Starting phenix.real_space_refine on Sun Jul 5 07:58:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwb_44963/07_2026/9bwb_44963.map" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14780 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9695 2.51 5 N 2320 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14820 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 106 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PX4:plan-1': 3, 'PX4:plan-2': 1, 'PIO:plan-2': 5} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 2.66, per 1000 atoms: 0.18 Number of scatterers: 14820 At special positions: 0 Unit cell: (95.76, 97.44, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2705 8.00 N 2320 7.00 C 9695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=1.52 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=1.52 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=1.52 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=1.52 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=1.52 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 592.2 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 39.8% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.752A pdb=" N PHE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.536A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 308 Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.823A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.753A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.536A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 308 Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.824A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.752A pdb=" N PHE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.535A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 240 Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 308 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.823A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.752A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.536A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 308 Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.823A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'E' and resid 9 through 18 removed outlier: 3.753A pdb=" N PHE E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.535A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.823A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 4.850A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 108 removed outlier: 6.710A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE A 108 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG A 131 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.071A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 85 removed outlier: 4.850A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 108 removed outlier: 6.710A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 108 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG B 131 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.070A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.850A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 removed outlier: 6.710A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 108 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG C 131 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.070A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 187 through 189 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 85 removed outlier: 4.850A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 108 removed outlier: 6.710A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE D 108 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG D 131 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.071A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 189 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 85 removed outlier: 4.850A pdb=" N LEU E 118 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 108 removed outlier: 6.711A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE E 108 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ARG E 131 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.071A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 187 through 189 815 hydrogen bonds defined for protein. 