: 0.6423 (m) REVERT: J 17 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6713 (mm-30) REVERT: P 51 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: S 1 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.3822 (mmp) REVERT: S 9 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7361 (t70) REVERT: U 3 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7102 (mtp85) REVERT: U 12 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6348 (mtp85) REVERT: V 13 GLU cc_start: 0.5990 (tm-30) cc_final: 0.5684 (tm-30) REVERT: W 1 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5460 (tpp) REVERT: W 9 ASP cc_start: 0.7756 (t70) cc_final: 0.7437 (t0) REVERT: W 11 ARG cc_start: 0.7163 (mtt90) cc_final: 0.6842 (mtt-85) REVERT: W 42 GLN cc_start: 0.8176 (tp40) cc_final: 0.7815 (tp40) REVERT: 1 36 GLU cc_start: 0.7874 (tt0) cc_final: 0.7541 (tt0) REVERT: 7 12 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7165 (mtt-85) REVERT: 8 23 MET cc_start: 0.8196 (mmp) cc_final: 0.7849 (mmm) REVERT: 8 38 PHE cc_start: 0.7864 (m-80) cc_final: 0.7624 (m-80) REVERT: 8 51 GLU cc_start: 0.7143 (pm20) cc_final: 0.6587 (pm20) outliers start: 79 outliers final: 52 residues processed: 357 average time/residue: 1.5904 time to fit residues: 653.3101 Evaluate side-chains 362 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 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 L residue 247 CYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 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 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 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 1 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 23 SER 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 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: 6.9990 chunk 92 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095526 restraints weight = 36787.625| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.15 r_work: 0.3078 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- 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 = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.491 30171 Z= 0.245 Angle : 0.915 19.284 41219 Z= 0.346 Chirality : 0.045 0.410 3955 Planarity : 0.005 0.066 4804 Dihedral : 22.416 167.349 7252 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.34 % Allowed : 13.75 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.16), residues: 2699 helix: 1.58 (0.12), residues: 1553 sheet: 0.06 (0.70), residues: 59 loop : -0.31 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 7 2 HIS 0.012 0.003 HIS M 182 PHE 0.027 0.002 PHE C 345 TYR 0.022 0.002 TYR L 164 ARG 0.005 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.05253 ( 1369) hydrogen bonds : angle 4.46730 ( 3861) metal coordination : bond 0.01076 ( 4) metal coordination : angle 6.30024 ( 12) covalent geometry : bond 0.00586 (30108) covalent geometry : angle 0.90837 (41207) Misc. bond : bond 0.08896 ( 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 382 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 3.286 Fit side-chains revert: symmetry clash REVERT: L 202 LYS cc_start: 0.6225 (mppt) cc_final: 0.5762 (tttt) REVERT: M 216 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8318 (t80) REVERT: H 53 ARG cc_start: 0.6952 (mpp-170) cc_final: 0.6697 (mpp80) REVERT: H 82 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6837 (mtt180) REVERT: H 92 THR cc_start: 0.6711 (m) cc_final: 0.6401 (m) REVERT: H 93 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.5960 (tt0) REVERT: H 194 LEU cc_start: 0.7753 (mm) cc_final: 0.7479 (mt) REVERT: G 14 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: J 17 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6719 (mm-30) REVERT: N 10 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6100 (tp) REVERT: P 51 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: S 1 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.3815 (mmp) REVERT: U 3 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7117 (mtp85) REVERT: U 12 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6377 (mtp85) REVERT: V 13 GLU cc_start: 0.6016 (tm-30) cc_final: 0.5678 (tm-30) REVERT: V 14 GLU cc_start: 0.7224 (tp30) cc_final: 0.6918 (tp30) REVERT: W 1 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5424 (tpp) REVERT: W 9 ASP cc_start: 0.7729 (t70) cc_final: 0.7422 (t0) REVERT: W 11 ARG cc_start: 0.7152 (mtt90) cc_final: 0.6835 (mtt-85) REVERT: W 42 GLN cc_start: 0.8158 (tp40) cc_final: 0.7806 (tp40) REVERT: 1 36 GLU cc_start: 0.7900 (tt0) cc_final: 0.7565 (tt0) REVERT: 7 12 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: 8 23 MET cc_start: 0.8208 (mmp) cc_final: 0.7863 (mmm) REVERT: 8 38 PHE cc_start: 0.7831 (m-80) cc_final: 0.7586 (m-80) REVERT: 8 51 GLU cc_start: 0.7143 (pm20) cc_final: 0.6578 (pm20) outliers start: 76 outliers final: 53 residues processed: 357 average time/residue: 1.6736 time to fit residues: 687.8258 Evaluate side-chains 365 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 3.049 ------------------------------------------------------------------------------- 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 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 277 VAL Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain 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 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 51 GLU Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 9 residue 16 LEU Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 17 GLU Chi-restraints excluded: chain 0 residue 30 ILE Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 228 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095291 restraints weight = 36638.671| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.14 r_work: 0.3071 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.501 30171 Z= 0.260 Angle : 0.956 20.722 41219 Z= 0.360 Chirality : 0.046 0.411 3955 Planarity : 0.005 0.067 4804 Dihedral : 22.539 160.033 7252 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.51 % Allowed : 14.02 % Favored : 82.47 % 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: 1.11 (0.16), residues: 2699 helix: 1.54 (0.12), residues: 1542 sheet: -0.20 (0.70), residues: 60 loop : -0.31 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 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 0.007 0.001 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 1369) hydrogen bonds : angle 4.50510 ( 3861) metal coordination : bond 0.01136 ( 4) metal coordination : angle 6.67369 ( 12) covalent geometry : bond 0.00622 (30108) covalent geometry : angle 0.94894 (41207) Misc. bond : bond 0.09068 ( 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 386 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 306 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: C 72 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6683 (mmp80) REVERT: L 202 LYS cc_start: 0.6345 (mppt) cc_final: 0.5801 (tttt) REVERT: M 216 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8330 (t80) REVERT: H 53 ARG cc_start: 0.6962 (mpp-170) cc_final: 0.6710 (mpp80) REVERT: H 82 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6833 (mtt180) REVERT: H 92 THR cc_start: 0.6714 (m) cc_final: 0.6404 (m) REVERT: H 93 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5958 (tt0) REVERT: H 193 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: G 14 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: J 17 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6722 (mm-30) REVERT: N 10 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6092 (tp) REVERT: P 51 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: S 1 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.3851 (mmp) REVERT: U 3 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7122 (mtp85) REVERT: U 12 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6377 (mtp85) REVERT: V 10 LEU cc_start: 0.7073 (mp) cc_final: 0.6857 (mt) REVERT: V 13 GLU cc_start: 0.5977 (tm-30) cc_final: 0.5685 (tm-30) REVERT: V 14 GLU cc_start: 0.7188 (tp30) cc_final: 0.6934 (tp30) REVERT: V 38 PHE cc_start: 0.8354 (m-80) cc_final: 0.8120 (m-80) REVERT: W 1 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5508 (tpp) REVERT: W 9 ASP cc_start: 0.7718 (t70) cc_final: 0.7415 (t0) REVERT: W 11 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6830 (mtt-85) REVERT: W 42 GLN cc_start: 0.8182 (tp40) cc_final: 0.7865 (tp40) REVERT: 1 36 GLU cc_start: 0.7870 (tt0) cc_final: 0.7535 (tt0) REVERT: 7 12 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7107 (mtt-85) REVERT: 8 23 MET cc_start: 0.8182 (mmp) cc_final: 0.7827 (mmm) REVERT: 8 38 PHE cc_start: 0.7848 (m-80) cc_final: 0.7605 (m-80) REVERT: 8 51 GLU cc_start: 0.7141 (pm20) cc_final: 0.6581 (pm20) REVERT: 9 11 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6735 (mtp180) outliers start: 80 outliers final: 54 residues processed: 363 average time/residue: 1.6009 time to fit residues: 668.9309 Evaluate side-chains 367 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ARG 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 252 CYS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 45 ASP 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 8 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain 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 I residue 21 MET Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 50 ASP Chi-restraints excluded: chain 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 