Starting phenix.real_space_refine on Sun May 3 12:00:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lex_63036/05_2026/9lex_63036.map" } resolution = 2.85 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= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 55 5.16 5 C 8285 2.51 5 N 2070 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.43, per 1000 atoms: 0.27 Number of scatterers: 12742 At special positions: 0 Unit cell: (98.792, 99.724, 124.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 55 16.00 O 2330 8.00 N 2070 7.00 C 8285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.05 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.05 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.05 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.05 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.05 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 55 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 55 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 55 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 55 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 658.6 milliseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 36.3% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.656A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 258 through 282 removed outlier: 4.398A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 4.031A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 391 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.656A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 258 through 282 removed outlier: 4.397A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 removed outlier: 4.031A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 391 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.655A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 258 through 282 removed outlier: 4.398A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 322 removed outlier: 4.030A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 391 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.655A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 258 through 282 removed outlier: 4.397A pdb=" N ILE D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 322 removed outlier: 4.030A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 391 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.655A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 282 removed outlier: 4.398A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 322 removed outlier: 4.029A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 128 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 80 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL A 74 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 86 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL A 68 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 66 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER A 90 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 64 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU A 92 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL A 62 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 68 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 128 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 74 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 86 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL B 68 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL B 66 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER B 90 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 64 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N LEU B 92 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL B 62 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 68 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL C 128 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 80 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 74 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 86 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL C 68 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG C 88 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 66 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER C 90 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL C 64 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU C 92 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL C 62 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 68 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL D 128 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR D 80 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 74 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 86 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL D 68 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG D 88 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL D 66 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER D 