2355 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: 2.01 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2292 1.32 - 1.44: 4153 1.44 - 1.56: 8260 1.56 - 1.69: 225 1.69 - 1.81: 165 Bond restraints: 15095 Sorted by residual: bond pdb=" C9 PX4 D 509 " pdb=" O5 PX4 D 509 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C9 PX4 A 509 " pdb=" O5 PX4 A 509 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C9 PX4 C 509 " pdb=" O5 PX4 C 509 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C9 PX4 E 503 " pdb=" O5 PX4 E 503 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C9 PX4 B 509 " pdb=" O5 PX4 B 509 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 15090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 19415 2.24 - 4.49: 740 4.49 - 6.73: 125 6.73 - 8.97: 25 8.97 - 11.22: 5 Bond angle restraints: 20310 Sorted by residual: angle pdb=" C THR D 112 " pdb=" CA THR D 112 " pdb=" CB THR D 112 " ideal model delta sigma weight residual 110.42 121.64 -11.22 1.99e+00 2.53e-01 3.18e+01 angle pdb=" C THR E 112 " pdb=" CA THR E 112 " pdb=" CB THR E 112 " ideal model delta sigma weight residual 110.42 121.63 -11.21 1.99e+00 2.53e-01 3.17e+01 angle pdb=" C THR C 112 " pdb=" CA THR C 112 " pdb=" CB THR C 112 " ideal model delta sigma weight residual 110.42 121.61 -11.19 1.99e+00 2.53e-01 3.16e+01 angle pdb=" C THR A 112 " pdb=" CA THR A 112 " pdb=" CB THR A 112 " ideal model delta sigma weight residual 110.42 121.60 -11.18 1.99e+00 2.53e-01 3.15e+01 angle pdb=" C THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta sigma weight residual 110.42 121.59 -11.17 1.99e+00 2.53e-01 3.15e+01 ... (remaining 20305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 7960 17.27 - 34.54: 904 34.54 - 51.81: 226 51.81 - 69.08: 60 69.08 - 86.35: 25 Dihedral angle restraints: 9175 sinusoidal: 4040 harmonic: 5135 Sorted by residual: dihedral pdb=" C THR D 112 " pdb=" N THR D 112 " pdb=" CA THR D 112 " pdb=" CB THR D 112 " ideal model delta harmonic sigma weight residual -122.00 -137.10 15.10 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C THR E 112 " pdb=" N THR E 112 " pdb=" CA THR E 112 " pdb=" CB THR E 112 " ideal model delta harmonic sigma weight residual -122.00 -137.09 15.09 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" C THR A 112 " pdb=" N THR A 112 " pdb=" CA THR A 112 " pdb=" CB THR A 112 " ideal model delta harmonic sigma weight residual -122.00 -137.06 15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 9172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1967 0.085 - 0.170: 238 0.170 - 0.255: 30 0.255 - 0.340: 5 0.340 - 0.425: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA THR D 112 " pdb=" N THR D 112 " pdb=" C THR D 112 " pdb=" CB THR D 112 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA THR E 112 " pdb=" N THR E 112 " pdb=" C THR E 112 " pdb=" CB THR E 112 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA THR A 112 " pdb=" N THR A 112 " pdb=" C THR A 112 " pdb=" CB THR A 112 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 2242 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 144 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASN B 144 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN B 144 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 145 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 144 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A 144 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN A 144 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 145 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 144 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASN C 144 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN C 144 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 145 " -0.019 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 97 2.55 - 3.14: 10762 3.14 - 3.72: 22258 3.72 - 4.31: 33508 4.31 - 4.90: 54870 Nonbonded interactions: 121495 Sorted by model distance: nonbonded pdb=" CG2 VAL E 111 " pdb=" O HOH D 607 " model vdw 1.962 3.460 nonbonded pdb=" CG2 VAL A 111 " pdb=" O HOH E 607 " model vdw 1.962 3.460 nonbonded pdb=" CG2 VAL C 111 " pdb=" O HOH B 607 " model vdw 1.962 3.460 nonbonded pdb=" CG2 VAL D 111 " pdb=" O HOH C 607 " model vdw 1.962 3.460 nonbonded pdb=" CG2 VAL B 111 " pdb=" O HOH A 607 " model vdw 1.962 3.460 ... (remaining 121490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'B' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'C' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'D' and (resid 8 through 427 or (resid 505 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'E' and (resid 8 through 427 or resid 504)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 : 0.015 0.510 15110 Z= 0.789 Angle : 1.097 28.479 20350 Z= 0.573 Chirality : 0.059 0.425 2245 Planarity : 0.006 0.061 2520 Dihedral : 16.624 86.350 5820 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.51 % Allowed : 17.07 % Favored : 82.42 % Cbeta Deviations : 0.30 % 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 are not related in a simple way. whole: 0.39 (0.20), residues: 1710 helix: 1.42 (0.21), residues: 605 sheet: 0.32 (0.26), residues: 405 loop : -0.76 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 196 TYR 0.030 0.002 TYR C 301 PHE 0.011 0.001 PHE D 99 TRP 0.006 0.001 TRP A 68 HIS 0.003 0.001 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01233 / 0.64 (15095) covalent geometry : angle 0.98400 / 0.52 (20310) SS BOND : bond 0.50936 / 25.34 ( 5) SS BOND : angle 21.86643 / 11.15 ( 10) hydrogen bonds : bond 0.12755 / 8.56 ( 720) hydrogen bonds : angle 5.06188 / 3.46 ( 2355) link_BETA1-4 : bond 0.00257 / 0.13 ( 5) link_BETA1-4 : angle 0.99747 / 0.52 ( 15) link_NAG-ASN : bond 0.00071 / 0.04 ( 5) link_NAG-ASN : angle 1.15069 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 0.385 Fit side-chains REVERT: B 56 MET cc_start: 0.8992 (mtt) cc_final: 0.8739 (mtt) REVERT: C 196 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7591 (mmp80) REVERT: D 196 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7503 (mmp80) REVERT: E 121 PHE cc_start: 0.7667 (m-80) cc_final: 0.7330 (m-10) REVERT: E 147 MET cc_start: 0.9115 (mtm) cc_final: 0.8908 (mtm) REVERT: E 196 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7517 (mmp80) outliers start: 8 outliers final: 2 residues processed: 217 average time/residue: 0.5934 time to fit residues: 139.9992 Evaluate side-chains 173 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 80 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 HIS B 171 GLN B 266 GLN B 427 HIS C 171 GLN C 266 GLN C 427 HIS D 427 HIS E 171 GLN E 427 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.072335 restraints weight = 20906.935| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.37 r_work: 0.2736 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15110 Z= 0.158 Angle : 0.585 6.030 20350 Z= 0.307 Chirality : 0.043 0.143 2245 Planarity : 0.005 0.049 2520 Dihedral : 7.830 100.055 2424 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.48 % Allowed : 19.49 % Favored : 78.03 % 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 are not related in a simple way. whole: 0.54 (0.20), residues: 1710 helix: 1.73 (0.21), residues: 605 sheet: 0.23 (0.26), residues: 410 loop : -0.75 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 59 TYR 0.028 0.002 TYR A 301 PHE 0.012 0.001 PHE E 99 TRP 0.008 0.001 TRP E 68 HIS 0.005 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (15095) covalent geometry : angle 0.58290 / 0.31 (20310) SS BOND : bond 0.00547 / 0.27 ( 5) SS BOND : angle 1.88216 / 0.97 ( 10) hydrogen bonds : bond 0.05191 / 3.50 ( 720) hydrogen bonds : angle 4.35374 / 2.99 ( 2355) link_BETA1-4 : bond 0.00234 / 0.12 ( 5) link_BETA1-4 : angle 1.16245 / 0.62 ( 15) link_NAG-ASN : bond 0.00078 / 0.04 ( 5) link_NAG-ASN : angle 0.89964 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.398 Fit side-chains REVERT: A 91 ASP cc_start: 0.8500 (t70) cc_final: 0.8252 (t70) REVERT: B 56 MET cc_start: 0.9292 (mtt) cc_final: 0.9089 (mtt) REVERT: C 147 MET cc_start: 0.9313 (mtm) cc_final: 0.8980 (mtm) REVERT: C 196 ARG cc_start: 0.8624 (mmt90) cc_final: 0.8346 (mmt90) REVERT: C 391 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7564 (mtm-85) REVERT: D 196 ARG cc_start: 0.8504 (mmt90) cc_final: 0.8188 (mmt90) REVERT: E 121 PHE cc_start: 0.8226 (m-80) cc_final: 0.7909 (m-10) REVERT: E 196 ARG cc_start: 0.8635 (mmt90) cc_final: 0.8347 (mmt90) outliers start: 39 outliers final: 12 residues processed: 211 average time/residue: 0.5170 time to fit residues: 120.3246 Evaluate side-chains 179 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 104 optimal weight: 0.0670 chunk 162 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 GLN B 266 GLN C 171 GLN C 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.074830 restraints weight = 21070.619| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.38 r_work: 0.2793 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15110 Z= 0.107 Angle : 0.530 5.821 20350 Z= 0.275 Chirality : 0.042 0.147 2245 Planarity : 0.005 0.061 2520 Dihedral : 7.234 94.789 2424 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.36 % Allowed : 20.38 % Favored : 77.26 % 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 are not related in a simple way. whole: 0.80 (0.20), residues: 1710 helix: 2.00 (0.22), residues: 605 sheet: 0.30 (0.25), residues: 410 loop : -0.62 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 59 TYR 0.025 0.001 TYR A 301 PHE 0.009 0.001 PHE D 99 TRP 0.008 0.001 TRP D 68 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15095) covalent geometry : angle 0.52822 / 0.27 (20310) SS BOND : bond 0.00043 / 0.02 ( 5) SS BOND : angle 1.15938 / 0.59 ( 10) hydrogen bonds : bond 0.04253 / 2.87 ( 720) hydrogen bonds : angle 4.06140 / 2.78 ( 2355) link_BETA1-4 : bond 0.00278 / 0.14 ( 5) link_BETA1-4 : angle 1.15823 / 0.62 ( 15) link_NAG-ASN : bond 0.00049 / 0.02 ( 5) link_NAG-ASN : angle 0.65075 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.534 Fit side-chains REVERT: A 8 MET cc_start: 0.8176 (tpp) cc_final: 0.7951 (tpp) REVERT: A 91 ASP cc_start: 0.8497 (t70) cc_final: 0.8256 (t70) REVERT: A 180 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: B 56 MET cc_start: 0.9286 (mtt) cc_final: 0.8881 (mtt) REVERT: B 140 MET cc_start: 0.9207 (mtm) cc_final: 0.8992 (mtt) REVERT: C 196 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8054 (mmp80) REVERT: C 391 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7656 (mtm-85) REVERT: D 175 PRO cc_start: 0.8989 (Cg_endo) cc_final: 0.8763 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8459 (mmt90) cc_final: 0.7925 (mmp80) REVERT: D 255 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (tt) REVERT: E 121 PHE cc_start: 0.8255 (m-80) cc_final: 0.7944 (m-10) REVERT: E 171 GLN cc_start: 0.8752 (tt0) cc_final: 0.8527 (tt0) REVERT: E 180 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: E 196 ARG cc_start: 0.8619 (mmt90) cc_final: 0.8348 (mmt90) outliers start: 37 outliers final: 15 residues processed: 208 average time/residue: 0.5535 time to fit residues: 127.0440 Evaluate side-chains 190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN B 266 GLN C 115 ASN C 266 GLN D 115 ASN E 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070912 restraints weight = 20980.215| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.37 r_work: 0.2709 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15110 Z= 0.185 Angle : 0.591 6.118 20350 Z= 0.311 Chirality : 0.044 0.151 2245 Planarity : 0.005 0.062 2520 Dihedral : 7.439 95.516 2424 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.06 % Allowed : 20.25 % Favored : 76.69 % 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 are not related in a simple way. whole: 0.70 (0.20), residues: 1710 helix: 1.86 (0.22), residues: 605 sheet: 0.29 (0.26), residues: 405 loop : -0.63 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 196 TYR 0.030 0.002 TYR A 301 PHE 0.012 0.002 PHE E 99 TRP 0.006 0.001 TRP C 68 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (15095) covalent geometry : angle 0.58855 / 0.31 (20310) SS BOND : bond 0.00588 / 0.29 ( 5) SS BOND : angle 1.54290 / 0.78 ( 10) hydrogen bonds : bond 0.05419 / 3.64 ( 720) hydrogen bonds : angle 4.35942 / 2.99 ( 2355) link_BETA1-4 : bond 0.00181 / 0.09 ( 5) link_BETA1-4 : angle 1.23766 / 0.66 ( 15) link_NAG-ASN : bond 0.00137 / 0.07 ( 5) link_NAG-ASN : angle 1.04398 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.550 Fit side-chains REVERT: A 91 ASP cc_start: 0.8602 (t70) cc_final: 0.8352 (t0) REVERT: B 56 MET cc_start: 0.9272 (mtt) cc_final: 0.8932 (mtt) REVERT: B 91 ASP cc_start: 0.8576 (p0) cc_final: 0.8135 (t0) REVERT: B 421 LEU cc_start: 0.7158 (mp) cc_final: 0.6923 (mt) REVERT: C 147 MET cc_start: 0.9337 (mtm) cc_final: 0.9045 (mtm) REVERT: C 196 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8408 (mmt90) REVERT: D 110 GLU cc_start: 0.8201 (pm20) cc_final: 0.7996 (pm20) REVERT: D 175 PRO cc_start: 0.9021 (Cg_endo) cc_final: 0.8795 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8182 (mmt90) REVERT: D 255 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8389 (tt) REVERT: E 91 ASP cc_start: 0.8513 (p0) cc_final: 0.8085 (t0) REVERT: E 121 PHE cc_start: 0.8257 (m-80) cc_final: 0.7940 (m-10) REVERT: E 180 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: E 190 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8612 (mmmm) REVERT: E 196 ARG cc_start: 0.8656 (mmt90) cc_final: 0.8414 (mmt90) outliers start: 48 outliers final: 18 residues processed: 215 average time/residue: 0.5577 time to fit residues: 132.1105 Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 GLN B 266 GLN C 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074185 restraints weight = 20979.393| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.38 r_work: 0.2774 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15110 Z= 0.109 Angle : 0.523 5.850 20350 Z= 0.273 Chirality : 0.042 0.151 2245 Planarity : 0.004 0.063 2520 Dihedral : 6.848 90.115 2424 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.10 % Allowed : 21.27 % Favored : 76.62 % 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 are not related in a simple way. whole: 0.85 (0.20), residues: 1710 helix: 2.04 (0.22), residues: 605 sheet: 0.34 (0.25), residues: 410 loop : -0.59 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 196 TYR 0.025 0.002 TYR A 301 PHE 0.009 0.001 PHE C 99 TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15095) covalent geometry : angle 0.52171 / 0.27 (20310) SS BOND : bond 0.00345 / 0.17 ( 5) SS BOND : angle 0.90976 / 0.46 ( 10) hydrogen bonds : bond 0.04221 / 2.85 ( 720) hydrogen bonds : angle 4.02894 / 2.76 ( 2355) link_BETA1-4 : bond 0.00200 / 0.10 ( 5) link_BETA1-4 : angle 1.14319 / 0.61 ( 15) link_NAG-ASN : bond 0.00044 / 0.02 ( 5) link_NAG-ASN : angle 0.73590 / 0.