Starting phenix.real_space_refine on Thu Sep 18 14:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.map" model { file = "/net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cz8_46063/09_2025/9cz8_46063.cif" } resolution = 1.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Fe 68 7.16 5 S 36 5.16 5 C 10656 2.51 5 N 2688 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "B" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "C" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "D" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "E" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "F" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "G" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "H" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "I" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "J" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "K" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "L" Number of atoms: 1378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1374 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1396 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' O': 7, ' FE': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' O': 7, ' FE': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' O': 7, ' FE': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' O': 7, ' FE': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' O': 5, ' FE': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Residues with excluded nonbonded symmetry interactions: 652 residue: pdb="FE FE A 201 " occ=0.60 residue: pdb="FE FE A 202 " occ=0.52 residue: pdb="FE FE A 203 " occ=0.28 residue: pdb=" O O A 204 " occ=0.79 residue: pdb="FE FE A 205 " occ=0.43 residue: pdb=" O O A 206 " occ=0.00 residue: pdb=" O O A 207 " occ=0.01 residue: pdb=" O O A 208 " occ=0.42 residue: pdb="FE FE A 209 " occ=0.14 residue: pdb=" O O A 210 " occ=0.53 residue: pdb="FE FE A 211 " occ=0.69 residue: pdb=" O O A 212 " occ=0.78 ... (remaining 640 not shown) Time building chain proxies: 7.03, per 1000 atoms: 0.41 Number of scatterers: 17188 At special positions: 0 Unit cell: (104.19, 110.4, 102.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 68 26.01 S 36 16.00 O 3740 8.00 N 2688 7.00 C 10656 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=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 104 through 131 Processing helix chain 'A' and resid 134 through 161 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'B' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 3.816A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 104 through 131 Processing helix chain 'B' and resid 134 through 161 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'C' and resid 15 through 43 removed outlier: 3.548A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 104 through 131 Processing helix chain 'C' and resid 134 through 161 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'D' and resid 15 through 43 removed outlier: 3.548A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 104 through 131 Processing helix chain 'D' and resid 134 through 161 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 15 through 43 removed outlier: 3.548A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 104 through 131 Processing helix chain 'E' and resid 134 through 161 Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 3.816A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 104 through 131 Processing helix chain 'F' and resid 134 through 161 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'G' and resid 15 through 43 removed outlier: 3.548A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 104 through 131 Processing helix chain 'G' and resid 134 through 161 Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'H' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 39 " --> pdb=" O TYR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 3.816A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 84 through 91 Processing helix chain 'H' and resid 104 through 131 Processing helix chain 'H' and resid 134 through 161 Processing helix chain 'H' and resid 178 through 182 Processing helix chain 'I' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE I 39 " --> pdb=" O TYR I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.816A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 72 - end of helix Processing helix chain 'I' and resid 84 through 91 Processing helix chain 'I' and resid 104 through 131 Processing helix chain 'I' and resid 134 through 161 Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'J' and resid 15 through 43 removed outlier: 3.548A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE J 39 " --> pdb=" O TYR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.816A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 72 - end of helix Processing helix chain 'J' and resid 84 through 91 Processing helix chain 'J' and resid 104 through 131 Processing helix chain 'J' and resid 134 through 161 Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'K' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 3.818A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 72 - end of helix Processing helix chain 'K' and resid 84 through 91 Processing helix chain 'K' and resid 104 through 131 Processing helix chain 'K' and resid 134 through 161 Processing helix chain 'K' and resid 178 through 182 Processing helix chain 'L' and resid 15 through 43 removed outlier: 3.549A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE L 39 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.817A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 72 - end of helix Processing helix chain 'L' and resid 84 through 91 Processing helix chain 'L' and resid 104 through 131 Processing helix chain 'L' and resid 134 through 161 Processing helix chain 'L' and resid 178 through 182 1188 hydrogen bonds defined for protein. 