90 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL D 64 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU D 92 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL D 62 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 68 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL E 128 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 80 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL E 74 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E 86 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL E 68 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG E 88 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL E 66 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER E 90 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL E 64 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N LEU E 92 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL E 62 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 68 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 750 hydrogen bonds defined for protein. 2190 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: 2.08 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2179 1.32 - 1.45: 3461 1.45 - 1.57: 7325 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13040 Sorted by residual: bond pdb=" C VAL A 64 " pdb=" O VAL A 64 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.07e-02 8.73e+03 1.12e+01 bond pdb=" C VAL E 64 " pdb=" O VAL E 64 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.07e-02 8.73e+03 1.11e+01 bond pdb=" C VAL D 64 " pdb=" O VAL D 64 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.07e-02 8.73e+03 1.06e+01 bond pdb=" C VAL B 64 " pdb=" O VAL B 64 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.07e-02 8.73e+03 1.05e+01 bond pdb=" CA ASN C 158 " pdb=" C ASN C 158 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.25e-02 6.40e+03 1.03e+01 ... (remaining 13035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 16982 1.86 - 3.72: 677 3.72 - 5.57: 131 5.57 - 7.43: 55 7.43 - 9.29: 5 Bond angle restraints: 17850 Sorted by residual: angle pdb=" N TRP C 391 " pdb=" CA TRP C 391 " pdb=" C TRP C 391 " ideal model delta sigma weight residual 109.54 118.83 -9.29 1.37e+00 5.33e-01 4.60e+01 angle pdb=" N TRP B 391 " pdb=" CA TRP B 391 " pdb=" C TRP B 391 " ideal model delta sigma weight residual 109.54 118.82 -9.28 1.37e+00 5.33e-01 4.59e+01 angle pdb=" N TRP E 391 " pdb=" CA TRP E 391 " pdb=" C TRP E 391 " ideal model delta sigma weight residual 109.54 118.80 -9.26 1.37e+00 5.33e-01 4.57e+01 angle pdb=" N TRP D 391 " pdb=" CA TRP D 391 " pdb=" C TRP D 391 " ideal model delta sigma weight residual 109.54 118.80 -9.26 1.37e+00 5.33e-01 4.56e+01 angle pdb=" N TRP A 391 " pdb=" CA TRP A 391 " pdb=" C TRP A 391 " ideal model delta sigma weight residual 109.54 118.74 -9.20 1.37e+00 5.33e-01 4.51e+01 ... (remaining 17845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 7565 21.15 - 42.31: 385 42.31 - 63.46: 50 63.46 - 84.61: 85 84.61 - 105.77: 40 Dihedral angle restraints: 8125 sinusoidal: 3515 harmonic: 4610 Sorted by residual: dihedral pdb=" CB CYS E 289 " pdb=" SG CYS E 289 " pdb=" SG CYS E 394 " pdb=" CB CYS E 394 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 394 " pdb=" CB CYS C 394 " ideal model delta sinusoidal sigma weight residual 93.00 156.93 -63.93 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 394 " pdb=" CB CYS B 394 " ideal model delta sinusoidal sigma weight residual 93.00 156.91 -63.91 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 8122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1919 0.075 - 0.150: 263 0.150 - 0.225: 33 0.225 - 0.299: 28 0.299 - 0.374: 12 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.72e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.72e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 ... (remaining 2252 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.198 2.00e-02 2.50e+03 1.68e-01 3.54e+02 pdb=" C7 NAG G 1 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.198 2.00e-02 2.50e+03 1.68e-01 3.53e+02 pdb=" C7 NAG I 1 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.198 2.00e-02 2.50e+03 1.68e-01 3.53e+02 pdb=" C7 NAG M 1 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.274 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.154 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1525 2.75 - 3.29: 11950 3.29 - 3.82: 21751 3.82 - 4.36: 25648 4.36 - 4.90: 44759 Nonbonded interactions: 105633 Sorted by model distance: nonbonded pdb=" OD2 ASP E 142 " pdb=" ND1 HIS E 144 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP D 142 " pdb=" ND1 HIS D 144 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP B 142 " pdb=" ND1 HIS B 144 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP C 142 " pdb=" ND1 HIS C 144 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 2.214 3.120 ... (remaining 105628 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 47 through 395) selection = chain 'B' selection = (chain 'C' and resid 47 through 395) selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.990 Find NCS groups from input model: 0.290 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:9.