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.412 Fit side-chains REVERT: A 8 MET cc_start: 0.8108 (tpp) cc_final: 0.7739 (tpp) REVERT: A 91 ASP cc_start: 0.8538 (t70) cc_final: 0.8277 (t0) REVERT: A 110 GLU cc_start: 0.8202 (pm20) cc_final: 0.7900 (pm20) REVERT: A 180 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: A 421 LEU cc_start: 0.7210 (mt) cc_final: 0.7005 (mp) REVERT: B 56 MET cc_start: 0.9285 (mtt) cc_final: 0.8933 (mtt) REVERT: B 91 ASP cc_start: 0.8556 (p0) cc_final: 0.8132 (t0) REVERT: B 110 GLU cc_start: 0.8259 (pm20) cc_final: 0.8021 (pm20) REVERT: C 89 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7394 (mtp) REVERT: C 196 ARG cc_start: 0.8624 (mmt90) cc_final: 0.8306 (mmt90) REVERT: C 391 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7611 (mtm-85) REVERT: D 110 GLU cc_start: 0.8157 (pm20) cc_final: 0.7872 (pm20) REVERT: D 175 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8767 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8145 (mmt90) REVERT: D 255 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8332 (tt) REVERT: E 91 ASP cc_start: 0.8491 (p0) cc_final: 0.8048 (t0) REVERT: E 110 GLU cc_start: 0.8229 (pm20) cc_final: 0.7992 (pm20) REVERT: E 121 PHE cc_start: 0.8260 (m-80) cc_final: 0.7926 (m-10) REVERT: E 180 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: E 196 ARG cc_start: 0.8650 (mmt90) cc_final: 0.8413 (mmt90) outliers start: 33 outliers final: 13 residues processed: 214 average time/residue: 0.4998 time to fit residues: 118.3880 Evaluate side-chains 202 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 0.0970 chunk 126 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 138 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 266 GLN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.072872 restraints weight = 20808.952| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.37 r_work: 0.2755 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15110 Z= 0.129 Angle : 0.541 5.981 20350 Z= 0.281 Chirality : 0.042 0.145 2245 Planarity : 0.005 0.064 2520 Dihedral : 6.825 101.561 2424 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.04 % Allowed : 20.89 % Favored : 77.07 % 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 are not related in a simple way. whole: 0.85 (0.20), residues: 1710 helix: 2.03 (0.22), residues: 605 sheet: 0.34 (0.25), residues: 410 loop : -0.59 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 196 TYR 0.028 0.002 TYR A 301 PHE 0.010 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15095) covalent geometry : angle 0.53964 / 0.28 (20310) SS BOND : bond 0.00452 / 0.22 ( 5) SS BOND : angle 1.09519 / 0.55 ( 10) hydrogen bonds : bond 0.04538 / 3.06 ( 720) hydrogen bonds : angle 4.08116 / 2.80 ( 2355) link_BETA1-4 : bond 0.00213 / 0.11 ( 5) link_BETA1-4 : angle 1.22888 / 0.66 ( 15) link_NAG-ASN : bond 0.00043 / 0.02 ( 5) link_NAG-ASN : angle 0.85033 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.597 Fit side-chains REVERT: A 8 MET cc_start: 0.8136 (tpp) cc_final: 0.7777 (tpp) REVERT: A 91 ASP cc_start: 0.8561 (t70) cc_final: 0.8324 (t0) REVERT: A 110 GLU cc_start: 0.8236 (pm20) cc_final: 0.7952 (pm20) REVERT: A 180 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: A 421 LEU cc_start: 0.7197 (mt) cc_final: 0.6981 (mp) REVERT: B 56 MET cc_start: 0.9295 (mtt) cc_final: 0.8978 (mtt) REVERT: B 91 ASP cc_start: 0.8541 (p0) cc_final: 0.8154 (t0) REVERT: B 110 GLU cc_start: 0.8295 (pm20) cc_final: 0.8048 (pm20) REVERT: B 196 ARG cc_start: 0.8579 (mmt90) cc_final: 0.7938 (mmt180) REVERT: C 196 ARG cc_start: 0.8630 (mmt90) cc_final: 0.8386 (mmt90) REVERT: D 110 GLU cc_start: 0.8244 (pm20) cc_final: 0.7999 (pm20) REVERT: D 171 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8395 (tp-100) REVERT: D 175 PRO cc_start: 0.8994 (Cg_endo) cc_final: 0.8777 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8182 (mmt90) REVERT: D 255 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8375 (tt) REVERT: E 91 ASP cc_start: 0.8447 (p0) cc_final: 0.8046 (t0) REVERT: E 110 GLU cc_start: 0.8268 (pm20) cc_final: 0.7991 (pm20) REVERT: E 121 PHE cc_start: 0.8258 (m-80) cc_final: 0.7924 (m-10) REVERT: E 171 GLN cc_start: 0.8784 (tt0) cc_final: 0.8527 (tt0) REVERT: E 190 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8600 (mmmm) REVERT: E 196 ARG cc_start: 0.8657 (mmt90) cc_final: 0.8427 (mmt90) outliers start: 32 outliers final: 12 residues processed: 213 average time/residue: 0.5104 time to fit residues: 120.5183 Evaluate side-chains 203 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074169 restraints weight = 20811.333| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.37 r_work: 0.2775 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15110 Z= 0.113 Angle : 0.535 8.539 20350 Z= 0.273 Chirality : 0.042 0.148 2245 Planarity : 0.005 0.066 2520 Dihedral : 5.855 43.543 2420 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.42 % Allowed : 20.51 % Favored : 77.07 % 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 are not related in a simple way. whole: 0.89 (0.20), residues: 1710 helix: 2.08 (0.22), residues: 605 sheet: 0.37 (0.25), residues: 410 loop : -0.57 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 196 TYR 0.027 0.002 TYR A 301 PHE 0.009 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (15095) covalent geometry : angle 0.53326 / 0.27 (20310) SS BOND : bond 0.00390 / 0.19 ( 5) SS BOND : angle 0.95536 / 0.48 ( 10) hydrogen bonds : bond 0.04244 / 2.86 ( 720) hydrogen bonds : angle 3.99153 / 2.74 ( 2355) link_BETA1-4 : bond 0.00247 / 0.12 ( 5) link_BETA1-4 : angle 1.20747 / 0.65 ( 15) link_NAG-ASN : bond 0.00025 / 0.01 ( 5) link_NAG-ASN : angle 0.77349 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.465 Fit side-chains REVERT: A 8 MET cc_start: 0.8116 (tpp) cc_final: 0.7764 (tpp) REVERT: A 91 ASP cc_start: 0.8543 (t70) cc_final: 0.8277 (t0) REVERT: A 110 GLU cc_start: 0.8243 (pm20) cc_final: 0.7945 (pm20) REVERT: A 180 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: A 421 LEU cc_start: 0.7199 (mt) cc_final: 0.6996 (mp) REVERT: B 56 MET cc_start: 0.9303 (mtt) cc_final: 0.8995 (mtt) REVERT: B 91 ASP cc_start: 0.8515 (p0) cc_final: 0.8145 (t0) REVERT: B 110 GLU cc_start: 0.8273 (pm20) cc_final: 0.8021 (pm20) REVERT: B 190 LYS cc_start: 0.8809 (mmpt) cc_final: 0.8468 (mmmm) REVERT: B 196 ARG cc_start: 0.8559 (mmt90) cc_final: 0.7939 (mmt180) REVERT: C 89 MET cc_start: 0.7635 (ptp) cc_final: 0.7200 (pp-130) REVERT: C 196 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8385 (mmt90) REVERT: D 89 MET cc_start: 0.7618 (ptp) cc_final: 0.7201 (pp-130) REVERT: D 110 GLU cc_start: 0.8232 (pm20) cc_final: 0.7943 (pm20) REVERT: D 171 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8387 (tp-100) REVERT: D 175 PRO cc_start: 0.8994 (Cg_endo) cc_final: 0.8780 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8246 (mmt90) REVERT: D 255 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8353 (tt) REVERT: E 8 MET cc_start: 0.8090 (tpp) cc_final: 0.7877 (tpp) REVERT: E 91 ASP cc_start: 0.8444 (p0) cc_final: 0.8045 (t0) REVERT: E 110 GLU cc_start: 0.8216 (pm20) cc_final: 0.7940 (pm20) REVERT: E 121 PHE cc_start: 0.8253 (m-80) cc_final: 0.7917 (m-10) REVERT: E 171 GLN cc_start: 0.8779 (tt0) cc_final: 0.8509 (tt0) REVERT: E 190 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8612 (mmmm) REVERT: E 196 ARG cc_start: 0.8654 (mmt90) cc_final: 0.8423 (mmt90) outliers start: 38 outliers final: 19 residues processed: 216 average time/residue: 0.4988 time to fit residues: 119.3994 Evaluate side-chains 211 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073836 restraints weight = 20796.686| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.40 r_work: 0.2772 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15110 Z= 0.115 Angle : 0.541 9.661 20350 Z= 0.275 Chirality : 0.042 0.150 2245 Planarity : 0.005 0.068 2520 Dihedral : 5.739 42.948 2420 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.17 % Allowed : 21.08 % Favored : 76.75 % 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 are not related in a simple way. whole: 0.90 (0.20), residues: 1710 helix: 2.09 (0.22), residues: 605 sheet: 0.36 (0.25), residues: 410 loop : -0.56 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 196 TYR 0.027 0.002 TYR A 301 PHE 0.009 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15095) covalent geometry : angle 0.53958 / 0.28 (20310) SS BOND : bond 0.00397 / 0.20 ( 5) SS BOND : angle 0.96444 / 0.49 ( 10) hydrogen bonds : bond 0.04234 / 2.85 ( 720) hydrogen bonds : angle 3.98069 / 2.73 ( 2355) link_BETA1-4 : bond 0.00217 / 0.11 ( 5) link_BETA1-4 : angle 1.21988 / 0.65 ( 15) link_NAG-ASN : bond 0.00025 / 0.01 ( 5) link_NAG-ASN : angle 0.77835 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.634 Fit side-chains REVERT: A 8 MET cc_start: 0.8105 (tpp) cc_final: 0.7751 (tpp) REVERT: A 91 ASP cc_start: 0.8550 (t70) cc_final: 