3480 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: 2.69 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4721 1.33 - 1.45: 2891 1.45 - 1.57: 9272 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 16920 Sorted by residual: bond pdb=" CB AVAL C 178 " pdb=" CG2AVAL C 178 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.57e+00 bond pdb=" CB AVAL G 178 " pdb=" CG2AVAL G 178 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.57e+00 bond pdb=" CB AVAL F 178 " pdb=" CG2AVAL F 178 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CB AVAL J 178 " pdb=" CG2AVAL J 178 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.53e+00 bond pdb=" CB AVAL D 178 " pdb=" CG2AVAL D 178 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 ... (remaining 16915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 19809 0.98 - 1.97: 2387 1.97 - 2.95: 477 2.95 - 3.93: 187 3.93 - 4.91: 96 Bond angle restraints: 22956 Sorted by residual: angle pdb=" CB GLU J 147 " pdb=" CG GLU J 147 " pdb=" CD GLU J 147 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.70e+00 3.46e-01 7.61e+00 angle pdb=" CB GLU I 147 " pdb=" CG GLU I 147 " pdb=" CD GLU I 147 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.70e+00 3.46e-01 7.53e+00 angle pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.70e+00 3.46e-01 7.48e+00 angle pdb=" CB GLU H 147 " pdb=" CG GLU H 147 " pdb=" CD GLU H 147 " ideal model delta sigma weight residual 112.60 117.24 -4.64 1.70e+00 3.46e-01 7.44e+00 angle pdb=" CB GLU D 147 " pdb=" CG GLU D 147 " pdb=" CD GLU D 147 " ideal model delta sigma weight residual 112.60 117.23 -4.63 1.70e+00 3.46e-01 7.43e+00 ... (remaining 22951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 9096 14.96 - 29.92: 900 29.92 - 44.87: 132 44.87 - 59.83: 36 59.83 - 74.79: 36 Dihedral angle restraints: 10200 sinusoidal: 4164 harmonic: 6036 Sorted by residual: dihedral pdb=" CA PHE G 167 " pdb=" C PHE G 167 " pdb=" N ARG G 168 " pdb=" CA ARG G 168 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE L 167 " pdb=" C PHE L 167 " pdb=" N ARG L 168 " pdb=" CA ARG L 168 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE D 167 " pdb=" C PHE D 167 " pdb=" N ARG D 168 " pdb=" CA ARG D 168 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 10197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 938 0.033 - 0.066: 997 0.066 - 0.099: 406 0.099 - 0.132: 165 0.132 - 0.164: 26 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CG LEU K 40 " pdb=" CB LEU K 40 " pdb=" CD1 LEU K 40 " pdb=" CD2 LEU K 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CG LEU C 40 " pdb=" CB LEU C 40 " pdb=" CD1 LEU C 40 " pdb=" CD2 LEU C 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CG LEU E 40 " pdb=" CB LEU E 40 " pdb=" CD1 LEU E 40 " pdb=" CD2 LEU E 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 2529 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 167 " 0.028 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE D 167 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE D 167 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 167 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 167 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE D 167 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 167 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 167 " -0.028 2.00e-02 2.50e+03 1.80e-02 5.67e+00 pdb=" CG PHE F 167 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE F 167 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE F 167 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE F 167 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 167 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 167 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 167 " 0.028 2.00e-02 2.50e+03 1.80e-02 5.67e+00 pdb=" CG PHE C 167 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE C 167 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 167 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 167 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 167 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 298 2.40 - 3.02: 10966 3.02 - 3.65: 29506 3.65 - 4.27: 45718 4.27 - 4.90: 71250 Nonbonded interactions: 157738 Sorted by model distance: nonbonded pdb=" OE2 GLU G 50 " pdb="FE FE G 208 " model vdw 1.774 2.260 nonbonded pdb="FE FE A 213 " pdb=" O O A 214 " model vdw 1.794 2.020 nonbonded pdb="FE FE J 211 " pdb=" O O J 212 " model vdw 1.794 2.020 nonbonded pdb="FE FE G 212 " pdb=" O O G 213 " model vdw 1.795 2.020 nonbonded pdb="FE FE D 213 " pdb=" O O D 214 " model vdw 1.795 2.020 ... (remaining 157733 