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.006 0.040 13080 Z= 0.408 Angle : 0.923 9.289 17960 Z= 0.517 Chirality : 0.064 0.374 2255 Planarity : 0.010 0.168 2150 Dihedral : 17.300 105.766 5075 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 1.47 (0.22), residues: 1535 helix: 2.15 (0.21), residues: 495 sheet: 1.31 (0.25), residues: 465 loop : -0.33 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.010 0.002 TYR A 272 PHE 0.020 0.002 PHE A 72 TRP 0.012 0.001 TRP D 112 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00630 (13040) covalent geometry : angle 0.89291 (17850) SS BOND : bond 0.01035 ( 10) SS BOND : angle 4.03306 ( 20) hydrogen bonds : bond 0.14441 ( 665) hydrogen bonds : angle 6.43187 ( 2190) link_BETA1-4 : bond 0.00445 ( 20) link_BETA1-4 : angle 1.41914 ( 60) link_NAG-ASN : bond 0.01202 ( 10) link_NAG-ASN : angle 4.53505 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: D 73 ASN cc_start: 0.8332 (m110) cc_final: 0.7992 (m110) REVERT: D 95 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7887 (mtm180) REVERT: E 50 ILE cc_start: 0.8646 (pt) cc_final: 0.8427 (mp) outliers start: 0 outliers final: 1 residues processed: 304 average time/residue: 0.7106 time to fit residues: 231.4327 Evaluate side-chains 177 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 73 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 382 GLN B 54 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 215 GLN B 221 GLN B 290 ASN C 51 GLN C 141 GLN C 156 ASN C 163 HIS C 180 ASN D 51 GLN D 73 ASN D 144 HIS D 158 ASN D 215 GLN D 281 GLN D 290 ASN D 382 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN E 281 GLN E 382 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122555 restraints weight = 14321.865| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.43 r_work: 0.3409 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13080 Z= 0.209 Angle : 0.681 7.841 17960 Z= 0.332 Chirality : 0.045 0.179 2255 Planarity : 0.005 0.038 2150 Dihedral : 9.925 56.903 2277 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.48 % Allowed : 10.76 % Favored : 84.77 % 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: 1.68 (0.21), residues: 1535 helix: 2.74 (0.20), residues: 480 sheet: 1.23 (0.25), residues: 465 loop : -0.36 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 320 TYR 0.024 0.002 TYR B 272 PHE 0.018 0.002 PHE B 67 TRP 0.041 0.002 TRP C 391 HIS 0.008 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00497 (13040) covalent geometry : angle 0.66791 (17850) SS BOND : bond 0.00365 ( 10) SS BOND : angle 1.64055 ( 20) hydrogen bonds : bond 0.05016 ( 665) hydrogen bonds : angle 4.69469 ( 2190) link_BETA1-4 : bond 0.00630 ( 20) link_BETA1-4 : angle 2.07134 ( 60) link_NAG-ASN : bond 0.00286 ( 10) link_NAG-ASN : angle 1.39738 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.404 Fit side-chains REVERT: A 121 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (t) REVERT: A 142 ASP cc_start: 0.7547 (p0) cc_final: 0.7267 (p0) REVERT: A 153 THR cc_start: 0.8983 (p) cc_final: 0.8768 (p) REVERT: A 201 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: A 215 GLN cc_start: 0.6389 (mt0) cc_final: 0.6094 (mm-40) REVERT: A 368 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6973 (mtt-85) REVERT: B 78 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6628 (ttp-170) REVERT: B 84 MET cc_start: 0.8951 (mtp) cc_final: 0.8689 (mtm) REVERT: B 179 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 186 GLU cc_start: 0.8216 (tt0) cc_final: 0.7927 (tt0) REVERT: C 201 GLU cc_start: 0.7826 (mp0) cc_final: 0.7536 (tt0) REVERT: C 215 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7160 (mm110) REVERT: C 248 ASP cc_start: 0.7993 (t70) cc_final: 0.7696 (t70) REVERT: C 259 ILE cc_start: 0.8333 (mm) cc_final: 0.8106 (pp) REVERT: C 390 MET cc_start: 0.7137 (mmp) cc_final: 0.6546 (ttp) REVERT: D 88 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7401 (mtm110) REVERT: D 114 SER cc_start: 0.8823 (m) cc_final: 0.8456 (p) REVERT: D 235 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8017 (mt) REVERT: D 390 MET cc_start: 0.8189 (mtt) cc_final: 0.7964 (mtp) REVERT: E 50 ILE cc_start: 0.8430 (pt) cc_final: 0.8081 (OUTLIER) REVERT: E 79 TYR cc_start: 0.8926 (m-80) cc_final: 0.8704 (m-10) REVERT: E 158 ASN cc_start: 0.8419 (m-40) cc_final: 0.7928 (t0) REVERT: E 183 MET cc_start: 0.8339 (mpp) cc_final: 0.8076 (mpp) REVERT: E 260 GLU cc_start: 0.8012 (pt0) cc_final: 0.7513 (mt-10) outliers start: 62 outliers final: 32 residues processed: 241 average time/residue: 0.5623 time to fit residues: 147.8909 Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 141 GLN A 163 HIS A 190 HIS A 382 GLN B 54 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 281 GLN D 