0.8305 (t0) REVERT: A 110 GLU cc_start: 0.8262 (pm20) cc_final: 0.7955 (pm20) REVERT: A 180 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 421 LEU cc_start: 0.7171 (mt) cc_final: 0.6960 (mp) REVERT: B 56 MET cc_start: 0.9303 (mtt) cc_final: 0.8996 (mtt) REVERT: B 91 ASP cc_start: 0.8518 (p0) cc_final: 0.8139 (t0) REVERT: B 110 GLU cc_start: 0.8288 (pm20) cc_final: 0.8040 (pm20) REVERT: B 190 LYS cc_start: 0.8794 (mmpt) cc_final: 0.8460 (mmmm) REVERT: B 196 ARG cc_start: 0.8569 (mmt90) cc_final: 0.7938 (mmt180) REVERT: C 89 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7191 (pp-130) REVERT: C 110 GLU cc_start: 0.8251 (pm20) cc_final: 0.7969 (pm20) REVERT: C 196 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8380 (mmt90) REVERT: D 89 MET cc_start: 0.7695 (ptp) cc_final: 0.7248 (pp-130) REVERT: D 91 ASP cc_start: 0.8617 (t70) cc_final: 0.8329 (t0) REVERT: D 110 GLU cc_start: 0.8251 (pm20) cc_final: 0.7960 (pm20) REVERT: D 171 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8401 (tp-100) REVERT: D 175 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8776 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8498 (mmt90) cc_final: 0.8251 (mmt90) REVERT: D 255 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8357 (tt) REVERT: E 8 MET cc_start: 0.8087 (tpp) cc_final: 0.7876 (tpp) REVERT: E 91 ASP cc_start: 0.8446 (p0) cc_final: 0.8054 (t0) REVERT: E 110 GLU cc_start: 0.8221 (pm20) cc_final: 0.7949 (pm20) REVERT: E 121 PHE cc_start: 0.8258 (m-80) cc_final: 0.7922 (m-10) REVERT: E 171 GLN cc_start: 0.8783 (tt0) cc_final: 0.8505 (tt0) REVERT: E 190 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: E 196 ARG cc_start: 0.8650 (mmt90) cc_final: 0.8421 (mmt90) outliers start: 34 outliers final: 17 residues processed: 212 average time/residue: 0.5682 time to fit residues: 133.2442 Evaluate side-chains 210 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073954 restraints weight = 20838.886| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.37 r_work: 0.2769 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15110 Z= 0.118 Angle : 0.546 10.149 20350 Z= 0.277 Chirality : 0.042 0.173 2245 Planarity : 0.005 0.071 2520 Dihedral : 5.662 41.698 2420 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.78 % Allowed : 21.66 % Favored : 76.56 % 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 are not related in a simple way. whole: 0.92 (0.20), residues: 1710 helix: 2.10 (0.22), residues: 605 sheet: 0.38 (0.25), residues: 410 loop : -0.56 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 196 TYR 0.027 0.002 TYR A 301 PHE 0.009 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15095) covalent geometry : angle 0.54443 / 0.28 (20310) SS BOND : bond 0.00417 / 0.21 ( 5) SS BOND : angle 0.98485 / 0.50 ( 10) hydrogen bonds : bond 0.04286 / 2.88 ( 720) hydrogen bonds : angle 3.97143 / 2.73 ( 2355) link_BETA1-4 : bond 0.00234 / 0.12 ( 5) link_BETA1-4 : angle 1.21773 / 0.65 ( 15) link_NAG-ASN : bond 0.00021 / 0.01 ( 5) link_NAG-ASN : angle 0.78883 / 0.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.685 Fit side-chains REVERT: A 8 MET cc_start: 0.8118 (tpp) cc_final: 0.7767 (tpp) REVERT: A 91 ASP cc_start: 0.8550 (t70) cc_final: 0.8276 (t0) REVERT: A 110 GLU cc_start: 0.8272 (pm20) cc_final: 0.7966 (pm20) REVERT: A 180 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: A 421 LEU cc_start: 0.7130 (mt) cc_final: 0.6921 (mp) REVERT: B 56 MET cc_start: 0.9303 (mtt) cc_final: 0.8992 (mtt) REVERT: B 89 MET cc_start: 0.7456 (ptp) cc_final: 0.7145 (pp-130) REVERT: B 91 ASP cc_start: 0.8531 (p0) cc_final: 0.8166 (t0) REVERT: B 110 GLU cc_start: 0.8301 (pm20) cc_final: 0.8063 (pm20) REVERT: B 190 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8462 (mmmm) REVERT: B 196 ARG cc_start: 0.8576 (mmt90) cc_final: 0.7948 (mmt180) REVERT: C 110 GLU cc_start: 0.8276 (pm20) cc_final: 0.7999 (pm20) REVERT: C 196 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8396 (mmt90) REVERT: D 91 ASP cc_start: 0.8621 (t70) cc_final: 0.8332 (t0) REVERT: D 110 GLU cc_start: 0.8285 (pm20) cc_final: 0.7994 (pm20) REVERT: D 171 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8406 (tp-100) REVERT: D 175 PRO cc_start: 0.8985 (Cg_endo) cc_final: 0.8779 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8510 (mmt90) cc_final: 0.8267 (mmt90) REVERT: D 255 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8363 (tt) REVERT: E 91 ASP cc_start: 0.8447 (p0) cc_final: 0.8055 (t0) REVERT: E 110 GLU cc_start: 0.8222 (pm20) cc_final: 0.7952 (pm20) REVERT: E 121 PHE cc_start: 0.8260 (m-80) cc_final: 0.7925 (m-10) REVERT: E 171 GLN cc_start: 0.8793 (tt0) cc_final: 0.8518 (tt0) REVERT: E 190 