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'B' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'C' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'D' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'E' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'F' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'G' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'H' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'I' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'J' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'K' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) selection = (chain 'L' and (resid 14 through 117 or resid 119 through 177 or resid 179 throu \ gh 203)) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.000 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.078 16920 Z= 0.421 Angle : 0.800 4.915 22956 Z= 0.437 Chirality : 0.057 0.164 2532 Planarity : 0.009 0.085 2976 Dihedral : 13.147 74.789 6336 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.17), residues: 2028 helix: 1.16 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : 1.14 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG J 136 TYR 0.025 0.004 TYR C 123 PHE 0.034 0.005 PHE D 167 TRP 0.008 0.003 TRP F 154 HIS 0.008 0.003 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00926 (16920) covalent geometry : angle 0.80004 (22956) hydrogen bonds : bond 0.16510 ( 1188) hydrogen bonds : angle 6.82172 ( 3480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8399 (tttt) cc_final: 0.8050 (tptp) REVERT: A 102 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7272 (tp30) REVERT: A 114 GLU cc_start: 0.8456 (tt0) cc_final: 0.8181 (tm-30) REVERT: B 18 LYS cc_start: 0.8462 (tttt) cc_final: 0.8098 (tptp) REVERT: B 114 GLU cc_start: 0.8501 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 174 GLU cc_start: 0.7784 (tt0) cc_final: 0.7348 (tm-30) REVERT: C 17 GLU cc_start: 0.7768 (mp0) cc_final: 0.7555 (mp0) REVERT: C 18 LYS cc_start: 0.8422 (tttt) cc_final: 0.8095 (tptt) REVERT: C 114 GLU cc_start: 0.8460 (tt0) cc_final: 0.8201 (tm-30) REVERT: D 18 LYS cc_start: 0.8435 (tttt) cc_final: 0.8089 (tptp) REVERT: D 114 GLU cc_start: 0.8488 (tt0) cc_final: 0.8269 (tm-30) REVERT: E 18 LYS cc_start: 0.8348 (tttt) cc_final: 0.8004 (tptm) REVERT: E 114 GLU cc_start: 0.8429 (tt0) cc_final: 0.8042 (mp0) REVERT: E 174 GLU cc_start: 0.7729 (tt0) cc_final: 0.7364 (tm-30) REVERT: F 18 LYS cc_start: 0.8408 (tttt) cc_final: 0.8067 (tptp) REVERT: G 18 LYS cc_start: 0.8457 (tttt) cc_final: 0.8118 (tptm) REVERT: H 18 LYS cc_start: 0.8295 (tttt) cc_final: 0.7927 (tptt) REVERT: H 21 GLU cc_start: 0.8265 (tt0) cc_final: 0.8046 (tm-30) REVERT: H 80 GLU cc_start: 0.7886 (pt0) cc_final: 0.7682 (mt-10) REVERT: H 102 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7293 (tp30) REVERT: H 114 GLU cc_start: 0.8329 (tt0) cc_final: 0.8077 (tm-30) REVERT: H 174 GLU cc_start: 0.7719 (tt0) cc_final: 0.7333 (tm-30) REVERT: I 18 LYS cc_start: 0.8329 (tttt) cc_final: 0.7993 (tptp) REVERT: J 18 LYS cc_start: 0.8412 (tttt) cc_final: 0.8053 (tptp) REVERT: J 114 GLU cc_start: 0.8497 (tt0) cc_final: 0.8294 (tm-30) REVERT: K 18 LYS cc_start: 0.8417 (tttt) cc_final: 0.8046 (tptp) REVERT: L 18 LYS cc_start: 0.8429 (tttt) cc_final: 0.8108 (tptp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.0609 time to fit residues: 420.3491 Evaluate side-chains 349 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131762 restraints weight = 32345.415| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.68 r_work: 0.3485 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16920 Z= 0.154 Angle : 0.560 4.491 22956 Z= 0.309 Chirality : 0.039 0.132 2532 Planarity : 0.004 0.024 2976 Dihedral : 4.255 18.321 2292 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.18), residues: 2028 helix: 1.99 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.38 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.022 0.002 TYR I 123 PHE 0.014 0.002 PHE F 31 TRP 0.005 0.001 TRP D 154 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00279 (16920) covalent geometry : angle 0.56020 (22956) hydrogen bonds : bond 0.07269 ( 1188) hydrogen bonds : angle 5.58847 ( 3480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.699 Fit side-chains REVERT: A 18 LYS cc_start: 0.8169 (tttt) cc_final: 0.7752 (tptm) REVERT: A 114 GLU cc_start: 0.8388 (tt0) cc_final: 0.8033 (tm-30) REVERT: B 18 LYS cc_start: 0.8166 (tttt) cc_final: 0.7704 (tptt) REVERT: B 114 GLU cc_start: 0.8350 (tt0) cc_final: 0.8094 (tm-30) REVERT: B 174 GLU cc_start: 0.7744 (tt0) cc_final: 0.7232 (tm-30) REVERT: C 18 LYS cc_start: 0.8233 (tttt) cc_final: 0.7783 (tptm) REVERT: C 102 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7081 (tp30) REVERT: C 114 GLU cc_start: 0.8411 (tt0) cc_final: 0.8004 (tm-30) REVERT: D 16 VAL cc_start: 0.8672 (t) cc_final: 0.8318 (p) REVERT: D 18 LYS cc_start: 0.8155 (tttt) cc_final: 0.7675 (tptp) REVERT: D 114 GLU cc_start: 0.8295 (tt0) cc_final: 0.7961 (tm-30) REVERT: E 18 LYS cc_start: 0.8147 (tttt) cc_final: 0.7648 (tptm) REVERT: E 106 GLU cc_start: 0.8127 (tp30) cc_final: 0.7895 (tm-30) REVERT: E 114 GLU cc_start: 0.8315 (tt0) cc_final: 0.8023 (tm-30) REVERT: F 17 GLU cc_start: 0.7833 (mp0) cc_final: 0.7432 (mp0) REVERT: F 18 LYS cc_start: 0.8288 (tttt) cc_final: 