382 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124315 restraints weight = 14438.297| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.45 r_work: 0.3422 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13080 Z= 0.128 Angle : 0.550 6.949 17960 Z= 0.271 Chirality : 0.041 0.134 2255 Planarity : 0.004 0.029 2150 Dihedral : 5.632 30.296 2277 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.90 % Allowed : 14.66 % Favored : 81.44 % 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: 1.81 (0.21), residues: 1535 helix: 3.02 (0.21), residues: 480 sheet: 1.19 (0.24), residues: 465 loop : -0.35 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.018 0.002 TYR C 176 PHE 0.013 0.001 PHE C 220 TRP 0.038 0.002 TRP C 391 HIS 0.003 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00284 (13040) covalent geometry : angle 0.54115 (17850) SS BOND : bond 0.00213 ( 10) SS BOND : angle 0.81182 ( 20) hydrogen bonds : bond 0.04521 ( 665) hydrogen bonds : angle 4.34445 ( 2190) link_BETA1-4 : bond 0.00523 ( 20) link_BETA1-4 : angle 1.61745 ( 60) link_NAG-ASN : bond 0.00117 ( 10) link_NAG-ASN : angle 1.13656 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.465 Fit side-chains REVERT: A 142 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7352 (p0) REVERT: A 153 THR cc_start: 0.8901 (p) cc_final: 0.8675 (p) REVERT: A 201 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 215 GLN cc_start: 0.6285 (mm-40) cc_final: 0.6033 (mm110) REVERT: A 223 THR cc_start: 0.8709 (m) cc_final: 0.8346 (p) REVERT: A 368 ARG cc_start: 0.7451 (mtm180) cc_final: 0.6971 (mtt-85) REVERT: B 179 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8553 (t) REVERT: B 181 THR cc_start: 0.8608 (t) cc_final: 0.8346 (p) REVERT: B 186 GLU cc_start: 0.8352 (tt0) cc_final: 0.8031 (tt0) REVERT: C 86 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8560 (tt) REVERT: C 201 GLU cc_start: 0.7870 (mp0) cc_final: 0.7586 (tt0) REVERT: C 390 MET cc_start: 0.6999 (mmp) cc_final: 0.6295 (tmt) REVERT: D 88 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7421 (mtm110) REVERT: D 114 SER cc_start: 0.8877 (m) cc_final: 0.8639 (p) REVERT: D 183 MET cc_start: 0.8681 (tpt) cc_final: 0.8441 (tmm) REVERT: D 235 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8049 (mt) REVERT: E 50 ILE cc_start: 0.8413 (pt) cc_final: 0.8088 (mp) REVERT: E 79 TYR cc_start: 0.8896 (m-80) cc_final: 0.8664 (m-10) REVERT: E 148 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7869 (p0) REVERT: E 183 MET cc_start: 0.8393 (mpp) cc_final: 0.8139 (mpp) REVERT: E 260 GLU cc_start: 0.7968 (pt0) cc_final: 0.7503 (mt-10) outliers start: 54 outliers final: 23 residues processed: 225 average time/residue: 0.5941 time to fit residues: 145.1571 Evaluate side-chains 205 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 190 HIS A 382 GLN B 54 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 281 GLN E 158 ASN E 163 HIS E 281 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115578 restraints weight = 14515.917| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.47 r_work: 0.3310 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13080 Z= 0.277 Angle : 0.685 7.645 17960 Z= 0.338 Chirality : 0.045 0.185 2255 Planarity : 0.004 0.034 2150 Dihedral : 5.025 30.071 2275 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.42 % Allowed : 16.97 % Favored : 77.62 % 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: 1.34 (0.21), residues: 1535 helix: 2.59 (0.21), residues: 480 sheet: 0.78 (0.24), residues: 465 loop : -0.44 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.020 0.002 TYR B 272 PHE 0.019 0.002 PHE C 305 TRP 0.029 0.002 TRP C 391 HIS 0.007 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00672 (13040) covalent geometry : angle 0.67753 (17850) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.07386 ( 20) hydrogen bonds : bond 0.05373 ( 665) hydrogen bonds : angle 4.65927 ( 2190) link_BETA1-4 : bond 0.00518 ( 20) link_BETA1-4 : angle 1.54932 ( 60) link_NAG-ASN : bond 0.00424 ( 10) link_NAG-ASN : angle 1.51599 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 182 time to evaluate : 0.491 Fit side-chains REVERT: A 201 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 270 LEU cc_start: 0.8589 (tp) cc_final: 0.8353 (tp) REVERT: A 368 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7018 (mtt-85) REVERT: B 179 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8667 (t) REVERT: B 181 THR cc_start: 0.8556 (t) cc_final: 0.8311 (p) REVERT: B 186 GLU cc_start: 0.8555 (tt0) cc_final: 0.8251 (tt0) REVERT: B 260 GLU cc_start: 0.8698 (pm20) cc_final: 0.8464 (pt0) REVERT: B 271 SER cc_start: 0.8761 (t) cc_final: 0.8541 (m) REVERT: C 86 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8616 (tt) REVERT: C 201 GLU cc_start: 0.8004 (mp0) cc_final: 0.7591 (tt0) REVERT: C 390 MET cc_start: 0.7072 (mmt) cc_final: 0.6446 (tmt) REVERT: D 88 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7760 (mtm110) REVERT: D 114 