36 GLU Chi-restraints excluded: chain U residue 12 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 23 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 0 24 GLN a 39 ASN ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098475 restraints weight = 36630.692| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.18 r_work: 0.3132 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.411 30171 Z= 0.132 Angle : 0.724 16.357 41219 Z= 0.279 Chirality : 0.038 0.375 3955 Planarity : 0.004 0.065 4804 Dihedral : 21.277 156.156 7252 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.28 % Allowed : 15.42 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.16), residues: 2699 helix: 1.99 (0.12), residues: 1546 sheet: -0.13 (0.74), residues: 55 loop : -0.19 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 7 2 HIS 0.006 0.001 HIS M 301 PHE 0.025 0.001 PHE G 26 TYR 0.016 0.001 TYR Y 8 ARG 0.004 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 1369) hydrogen bonds : angle 4.23331 ( 3861) metal coordination : bond 0.00600 ( 4) metal coordination : angle 5.38760 ( 12) covalent geometry : bond 0.00302 (30108) covalent geometry : angle 0.71843 (41207) Misc. bond : bond 0.07183 ( 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 : 2.810 Fit side-chains REVERT: C 241 MET cc_start: 0.8768 (mmt) cc_final: 0.8521 (mmt) REVERT: C 311 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: L 202 LYS cc_start: 0.6158 (mppt) cc_final: 0.5687 (tttt) REVERT: M 216 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8138 (t80) REVERT: H 53 ARG cc_start: 0.6964 (mpp-170) cc_final: 0.6711 (mpp80) REVERT: H 92 THR cc_start: 0.6764 (m) cc_final: 0.6433 (m) REVERT: H 93 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: H 194 LEU cc_start: 0.7634 (mm) cc_final: 0.7370 (mt) REVERT: J 17 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6652 (mm-30) REVERT: U 3 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7151 (mtp85) REVERT: V 10 LEU cc_start: 0.7052 (mp) cc_final: 0.6849 (mt) REVERT: V 13 GLU cc_start: 0.6053 (tm-30) cc_final: 0.5713 (tm-30) REVERT: V 14 GLU cc_start: 0.7319 (tp30) cc_final: 0.7030 (tp30) REVERT: W 1 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5400 (tpp) REVERT: W 9 ASP cc_start: 0.7676 (t70) cc_final: 0.7315 (t0) REVERT: W 42 GLN cc_start: 0.8140 (tp40) cc_final: 0.7826 (tp40) REVERT: 1 36 GLU cc_start: 0.7922 (tt0) cc_final: 0.7703 (tp30) REVERT: 6 16 LYS cc_start: 0.7808 (mttp) cc_final: 0.7506 (mmmm) REVERT: 7 12 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6690 (mtt-85) REVERT: 8 23 MET cc_start: 0.8146 (mmp) cc_final: 0.7832 (mmm) REVERT: 8 38 PHE cc_start: 0.7878 (m-80) cc_final: 0.7649 (m-80) REVERT: 8 51 GLU cc_start: 0.7100 (pm20) cc_final: 0.6657 (pm20) REVERT: a 70 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5755 (p0) REVERT: a 81 PHE cc_start: 0.7273 (m-80) cc_final: 0.6632 (m-80) outliers start: 52 outliers final: 30 residues processed: 350 average time/residue: 1.5973 time to fit residues: 642.9932 Evaluate side-chains 339 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 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 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 93 GLN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain Q residue 36 ASP Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain 3 residue 7 LEU Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain 5 residue 16 LEU Chi-restraints excluded: chain 7 residue 12 ARG Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 6 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 a 39 ASN ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096471 restraints weight = 36710.913| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.18 r_work: 0.3098 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 30171 Z= 0.181 Angle : 0.806 16.666 41219 Z= 0.308 Chirality : 0.041 0.380 3955 Planarity : 0.004 0.065 4804 Dihedral : 21.317 157.315 7252 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 15.69 % Favored : 82.03 % 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: 1.91 (0.12), residues: 1547 sheet: -0.04 (0.69), residues: 59 loop : -0.20 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 7 2 HIS 0.009 0.002 HIS M 182 PHE 0.023 0.002 PHE C 345 TYR 0.018 0.002 TYR L 164 ARG 0.008 0.001 ARG S 3 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1369) hydrogen bonds : angle 4.29272 ( 3861) metal coordination : bond 0.00897 ( 4) metal coordination : angle 5.85270 ( 12) covalent geometry : bond 0.00424 (30108) covalent geometry : angle 0.79948 (41207) Misc. bond : bond 0.08051 ( 59) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24122.36 seconds wall clock time: 415 minutes 8.57 seconds (24908.57 seconds total)