0.7816 (tptm) REVERT: G 18 LYS cc_start: 0.8260 (tttt) cc_final: 0.7802 (tptm) REVERT: G 106 GLU cc_start: 0.8061 (tp30) cc_final: 0.7659 (mp0) REVERT: H 16 VAL cc_start: 0.8511 (t) cc_final: 0.8154 (p) REVERT: H 18 LYS cc_start: 0.8159 (tttt) cc_final: 0.7647 (tptt) REVERT: H 21 GLU cc_start: 0.8221 (tt0) cc_final: 0.7885 (tm-30) REVERT: H 80 GLU cc_start: 0.7967 (pt0) cc_final: 0.7657 (mt-10) REVERT: H 102 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7087 (tp30) REVERT: H 114 GLU cc_start: 0.8313 (tt0) cc_final: 0.8056 (tm-30) REVERT: H 174 GLU cc_start: 0.7671 (tt0) cc_final: 0.7294 (tm-30) REVERT: I 18 LYS cc_start: 0.8272 (tttt) cc_final: 0.7867 (tptm) REVERT: I 87 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7411 (tp30) REVERT: J 18 LYS cc_start: 0.8177 (tttt) cc_final: 0.7750 (tptm) REVERT: J 114 GLU cc_start: 0.8381 (tt0) cc_final: 0.8142 (tm-30) REVERT: K 18 LYS cc_start: 0.8226 (tttt) cc_final: 0.7704 (tptm) REVERT: K 114 GLU cc_start: 0.8289 (tt0) cc_final: 0.7991 (tm-30) REVERT: L 18 LYS cc_start: 0.8238 (tttt) cc_final: 0.7853 (tptm) REVERT: L 106 GLU cc_start: 0.8052 (tp30) cc_final: 0.7726 (mp0) REVERT: L 114 GLU cc_start: 0.8231 (tt0) cc_final: 0.8013 (tm-30) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 1.0286 time to fit residues: 434.9833 Evaluate side-chains 379 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS B 166 HIS C 166 HIS F 166 HIS G 166 HIS J 166 HIS L 166 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130355 restraints weight = 31342.040| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.65 r_work: 0.3468 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16920 Z= 0.153 Angle : 0.543 4.704 22956 Z= 0.302 Chirality : 0.038 0.128 2532 Planarity : 0.004 0.034 2976 Dihedral : 4.194 18.648 2292 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.19), residues: 2028 helix: 2.06 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.59 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 136 TYR 0.020 0.002 TYR I 123 PHE 0.011 0.002 PHE F 31 TRP 0.005 0.001 TRP D 154 HIS 0.005 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00281 (16920) covalent geometry : angle 0.54304 (22956) hydrogen bonds : bond 0.07165 ( 1188) hydrogen bonds : angle 5.44853 ( 3480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 0.686 Fit side-chains REVERT: A 18 LYS cc_start: 0.8180 (tttt) cc_final: 0.7731 (tmtm) REVERT: A 114 GLU cc_start: 0.8369 (tt0) cc_final: 0.8028 (tm-30) REVERT: B 18 LYS cc_start: 0.8174 (tttt) cc_final: 0.7733 (tptt) REVERT: B 114 GLU cc_start: 0.8330 (tt0) cc_final: 0.8049 (tm-30) REVERT: B 174 GLU cc_start: 0.7747 (tt0) cc_final: 0.7242 (tm-30) REVERT: C 18 LYS cc_start: 0.8222 (tttt) cc_final: 0.7758 (tptt) REVERT: C 114 GLU cc_start: 0.8378 (tt0) cc_final: 0.8015 (tm-30) REVERT: D 16 VAL cc_start: 0.8651 (t) cc_final: 0.8299 (p) REVERT: D 18 LYS cc_start: 0.8148 (tttt) cc_final: 0.7668 (tptp) REVERT: D 114 GLU cc_start: 0.8287 (tt0) cc_final: 0.7947 (tm-30) REVERT: E 17 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: E 18 LYS cc_start: 0.8196 (tttt) cc_final: 0.7707 (tptm) REVERT: E 114 GLU cc_start: 0.8312 (tt0) cc_final: 0.8029 (tm-30) REVERT: E 174 GLU cc_start: 0.7697 (tt0) cc_final: 0.7327 (tm-30) REVERT: F 18 LYS cc_start: 0.8266 (tttt) cc_final: 0.7825 (tptt) REVERT: G 18 LYS cc_start: 0.8235 (tttt) cc_final: 0.7792 (tptm) REVERT: H 17 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: H 18 LYS cc_start: 0.8208 (tttt) cc_final: 0.7736 (tptt) REVERT: H 102 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7084 (tp30) REVERT: H 114 GLU cc_start: 0.8270 (tt0) cc_final: 0.8022 (tm-30) REVERT: H 174 GLU cc_start: 0.7655 (tt0) cc_final: 0.7261 (tm-30) REVERT: I 18 LYS cc_start: 0.8274 (tttt) cc_final: 0.7844 (tptm) REVERT: I 87 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7466 (tp30) REVERT: J 16 VAL cc_start: 0.8603 (t) cc_final: 0.8242 (p) REVERT: J 18 LYS cc_start: 0.8234 (tttt) cc_final: 0.7824 (tptm) REVERT: J 114 GLU cc_start: 0.8358 (tt0) cc_final: 0.8096 (tm-30) REVERT: K 18 LYS cc_start: 0.8207 (tttt) cc_final: 0.7684 (tptm) REVERT: K 114 GLU cc_start: 0.8314 (tt0) cc_final: 0.7984 (tm-30) REVERT: L 18 LYS cc_start: 0.8252 (tttt) cc_final: 0.7862 (tptt) REVERT: L 114 GLU cc_start: 0.8248 (tt0) cc_final: 0.7974 (tm-30) outliers start: 3 outliers final: 0 residues processed: 398 average time/residue: 1.0365 time to fit residues: 440.8101 Evaluate side-chains 376 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 5 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 125 optimal weight: 0.0050 chunk 100 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133102 restraints weight = 29828.154| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.61 r_work: 0.3505 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16920 Z= 0.140 Angle : 0.515 4.497 22956 Z= 0.285 Chirality : 0.036 0.120 2532 Planarity : 0.004 0.034 2976 Dihedral : 4.088 18.242 2292 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.19), residues: 2028 helix: 2.17 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.66 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.018 0.002 TYR I 123 PHE 0.012 0.002 PHE F 31 TRP 0.004 0.001 TRP D 154 HIS 0.004 0.001 HIS J 146 Details of bonding type rmsd covalent