SER cc_start: 0.8898 (m) cc_final: 0.8556 (p) REVERT: D 183 MET cc_start: 0.8737 (tpt) cc_final: 0.8477 (tmm) REVERT: D 235 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (mt) REVERT: D 305 PHE cc_start: 0.8310 (m-80) cc_final: 0.7401 (t80) REVERT: E 50 ILE cc_start: 0.8405 (pt) cc_final: 0.8029 (OUTLIER) REVERT: E 79 TYR cc_start: 0.8965 (m-80) cc_final: 0.8747 (m-10) REVERT: E 84 MET cc_start: 0.8606 (mtp) cc_final: 0.8367 (mtm) REVERT: E 148 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8002 (p0) REVERT: E 160 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: E 257 ARG cc_start: 0.8176 (ptt-90) cc_final: 0.7701 (ptp-110) outliers start: 75 outliers final: 36 residues processed: 228 average time/residue: 0.5768 time to fit residues: 143.0377 Evaluate side-chains 202 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 141 GLN A 190 HIS A 210 GLN A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 281 GLN E 158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119830 restraints weight = 14447.967| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.47 r_work: 0.3364 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13080 Z= 0.125 Angle : 0.542 7.042 17960 Z= 0.267 Chirality : 0.040 0.135 2255 Planarity : 0.004 0.028 2150 Dihedral : 4.700 26.145 2275 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.61 % Allowed : 19.06 % Favored : 77.33 % 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: 1.59 (0.21), residues: 1535 helix: 2.94 (0.21), residues: 480 sheet: 0.86 (0.25), residues: 465 loop : -0.37 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.020 0.002 TYR B 272 PHE 0.017 0.001 PHE D 385 TRP 0.032 0.001 TRP C 391 HIS 0.002 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00276 (13040) covalent geometry : angle 0.53487 (17850) SS BOND : bond 0.00476 ( 10) SS BOND : angle 0.82783 ( 20) hydrogen bonds : bond 0.04462 ( 665) hydrogen bonds : angle 4.35502 ( 2190) link_BETA1-4 : bond 0.00480 ( 20) link_BETA1-4 : angle 1.38822 ( 60) link_NAG-ASN : bond 0.00168 ( 10) link_NAG-ASN : angle 1.12354 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.413 Fit side-chains REVERT: A 153 THR cc_start: 0.8888 (p) cc_final: 0.8642 (p) REVERT: A 201 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 368 ARG cc_start: 0.7500 (mtm180) cc_final: 0.7014 (mtt-85) REVERT: B 160 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: B 181 THR cc_start: 0.8538 (t) cc_final: 0.8320 (p) REVERT: B 186 GLU cc_start: 0.8523 (tt0) cc_final: 0.8196 (tt0) REVERT: B 238 LEU cc_start: 0.8349 (mt) cc_final: 0.8146 (mm) REVERT: C 86 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8548 (tt) REVERT: C 117 THR cc_start: 0.8727 (m) cc_final: 0.8439 (p) REVERT: C 194 GLU cc_start: 0.8036 (pt0) cc_final: 0.7809 (pt0) REVERT: C 201 GLU cc_start: 0.7972 (mp0) cc_final: 0.7595 (tt0) REVERT: C 390 MET cc_start: 0.6992 (mmt) cc_final: 0.6333 (tmt) REVERT: D 88 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7620 (mtm110) REVERT: D 114 SER cc_start: 0.8947 (m) cc_final: 0.8716 (p) REVERT: D 179 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8486 (t) REVERT: D 183 MET cc_start: 0.8768 (tpt) cc_final: 0.8557 (tmm) REVERT: D 235 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8081 (mt) REVERT: D 270 LEU cc_start: 0.8713 (tp) cc_final: 0.8503 (tp) REVERT: E 50 ILE cc_start: 0.8318 (pt) cc_final: 0.7991 (OUTLIER) REVERT: E 79 TYR cc_start: 0.8937 (m-80) cc_final: 0.8627 (m-10) REVERT: E 84 MET cc_start: 0.8610 (mtp) cc_final: 0.8364 (mtm) REVERT: E 257 ARG cc_start: 0.8158 (ptt-90) cc_final: 0.7695 (ptp-110) outliers start: 50 outliers final: 27 residues processed: 206 average time/residue: 0.6079 time to fit residues: 135.7453 Evaluate side-chains 191 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 190 HIS A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 210 GLN D 281 GLN E 158 ASN E 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118453 restraints weight = 14399.462| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.45 r_work: 0.3344 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13080 Z= 0.163 Angle : 0.565 7.409 17960 Z= 0.279 Chirality : 0.041 0.146 2255 Planarity : 0.004 0.032 2150 Dihedral : 4.556 24.845 2275 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.33 % Allowed : 19.49 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1535 helix: 2.96 (0.21), residues: 480 sheet: 0.76 (0.25), residues: 465 loop : -0.29 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.019 0.002 TYR B 272 PHE 0.013 0.002 PHE D 385 TRP 0.022 0.001 TRP C 391 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00385 (13040) covalent geometry : angle 0.55676 (17850) SS BOND : bond 0.00267 ( 10) SS BOND : angle 1.13927 ( 20) hydrogen bonds : bond 0.04601 ( 665) hydrogen bonds : angle 4.33202 ( 2190) link_BETA1-4 : bond 0.00503 ( 20) link_BETA1-4 : angle 1.40817 ( 60) link_NAG-ASN : bond 0.00230 ( 10) link_NAG-ASN : angle 1.23518 