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8610 (mmmm) REVERT: E 196 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8429 (mmt90) outliers start: 28 outliers final: 16 residues processed: 216 average time/residue: 0.5558 time to fit residues: 132.9257 Evaluate side-chains 210 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.075005 restraints weight = 20734.132| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.36 r_work: 0.2792 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15110 Z= 0.106 Angle : 0.539 11.455 20350 Z= 0.271 Chirality : 0.042 0.189 2245 Planarity : 0.005 0.072 2520 Dihedral : 5.452 39.371 2420 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.53 % Allowed : 21.78 % Favored : 76.69 % 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 are not related in a simple way. whole: 0.97 (0.20), residues: 1710 helix: 2.14 (0.22), residues: 605 sheet: 0.42 (0.25), residues: 410 loop : -0.54 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 196 TYR 0.025 0.002 TYR A 301 PHE 0.008 0.001 PHE C 99 TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15095) covalent geometry : angle 0.53773 / 0.27 (20310) SS BOND : bond 0.00355 / 0.18 ( 5) SS BOND : angle 0.85569 / 0.43 ( 10) hydrogen bonds : bond 0.03984 / 2.68 ( 720) hydrogen bonds : angle 3.87656 / 2.67 ( 2355) link_BETA1-4 : bond 0.00249 / 0.12 ( 5) link_BETA1-4 : angle 1.19871 / 0.64 ( 15) link_NAG-ASN : bond 0.00040 / 0.02 ( 5) link_NAG-ASN : angle 0.68134 / 0.34 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.631 Fit side-chains REVERT: A 8 MET cc_start: 0.8100 (tpp) cc_final: 0.7759 (tpp) REVERT: A 91 ASP cc_start: 0.8492 (t70) cc_final: 0.8232 (t0) REVERT: A 110 GLU cc_start: 0.8239 (pm20) cc_final: 0.7956 (pm20) REVERT: A 180 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: B 56 MET cc_start: 0.9345 (mtt) cc_final: 0.9048 (mtt) REVERT: B 89 MET cc_start: 0.7417 (ptp) cc_final: 0.7045 (pp-130) REVERT: B 91 ASP cc_start: 0.8512 (p0) cc_final: 0.8149 (t0) REVERT: B 110 GLU cc_start: 0.8261 (pm20) cc_final: 0.8042 (pm20) REVERT: B 190 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8436 (mmmm) REVERT: B 196 ARG cc_start: 0.8588 (mmt90) cc_final: 0.7970 (mmt180) REVERT: C 89 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7267 (ppp) REVERT: C 110 GLU cc_start: 0.8274 (pm20) cc_final: 0.8006 (pm20) REVERT: C 196 ARG cc_start: 0.8638 (mmt90) cc_final: 0.8382 (mmt90) REVERT: D 91 ASP cc_start: 0.8650 (t70) cc_final: 0.8355 (t0) REVERT: D 110 GLU cc_start: 0.8296 (pm20) cc_final: 0.8009 (pm20) REVERT: D 171 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: D 175 PRO cc_start: 0.8981 (Cg_endo) cc_final: 0.8779 (Cg_exo) REVERT: D 196 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8253 (mmt90) REVERT: D 255 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8347 (tt) REVERT: E 91 ASP cc_start: 0.8456 (p0) cc_final: 0.8045 (t0) REVERT: E 110 GLU cc_start: 0.8256 (pm20) cc_final: 0.7980 (pm20) REVERT: E 121 PHE cc_start: 0.8231 (m-80) cc_final: 0.7926 (m-10) REVERT: E 171 GLN cc_start: 0.8799 (tt0) cc_final: 0.8529 (tt0) REVERT: E 190 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8662 (mmmm) REVERT: E 196 ARG cc_start: 0.8651 (mmt90) cc_final: 0.8424 (mmt90) outliers start: 24 outliers final: 15 residues processed: 214 average time/residue: 0.5577 time to fit residues: 132.4619 Evaluate side-chains 212 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074357 restraints weight = 20644.868| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.36 r_work: 0.2778 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15110 Z= 0.115 Angle : 0.544 11.255 20350 Z= 0.274 Chirality : 0.042 0.165 2245 Planarity : 0.005 0.071 2520 Dihedral : 5.420 36.938 2420 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.59 % Allowed : 21.85 % Favored : 76.56 % 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 are not related in a simple way. whole: 0.99 (0.20), residues: 1710 helix: 2.14 (0.22), residues: 605 sheet: 0.47 (0.25), residues: 410 loop : -0.54 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 196 TYR 0.027 0.002 TYR A 301 PHE 0.009 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (15095) covalent geometry : angle 0.54287 / 0.27 (20310) SS BOND : bond 0.00404 / 0.20 ( 5) SS BOND : angle 0.94822 / 0.48 ( 10) hydrogen bonds : bond 0.04144 / 2.78 ( 720) hydrogen bonds : angle 3.91589 / 2.70 ( 2355) link_BETA1-4 : bond 0.00195 / 0.10 ( 5) link_BETA1-4 : angle 1.19178 / 0.64 ( 15) link_NAG-ASN : bond 0.00024 / 0.01 ( 5) link_NAG-ASN : angle 0.73210 / 0.36 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.79 seconds wall clock time: 107 minutes 55.69 seconds (6475.69 seconds total)