geometry : bond 0.00253 (16920) covalent geometry : angle 0.51498 (22956) hydrogen bonds : bond 0.06581 ( 1188) hydrogen bonds : angle 5.30827 ( 3480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8109 (tttt) cc_final: 0.7679 (tmtm) REVERT: A 48 GLU cc_start: 0.7454 (pt0) cc_final: 0.7249 (pt0) REVERT: A 106 GLU cc_start: 0.8012 (tp30) cc_final: 0.7575 (mp0) REVERT: A 114 GLU cc_start: 0.8351 (tt0) cc_final: 0.8001 (tm-30) REVERT: B 18 LYS cc_start: 0.8153 (tttt) cc_final: 0.7948 (tttm) REVERT: B 114 GLU cc_start: 0.8307 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 174 GLU cc_start: 0.7713 (tt0) cc_final: 0.7201 (tm-30) REVERT: C 18 LYS cc_start: 0.8145 (tttt) cc_final: 0.7705 (tptt) REVERT: C 114 GLU cc_start: 0.8365 (tt0) cc_final: 0.7994 (tm-30) REVERT: D 16 VAL cc_start: 0.8606 (t) cc_final: 0.8257 (p) REVERT: D 18 LYS cc_start: 0.8098 (tttt) cc_final: 0.7639 (tptp) REVERT: D 114 GLU cc_start: 0.8261 (tt0) cc_final: 0.7906 (tm-30) REVERT: E 18 LYS cc_start: 0.8164 (tttt) cc_final: 0.7648 (tptt) REVERT: E 95 ARG cc_start: 0.7368 (mtt180) cc_final: 0.7144 (tmt170) REVERT: E 114 GLU cc_start: 0.8252 (tt0) cc_final: 0.8002 (tm-30) REVERT: E 174 GLU cc_start: 0.7657 (tt0) cc_final: 0.7283 (tm-30) REVERT: F 17 GLU cc_start: 0.7812 (mp0) cc_final: 0.7388 (mp0) REVERT: F 18 LYS cc_start: 0.8193 (tttt) cc_final: 0.7694 (tptt) REVERT: F 106 GLU cc_start: 0.7839 (tp30) cc_final: 0.7504 (mp0) REVERT: G 18 LYS cc_start: 0.8157 (tttt) cc_final: 0.7707 (tptm) REVERT: H 16 VAL cc_start: 0.8518 (t) cc_final: 0.8173 (p) REVERT: H 17 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: H 18 LYS cc_start: 0.8141 (tttt) cc_final: 0.7649 (tptt) REVERT: H 174 GLU cc_start: 0.7563 (tt0) cc_final: 0.7122 (tm-30) REVERT: I 18 LYS cc_start: 0.8227 (tttt) cc_final: 0.7811 (tptt) REVERT: I 87 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7414 (tp30) REVERT: J 16 VAL cc_start: 0.8566 (t) cc_final: 0.8199 (p) REVERT: J 18 LYS cc_start: 0.8136 (tttt) cc_final: 0.7711 (tptm) REVERT: J 114 GLU cc_start: 0.8341 (tt0) cc_final: 0.8082 (tm-30) REVERT: K 18 LYS cc_start: 0.8136 (tttt) cc_final: 0.7614 (tptt) REVERT: K 95 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7119 (tmt170) REVERT: K 114 GLU cc_start: 0.8271 (tt0) cc_final: 0.7995 (tm-30) REVERT: L 18 LYS cc_start: 0.8145 (tttt) cc_final: 0.7762 (tptt) outliers start: 3 outliers final: 0 residues processed: 390 average time/residue: 1.0081 time to fit residues: 420.3167 Evaluate side-chains 380 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 HIS H 166 HIS I 166 HIS K 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123204 restraints weight = 27936.465| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.60 r_work: 0.3348 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16920 Z= 0.153 Angle : 0.542 4.590 22956 Z= 0.299 Chirality : 0.037 0.125 2532 Planarity : 0.004 0.035 2976 Dihedral : 4.107 17.940 2292 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.19), residues: 2028 helix: 2.10 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.73 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.021 0.002 TYR I 123 PHE 0.009 0.002 PHE B 31 TRP 0.003 0.001 TRP D 154 HIS 0.004 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00283 (16920) covalent geometry : angle 0.54157 (22956) hydrogen bonds : bond 0.07113 ( 1188) hydrogen bonds : angle 5.35795 ( 3480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.723 Fit side-chains REVERT: A 18 LYS cc_start: 0.8242 (tttt) cc_final: 0.7804 (tmtm) REVERT: A 48 GLU cc_start: 0.7544 (pt0) cc_final: 0.7335 (pt0) REVERT: A 114 GLU cc_start: 0.8447 (tt0) cc_final: 0.8094 (tm-30) REVERT: B 114 GLU cc_start: 0.8440 (tt0) cc_final: 0.8129 (tm-30) REVERT: B 174 GLU cc_start: 0.7765 (tt0) cc_final: 0.7280 (tm-30) REVERT: C 18 LYS cc_start: 0.8293 (tttt) cc_final: 0.7850 (tptt) REVERT: C 102 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7037 (tp30) REVERT: C 114 GLU cc_start: 0.8493 (tt0) cc_final: 0.8123 (tm-30) REVERT: D 16 VAL cc_start: 0.8660 (t) cc_final: 0.8320 (p) REVERT: D 18 LYS cc_start: 0.8152 (tttt) cc_final: 0.7680 (tptp) REVERT: D 114 GLU cc_start: 0.8423 (tt0) cc_final: 0.8056 (tm-30) REVERT: E 17 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: E 18 LYS cc_start: 0.8289 (tttt) cc_final: 0.7796 (tptt) REVERT: E 95 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7246 (tmt170) REVERT: E 114 GLU cc_start: 0.8326 (tt0) cc_final: 0.8067 (tm-30) REVERT: E 174 GLU cc_start: 0.7742 (tt0) cc_final: 0.7366 (tm-30) REVERT: F 17 GLU cc_start: 0.7914 (mp0) cc_final: 0.7496 (mp0) REVERT: F 18 LYS cc_start: 0.8288 (tttt) cc_final: 0.8026 (tttm) REVERT: G 18 LYS cc_start: 0.8279 (tttt) cc_final: 0.7827 (tptm) REVERT: H 17 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: H 18 LYS cc_start: 0.8249 (tttt) cc_final: 0.7759 (tptt) REVERT: H 114 GLU cc_start: 0.8439 (tt0) cc_final: 0.7934 (tm-30) REVERT: I 18 LYS cc_start: 0.8330 (tttt) cc_final: 0.7902 (tptm) REVERT: J 16 VAL cc_start: 0.8645 (t) cc_final: 0.8284 (p) REVERT: J 18 LYS cc_start: 0.8284 (tttt) cc_final: 0.7881 (tptm) REVERT: J 114 GLU cc_start: 0.8443 (tt0) cc_final: 0.8175 (tm-30) REVERT: K 18 LYS cc_start: 0.8260 (tttt) cc_final: 0.7760 (tptt) REVERT: K 95 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7186 (tmt170) REVERT: K 114 GLU cc_start: 0.8386 (tt0) cc_final: 0.8050 (tm-30) REVERT: L 18 LYS cc_start: 0.8302 (tttt) cc_final: 0.7893 (tptt) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 1.0202 time to fit residues: 413.2303 Evaluate side-chains 369 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 161 optimal weight: 0.0000 chunk 189 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124359 restraints weight = 39727.345| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.87 r_work: 0.3362 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16920 Z= 0.139 Angle : 0.525 5.716 22956 Z= 0.286 Chirality : 0.036 0.119 2532 Planarity : 0.004 0.029 2976 Dihedral : 4.019 17.629 2292 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.19), residues: 2028 helix: 2.17 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.83 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.018 0.002 TYR I 123 PHE 0.011 0.002 PHE F 31 TRP 0.004 0.001 TRP F 154 HIS 0.003 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00250 (16920) covalent geometry : angle 0.52467 (22956) hydrogen bonds : bond 0.06528 ( 1188) hydrogen bonds : angle 5.25111 ( 3480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.632 Fit side-chains REVERT: A 18 LYS cc_start: 0.8233 (tttt) cc_final: 0.7796 (tmtm) REVERT: A 48 GLU cc_start: 0.7483 (pt0) cc_final: 0.7265 (pt0) REVERT: A 87 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7333 (tp30) REVERT: A 114 GLU cc_start: 0.8443 (tt0) cc_final: 0.8079 (tm-30) REVERT: B 114 GLU cc_start: 0.8457 (tt0) cc_final: 0.8136 (tm-30) REVERT: B 174 GLU cc_start: 0.7784 (tt0) cc_final: 0.7234 (tm-30) REVERT: C 18 LYS cc_start: 0.8260 (tttt) cc_final: 0.7809 (tptt) REVERT: C 102 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7038 (tp30) REVERT: C 114 GLU cc_start: 0.8520 (tt0) cc_final: 0.8131 (tm-30) REVERT: D 16 VAL cc_start: 0.8647 (t) cc_final: 0.8306 (p) REVERT: D 18 LYS cc_start: 0.8162 (tttt) cc_final: 0.7693 (tptp) REVERT: D 114 GLU cc_start: 0.8434 (tt0) cc_final: 0.8042 (tm-30) REVERT: E 18 LYS cc_start: 0.8265 (tttt) cc_final: 0.7773 (tptt) REVERT: E 95 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7276 (tmt170) REVERT: E 114 GLU cc_start: 0.8344 (tt0) cc_final: 0.8090 (tm-30) REVERT: E 174 GLU cc_start: 0.7745 (tt0) cc_final: 0.7361 (tm-30) REVERT: F 17 GLU cc_start: 0.7955 (mp0) cc_final: 0.7546 (mp0) REVERT: F 18 LYS cc_start: 0.8274 (tttt) cc_final: 0.8017 (tttm) REVERT: F 87 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7423 (tp30) REVERT: G 18 LYS cc_start: 0.8254 (tttt) cc_final: 0.7797 (tptm) REVERT: H 17 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: H 18 LYS cc_start: 0.8228 (tttt) cc_final: 0.7734 (tptt) REVERT: H 114 GLU cc_start: 0.8432 (tt0) cc_final: 0.7914 (tm-30) REVERT: I 18 LYS cc_start: 0.8286 (tttt) cc_final: 0.7864 (tptt) REVERT: I 87 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7514 (tp30) REVERT: J 16 VAL cc_start: 0.8633 (t) cc_final: 0.8269 (p) REVERT: J 18 LYS cc_start: 0.8270 (tttt) cc_final: 0.7848 (tptt) REVERT: J 114 GLU cc_start: 0.8464 (tt0) cc_final: 0.8180 (tm-30) REVERT: K 18 LYS cc_start: 0.8241 (tttt) cc_final: 0.7758 (tptt) REVERT: K 114 GLU cc_start: 0.8390 (tt0) cc_final: 0.8093 (tm-30) REVERT: L 18 LYS cc_start: 0.8268 (tttt) cc_final: 0.7862 (tptt) outliers start: 1 outliers final: 0 residues processed: 384 average time/residue: 1.0133 time to fit residues: 415.5023 Evaluate side-chains 366 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 51 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 143 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123134 restraints weight = 35946.754| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.79 r_work: 0.3343 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16920 Z= 0.149 Angle : 0.548 6.496 22956 Z= 0.298 Chirality : 0.036 0.124 2532 Planarity : 0.004 0.032 2976 Dihedral : 4.048 17.486 2292 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.19), residues: 2028 helix: 2.12 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.80 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 41 TYR 0.020 0.002 TYR I 123 PHE 0.010 0.002 PHE B 31 TRP 0.002 0.001 TRP C 154 HIS 0.004 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00274 (16920) covalent geometry : angle 0.54775 (22956) hydrogen bonds : bond 0.06890 ( 1188) hydrogen bonds : angle 5.28430 ( 3480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.705 Fit side-chains REVERT: A 18 LYS cc_start: 0.8233 (tttt) cc_final: 0.7790 (tmtm) REVERT: A 48 GLU cc_start: 0.7493 (pt0) cc_final: 0.7276 (pt0) REVERT: A 114 GLU cc_start: 0.8464 (tt0) cc_final: 0.8078 (tm-30) REVERT: B 114 GLU cc_start: 0.8472 (tt0) cc_final: 0.8125 (tm-30) REVERT: B 174 GLU cc_start: 0.7770 (tt0) cc_final: 0.7280 (tm-30) REVERT: C 18 LYS cc_start: 0.8298 (tttt) cc_final: 0.7834 (tptt) REVERT: C 102 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7043 (tp30) REVERT: C 114 GLU cc_start: 0.8537 (tt0) cc_final: 0.8123 (tm-30) REVERT: D 16 VAL cc_start: 0.8637 (t) cc_final: 0.8293 (p) REVERT: D 18 LYS cc_start: 0.8152 (tttt) cc_final: 0.7666 (tptp) REVERT: D 114 GLU cc_start: 0.8456 (tt0) cc_final: 0.8048 (tm-30) REVERT: E 18 LYS cc_start: 0.8273 (tttt) cc_final: 0.7786 (tptt) REVERT: E 95 