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.374 Fit side-chains REVERT: A 65 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8321 (mmm-85) REVERT: A 153 THR cc_start: 0.8911 (p) cc_final: 0.8681 (p) REVERT: A 201 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 368 ARG cc_start: 0.7536 (mtm180) cc_final: 0.7032 (mtt-85) REVERT: B 179 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8661 (t) REVERT: B 181 THR cc_start: 0.8494 (t) cc_final: 0.8273 (p) REVERT: B 186 GLU cc_start: 0.8496 (tt0) cc_final: 0.8182 (tt0) REVERT: B 238 LEU cc_start: 0.8371 (mt) cc_final: 0.8167 (mm) REVERT: B 260 GLU cc_start: 0.8704 (pm20) cc_final: 0.8451 (pt0) REVERT: C 86 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8595 (tt) REVERT: C 117 THR cc_start: 0.8760 (m) cc_final: 0.8457 (p) REVERT: C 194 GLU cc_start: 0.8075 (pt0) cc_final: 0.7864 (pt0) REVERT: C 201 GLU cc_start: 0.7993 (mp0) cc_final: 0.7626 (tt0) REVERT: C 259 ILE cc_start: 0.8430 (mp) cc_final: 0.7944 (tt) REVERT: C 390 MET cc_start: 0.6828 (mmt) cc_final: 0.6345 (ttp) REVERT: D 88 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7657 (mtp-110) REVERT: D 114 SER cc_start: 0.8963 (m) cc_final: 0.8739 (p) REVERT: D 183 MET cc_start: 0.8781 (tpt) cc_final: 0.8565 (tmm) REVERT: D 235 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (mt) REVERT: E 50 ILE cc_start: 0.8337 (pt) cc_final: 0.8021 (OUTLIER) REVERT: E 79 TYR cc_start: 0.8936 (m-80) cc_final: 0.8646 (m-10) REVERT: E 84 MET cc_start: 0.8617 (mtp) cc_final: 0.8369 (mtm) REVERT: E 160 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: E 227 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8622 (pttm) REVERT: E 257 ARG cc_start: 0.8265 (ptt-90) cc_final: 0.7749 (ptp-110) outliers start: 60 outliers final: 34 residues processed: 200 average time/residue: 0.5778 time to fit residues: 125.6964 Evaluate side-chains 195 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 140 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 95 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.0050 overall best weight: 0.5632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 190 HIS A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 156 ASN D 281 GLN E 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121033 restraints weight = 14284.736| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.44 r_work: 0.3379 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13080 Z= 0.110 Angle : 0.528 9.939 17960 Z= 0.260 Chirality : 0.039 0.139 2255 Planarity : 0.003 0.029 2150 Dihedral : 4.377 20.615 2275 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.75 % Allowed : 19.86 % Favored : 76.39 % 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: 1.72 (0.22), residues: 1535 helix: 3.16 (0.21), residues: 480 sheet: 0.76 (0.25), residues: 465 loop : -0.24 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.024 0.001 TYR A 176 PHE 0.012 0.001 PHE D 385 TRP 0.023 0.001 TRP C 391 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00235 (13040) covalent geometry : angle 0.51461 (17850) SS BOND : bond 0.00256 ( 10) SS BOND : angle 2.50927 ( 20) hydrogen bonds : bond 0.04250 ( 665) hydrogen bonds : angle 4.18303 ( 2190) link_BETA1-4 : bond 0.00492 ( 20) link_BETA1-4 : angle 1.35157 ( 60) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 1.15458 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.509 Fit side-chains REVERT: A 65 ARG cc_start: 0.8481 (ttm170) cc_final: 0.8114 (mtt-85) REVERT: A 153 THR cc_start: 0.8858 (p) cc_final: 0.8644 (p) REVERT: A 368 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7021 (mtt-85) REVERT: B 179 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8655 (t) REVERT: B 181 THR cc_start: 0.8541 (t) cc_final: 0.8323 (p) REVERT: B 186 GLU cc_start: 0.8497 (tt0) cc_final: 0.8165 (tt0) REVERT: B 250 CYS cc_start: 0.8616 (m) cc_final: 0.8377 (m) REVERT: C 86 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8566 (tt) REVERT: C 117 THR cc_start: 0.8728 (m) cc_final: 0.8482 (p) REVERT: C 167 ASP cc_start: 0.8322 (p0) cc_final: 0.8026 (p0) REVERT: C 201 GLU cc_start: 0.7887 (mp0) cc_final: 0.7496 (tt0) REVERT: C 259 ILE cc_start: 0.8405 (mp) cc_final: 0.7913 (tt) REVERT: C 390 MET cc_start: 0.6837 (mmt) cc_final: 0.6384 (ttp) REVERT: D 88 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7610 (mtp-110) REVERT: D 179 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8407 (t) REVERT: D 183 MET cc_start: 0.8744 (tpt) cc_final: 0.8525 (tmm) REVERT: D 235 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8073 (mt) REVERT: E 50 ILE cc_start: 0.8311 (pt) cc_final: 0.8020 (mp) REVERT: E 79 TYR cc_start: 0.8918 (m-80) cc_final: 0.8618 (m-10) REVERT: E 84 MET cc_start: 0.8599 (mtp) cc_final: 0.8332 (mtm) REVERT: E 167 ASP cc_start: 0.8350 (p0) cc_final: 0.8067 (p0) REVERT: E 211 VAL cc_start: 0.7946 (t) cc_final: 0.7684 (m) REVERT: E 227 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8598 (pttm) REVERT: E 257 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.7781 (ptp-110) outliers start: 52 outliers final: 25 residues processed: 207 average time/residue: 0.5571 time to fit residues: 126.1038 Evaluate side-chains 195 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.0770 chunk 141 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 190 HIS ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 221 GLN D 281 GLN E 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118037 restraints weight = 14292.574| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.42 r_work: 0.3338 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13080 Z= 0.181 Angle : 0.580 7.841 17960 Z= 0.284 Chirality : 0.041 0.150 2255 Planarity : 0.004 0.031 2150 Dihedral : 4.518 23.755 2275 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.54 % Allowed : 20.87 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1535 helix: 3.02 (0.21), residues: 480 sheet: 0.64 (0.25), residues: 465 loop : -0.24 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.029 0.002 TYR A 176 PHE 0.014 0.002 PHE B 220 TRP 0.023 0.001 TRP C 391 HIS 0.004 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00430 (13040) covalent geometry : angle 0.57194 (17850) SS BOND : bond 0.00320 ( 10) SS BOND : angle 1.43543 ( 20) hydrogen bonds : bond 0.04637 ( 665) hydrogen bonds : angle 4.27437 ( 2190) link_BETA1-4 : bond 0.00493 ( 20) link_BETA1-4 : angle 1.41487 ( 60) link_NAG-ASN : bond 0.00358 ( 10) link_NAG-ASN : angle 1.29844 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.482 Fit side-chains REVERT: A 153 THR cc_start: 0.8957 (p) cc_final: 0.8723 (p) REVERT: A 201 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 233 SER cc_start: 0.8139 (m) cc_final: 0.7853 (p) REVERT: A 368 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7051 (mtt-85) REVERT: B 179 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8650 (t) REVERT: B 181 THR cc_start: 0.8460 (t) cc_final: 0.8243 (p) REVERT: B 186 GLU cc_start: 0.8499 (tt0) cc_final: 0.8193 (tt0) REVERT: B 260 GLU cc_start: 0.8673 (pm20) cc_final: 0.8428 (pt0) REVERT: C 86 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8611 (tt) REVERT: C 117 THR cc_start: 0.8759 (m) cc_final: 0.8476 (p) REVERT: C 201 GLU cc_start: 0.7997 (mp0) cc_final: 0.7623 (tt0) REVERT: C 259 ILE cc_start: 0.8408 (mp) cc_final: 0.7932 (tt) REVERT: C 390 MET cc_start: 0.6870 (mmt) cc_final: 0.6381 (ttp) REVERT: D 88 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7653 (mtp-110) REVERT: D 235 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8109 (mt) REVERT: E 50 ILE cc_start: 0.8334 (pt) cc_final: 0.8006 (OUTLIER) REVERT: E 79 TYR cc_start: 0.8934 (m-80) cc_final: 0.8711 (m-10) REVERT: E 84 MET cc_start: 0.8636 (mtp) cc_final: 0.8376 (mtm) REVERT: E 167 ASP cc_start: 0.8438 (p0) cc_final: 0.8019 (p0) REVERT: E 227 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8590 (pttm) REVERT: E 257 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.7808 (ptp-110) outliers start: 49 outliers final: 30 residues processed: 195 average time/residue: 0.5891 time to fit residues: 124.8058 Evaluate side-chains 191 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 190 HIS A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 281 GLN E 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118951 restraints weight = 14310.485| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.43 r_work: 0.3352 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13080 Z= 0.147 Angle : 0.550 8.087 17960 Z= 0.270 Chirality : 0.040 0.149 2255 Planarity : 0.003 0.030 2150 Dihedral : 4.463 22.921 2275 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.18 % Allowed : 21.44 % Favored : 75.38 % 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: 1.62 (0.21), residues: 1535 helix: 3.09 (0.21), residues: 480 sheet: 0.62 (0.25), residues: 465 loop : -0.22 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.036 0.002 TYR A 176 PHE 0.012 0.001 PHE B 220 TRP 0.022 0.001 TRP C 391 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00343 (13040) covalent geometry : angle 0.54209 (17850) SS BOND : bond 0.00348 ( 10) SS BOND : angle 1.33778 ( 20) hydrogen bonds : bond 0.04445 ( 665) hydrogen bonds : angle 4.19233 ( 2190) link_BETA1-4 : bond 0.00468 ( 20) link_BETA1-4 : angle 1.38319 ( 60) link_NAG-ASN : bond 0.00258 ( 10) link_NAG-ASN : angle 1.18793 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.464 Fit side-chains REVERT: A 153 THR cc_start: 0.8895 (p) cc_final: 0.8680 (p) REVERT: A 201 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 233 SER cc_start: 0.8118 (m) cc_final: 0.7855 (p) REVERT: A 368 ARG cc_start: 0.7531 (mtm180) cc_final: 0.7041 (mtt-85) REVERT: B 179 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (t) REVERT: B 181 THR cc_start: 0.8451 (t) cc_final: 0.8248 (p) REVERT: B 186 GLU cc_start: 0.8505 (tt0) cc_final: 0.8177 (tt0) REVERT: B 250 CYS cc_start: 0.8622 (m) cc_final: 0.8373 (m) REVERT: B 260 GLU cc_start: 0.8662 (pm20) cc_final: 