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7235 (tmt170) REVERT: E 114 GLU cc_start: 0.8353 (tt0) cc_final: 0.8060 (tm-30) REVERT: E 174 GLU cc_start: 0.7741 (tt0) cc_final: 0.7284 (tm-30) REVERT: F 17 GLU cc_start: 0.7943 (mp0) cc_final: 0.7525 (mp0) REVERT: F 18 LYS cc_start: 0.8283 (tttt) cc_final: 0.8010 (tttm) REVERT: F 87 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7415 (tp30) REVERT: G 18 LYS cc_start: 0.8267 (tttt) cc_final: 0.7802 (tptm) REVERT: H 17 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: H 18 LYS cc_start: 0.8256 (tttt) cc_final: 0.7748 (tptt) REVERT: H 114 GLU cc_start: 0.8453 (tt0) cc_final: 0.7927 (tm-30) REVERT: I 18 LYS cc_start: 0.8318 (tttt) cc_final: 0.7880 (tptt) REVERT: I 87 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7512 (tp30) REVERT: J 16 VAL cc_start: 0.8635 (t) cc_final: 0.8272 (p) REVERT: J 18 LYS cc_start: 0.8287 (tttt) cc_final: 0.7864 (tptt) REVERT: J 114 GLU cc_start: 0.8490 (tt0) cc_final: 0.8182 (tm-30) REVERT: K 18 LYS cc_start: 0.8261 (tttt) cc_final: 0.7767 (tptt) REVERT: K 114 GLU cc_start: 0.8399 (tt0) cc_final: 0.8037 (tm-30) REVERT: L 18 LYS cc_start: 0.8289 (tttt) cc_final: 0.7864 (tptt) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.9929 time to fit residues: 398.0930 Evaluate side-chains 368 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103060 restraints weight = 30244.150| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.85 r_work: 0.2984 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16920 Z= 0.268 Angle : 0.721 7.338 22956 Z= 0.395 Chirality : 0.045 0.143 2532 Planarity : 0.007 0.062 2976 Dihedral : 4.387 16.845 2292 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.18), residues: 2028 helix: 1.78 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.72 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 41 TYR 0.029 0.004 TYR L 75 PHE 0.015 0.004 PHE D 167 TRP 0.006 0.002 TRP I 154 HIS 0.008 0.002 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00563 (16920) covalent geometry : angle 0.72119 (22956) hydrogen bonds : bond 0.08960 ( 1188) hydrogen bonds : angle 5.73515 ( 3480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.714 Fit side-chains REVERT: A 18 LYS cc_start: 0.8090 (tttt) cc_final: 0.7617 (ttmt) REVERT: A 114 GLU cc_start: 0.8228 (tt0) cc_final: 0.7715 (tm-30) REVERT: B 114 GLU cc_start: 0.8311 (tt0) cc_final: 0.7830 (tm-30) REVERT: B 174 GLU cc_start: 0.7572 (tt0) cc_final: 0.7038 (tm-30) REVERT: C 18 LYS cc_start: 0.8162 (tttt) cc_final: 0.7576 (tptt) REVERT: C 102 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6757 (tp30) REVERT: C 114 GLU cc_start: 0.8300 (tt0) cc_final: 0.7739 (tm-30) REVERT: D 18 LYS cc_start: 0.7950 (tttt) cc_final: 0.7380 (tptm) REVERT: D 114 GLU cc_start: 0.8301 (tt0) cc_final: 0.7778 (tm-30) REVERT: E 17 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: E 18 LYS cc_start: 0.8179 (tttt) cc_final: 0.7592 (tptt) REVERT: E 114 GLU cc_start: 0.8178 (tt0) cc_final: 0.7716 (tm-30) REVERT: E 174 GLU cc_start: 0.7560 (tt0) cc_final: 0.7035 (tm-30) REVERT: F 18 LYS cc_start: 0.8173 (tttt) cc_final: 0.7590 (tptt) REVERT: G 18 LYS cc_start: 0.8120 (tttt) cc_final: 0.7576 (tptm) REVERT: H 17 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: H 18 LYS cc_start: 0.8094 (tttt) cc_final: 0.7469 (tptm) REVERT: H 114 GLU cc_start: 0.8352 (tt0) cc_final: 0.7676 (tm-30) REVERT: I 18 LYS cc_start: 0.8185 (tttt) cc_final: 0.7651 (tptt) REVERT: J 18 LYS cc_start: 0.8142 (tttt) cc_final: 0.7563 (tptp) REVERT: J 114 GLU cc_start: 0.8339 (tt0) cc_final: 0.7889 (tm-30) REVERT: K 18 LYS cc_start: 0.8087 (tttt) cc_final: 0.7483 (tptm) REVERT: K 114 GLU cc_start: 0.8233 (tt0) cc_final: 0.7727 (tm-30) REVERT: L 18 LYS cc_start: 0.8173 (tttt) cc_final: 0.7651 (tptm) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 1.0457 time to fit residues: 422.5879 Evaluate side-chains 372 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain H residue 17 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132660 restraints weight = 30797.724| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.62 r_work: 0.3553 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16920 Z= 0.157 Angle : 0.579 7.179 22956 Z= 0.315 Chirality : 0.037 0.124 2532 Planarity : 0.004 0.033 2976 Dihedral : 4.197 17.943 2292 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.19), residues: 2028 helix: 2.00 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.70 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.021 0.002 TYR I 123 PHE 0.010 0.002 PHE F 31 TRP 0.004 0.001 TRP D 154 HIS 0.004 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00291 (16920) covalent geometry : angle 0.57880 (22956) hydrogen bonds : bond 0.07122 ( 1188) hydrogen bonds : angle 5.40339 ( 3480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.442 Fit side-chains REVERT: A 18 LYS cc_start: 0.8274 (tttt) cc_final: 0.7878 (tmtm) REVERT: A 114 GLU cc_start: 0.8493 (tt0) cc_final: 0.8207 (tm-30) REVERT: B 114 GLU cc_start: 0.8487 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 174 GLU cc_start: 0.7871 (tt0) cc_final: 0.7439 (tm-30) REVERT: C 18 LYS cc_start: 0.8384 (tttt) cc_final: 0.7985 (tptt) REVERT: C 102 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7259 (tp30) REVERT: C 114 GLU cc_start: 0.8489 (tt0) cc_final: 0.8166 (tm-30) REVERT: D 16 VAL cc_start: 0.8735 (t) cc_final: 0.8414 (p) REVERT: D 18 LYS cc_start: 0.8268 (tttt) cc_final: 0.7833 (tptp) REVERT: D 114 GLU cc_start: 0.8444 (tt0) cc_final: 0.8132 (tm-30) REVERT: E 18 LYS cc_start: 0.8351 (tttt) cc_final: 0.7912 (tptm) REVERT: E 95 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7259 (tmt170) REVERT: E 114 GLU cc_start: 0.8405 (tt0) cc_final: 0.8201 (tm-30) REVERT: E 174 GLU cc_start: 0.7832 (tt0) cc_final: 0.7423 (tm-30) REVERT: F 17 GLU cc_start: 0.8028 (mp0) cc_final: 0.7628 (mp0) REVERT: F 18 LYS cc_start: 0.8423 (tttt) cc_final: 0.8180 (tttm) REVERT: G 18 LYS cc_start: 0.8329 (tttt) cc_final: 0.7930 (tptm) REVERT: H 18 LYS cc_start: 0.8334 (tttt) cc_final: 0.7893 (tptm) REVERT: H 114 GLU cc_start: 0.8429 (tt0) cc_final: 0.8014 (tm-30) REVERT: I 18 LYS cc_start: 0.8373 (tttt) cc_final: 0.8007 (tptt) REVERT: J 16 VAL cc_start: 0.8714 (t) cc_final: 0.8352 (p) REVERT: J 18 LYS cc_start: 0.8307 (tttt) cc_final: 0.7933 (tptm) REVERT: J 114 GLU cc_start: 0.8519 (tt0) cc_final: 0.8307 (tm-30) REVERT: K 18 LYS cc_start: 0.8349 (tttt) cc_final: 0.7889 (tptm) REVERT: K 114 GLU cc_start: 0.8399 (tt0) cc_final: 0.8145 (tm-30) REVERT: L 18 LYS cc_start: 0.8304 (tttt) cc_final: 0.7938 (tptm) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.9969 time to fit residues: 406.1449 Evaluate side-chains 370 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133620 restraints weight = 31941.428| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.65 r_work: 0.3562 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16920 Z= 0.150 Angle : 0.572 6.802 22956 Z= 0.311 Chirality : 0.037 0.125 2532 Planarity : 0.004 0.031 2976 Dihedral : 4.135 17.767 2292 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.19), residues: 2028 helix: 2.06 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.72 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 41 TYR 0.020 0.002 TYR I 123 PHE 0.010 0.002 PHE F 31 TRP 0.004 0.001 TRP C 154 HIS 0.004 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00278 (16920) covalent geometry : angle 0.57199 (22956) hydrogen bonds : bond 0.06862 ( 1188) hydrogen bonds : angle 5.32178 ( 3480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.468 Fit side-chains REVERT: A 18 LYS cc_start: 0.8268 (tttt) cc_final: 0.7871 (tmtm) REVERT: A 114 GLU cc_start: 0.8489 (tt0) cc_final: 0.8196 (tm-30) REVERT: B 87 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7637 (tp30) REVERT: B 114 GLU cc_start: 0.8466 (tt0) cc_final: 0.8226 (tm-30) REVERT: B 174 GLU cc_start: 0.7876 (tt0) cc_final: 0.7439 (tm-30) REVERT: C 18 LYS cc_start: 0.8337 (tttt) cc_final: 0.7945 (tptt) REVERT: C 102 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7247 (tp30) REVERT: C 114 GLU cc_start: 0.8519 (tt0) cc_final: 0.8183 (tm-30) REVERT: D 16 VAL cc_start: 0.8734 (t) cc_final: 0.8413 (p) REVERT: D 18 LYS cc_start: 0.8252 (tttt) cc_final: 0.7820 (tptp) REVERT: D 114 GLU cc_start: 0.8463 (tt0) cc_final: 0.8131 (tm-30) REVERT: E 18 LYS cc_start: 0.8327 (tttt) cc_final: 0.7865 (tptt) REVERT: E 95 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7239 (tmt170) REVERT: E 114 GLU cc_start: 0.8426 (tt0) cc_final: 0.8211 (tm-30) REVERT: E 174 GLU cc_start: 0.7830 (tt0) cc_final: 0.7416 (tm-30) REVERT: F 17 GLU cc_start: 0.8059 (mp0) cc_final: 0.7661 (mp0) REVERT: F 18 LYS cc_start: 0.8387 (tttt) cc_final: 0.8147 (tttm) REVERT: G 18 LYS cc_start: 0.8311 (tttt) cc_final: 0.7917 (tptm) REVERT: H 18 LYS cc_start: 0.8282 (tttt) cc_final: 0.7838 (tptt) REVERT: H 114 GLU cc_start: 0.8416 (tt0) cc_final: 0.7996 (tm-30) REVERT: I 18 LYS cc_start: 0.8380 (tttt) cc_final: 0.8008 (tptt) REVERT: J 16 VAL cc_start: 0.8687 (t) cc_final: 0.8325 (p) REVERT: J 18 LYS cc_start: 0.8288 (tttt) cc_final: 0.7920 (tptm) REVERT: J 114 GLU cc_start: 0.8521 (tt0) cc_final: 0.8303 (tm-30) REVERT: K 18 LYS cc_start: 0.8359 (tttt) cc_final: 0.7893 (tptt) REVERT: K 114 GLU cc_start: 0.8393 (tt0) cc_final: 0.8131 (tm-30) REVERT: L 18 LYS cc_start: 0.8308 (tttt) cc_final: 0.7936 (tptt) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.9879 time to fit residues: 396.1340 Evaluate side-chains 369 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 134 optimal weight: 0.0030 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130312 restraints weight = 33366.913| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.71 r_work: 0.3471 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16920 Z= 0.159 Angle : 0.594 6.861 22956 Z= 0.323 Chirality : 0.037 0.125 2532 Planarity : 0.004 0.035 2976 Dihedral : 4.162 17.917 2292 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.19), residues: 2028 helix: 2.00 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : 1.72 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 41 TYR 0.021 0.002 TYR I 123 PHE 0.009 0.002 PHE B 31 TRP 0.003 0.001 TRP C 154 HIS 0.004 0.001 HIS I 146 Details of bonding type rmsd covalent geometry : bond 0.00298 (16920) covalent geometry : angle 0.59350 (22956) hydrogen bonds : bond 0.07128 ( 1188) hydrogen bonds : angle 5.35363 ( 3480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10757.61 seconds wall clock time: 182 minutes 48.46 seconds (10968.46 seconds total)