0.8417 (pt0) REVERT: C 86 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8595 (tt) REVERT: C 117 THR cc_start: 0.8735 (m) cc_final: 0.8494 (p) REVERT: C 201 GLU cc_start: 0.7936 (mp0) cc_final: 0.7514 (tt0) REVERT: C 259 ILE cc_start: 0.8398 (mp) cc_final: 0.7921 (tt) REVERT: C 390 MET cc_start: 0.6813 (mmt) cc_final: 0.6392 (ttp) REVERT: D 88 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7635 (mtp-110) REVERT: D 235 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8098 (mt) REVERT: E 50 ILE cc_start: 0.8312 (pt) cc_final: 0.8020 (mp) REVERT: E 79 TYR cc_start: 0.8911 (m-80) cc_final: 0.8689 (m-10) REVERT: E 84 MET cc_start: 0.8617 (mtp) cc_final: 0.8352 (mtm) REVERT: E 167 ASP cc_start: 0.8391 (p0) cc_final: 0.8039 (p0) REVERT: E 227 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8591 (pttm) REVERT: E 257 ARG cc_start: 0.8376 (ptt-90) cc_final: 0.7830 (ptp-110) outliers start: 44 outliers final: 27 residues processed: 196 average time/residue: 0.5939 time to fit residues: 126.6271 Evaluate side-chains 197 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 190 HIS A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 210 GLN D 281 GLN E 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119680 restraints weight = 14324.571| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.41 r_work: 0.3361 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13080 Z= 0.134 Angle : 0.547 8.469 17960 Z= 0.268 Chirality : 0.040 0.154 2255 Planarity : 0.003 0.030 2150 Dihedral : 4.396 21.205 2275 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.96 % Allowed : 22.02 % Favored : 75.02 % 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: 1.66 (0.22), residues: 1535 helix: 3.15 (0.21), residues: 480 sheet: 0.62 (0.25), residues: 465 loop : -0.21 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.034 0.002 TYR A 176 PHE 0.012 0.001 PHE B 220 TRP 0.020 0.001 TRP C 391 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00307 (13040) covalent geometry : angle 0.53940 (17850) SS BOND : bond 0.00441 ( 10) SS BOND : angle 1.18246 ( 20) hydrogen bonds : bond 0.04368 ( 665) hydrogen bonds : angle 4.12005 ( 2190) link_BETA1-4 : bond 0.00485 ( 20) link_BETA1-4 : angle 1.37276 ( 60) link_NAG-ASN : bond 0.00206 ( 10) link_NAG-ASN : angle 1.14366 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.562 Fit side-chains REVERT: A 65 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8290 (mmm-85) REVERT: A 153 THR cc_start: 0.8882 (p) cc_final: 0.8671 (p) REVERT: A 201 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 233 SER cc_start: 0.8133 (m) cc_final: 0.7853 (p) REVERT: A 368 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7006 (mtt-85) REVERT: B 179 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8600 (t) REVERT: B 181 THR cc_start: 0.8432 (t) cc_final: 0.8227 (p) REVERT: B 250 CYS cc_start: 0.8608 (m) cc_final: 0.8359 (m) REVERT: B 260 GLU cc_start: 0.8652 (pm20) cc_final: 0.8384 (pt0) REVERT: C 117 THR cc_start: 0.8714 (m) cc_final: 0.8501 (p) REVERT: C 201 GLU cc_start: 0.7882 (mp0) cc_final: 0.7507 (tt0) REVERT: C 259 ILE cc_start: 0.8367 (mp) cc_final: 0.7872 (tt) REVERT: C 390 MET cc_start: 0.6814 (mmt) cc_final: 0.6400 (ttp) REVERT: D 88 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7634 (mtp-110) REVERT: D 183 MET cc_start: 0.8587 (tmt) cc_final: 0.8315 (mpt) REVERT: D 235 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8078 (mt) REVERT: E 50 ILE cc_start: 0.8298 (pt) cc_final: 0.8025 (mp) REVERT: E 79 TYR cc_start: 0.8884 (m-80) cc_final: 0.8661 (m-10) REVERT: E 84 MET cc_start: 0.8587 (mtp) cc_final: 0.8339 (mtm) REVERT: E 167 ASP cc_start: 0.8384 (p0) cc_final: 0.8073 (p0) REVERT: E 227 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8597 (pttm) REVERT: E 257 ARG cc_start: 0.8346 (ptt-90) cc_final: 0.7807 (ptp-110) outliers start: 41 outliers final: 28 residues processed: 207 average time/residue: 0.6206 time to fit residues: 139.3679 Evaluate side-chains 205 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 215 GLN Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 0.0070 chunk 134 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 190 HIS A 210 GLN A 221 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 382 GLN C 156 ASN C 210 GLN D 281 GLN E 158 ASN E 281 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.148671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121902 restraints weight = 14310.136| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.41 r_work: 0.3404 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13080 Z= 0.109 Angle : 0.521 8.651 17960 Z= 0.256 Chirality : 0.039 0.148 2255 Planarity : 0.003 0.029 2150 Dihedral : 4.264 20.535 2275 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.60 % Allowed : 22.38 % Favored : 75.02 % 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: 1.74 (0.22), residues: 1535 helix: 3.29 (0.21), residues: 480 sheet: 0.63 (0.25), residues: 465 loop : -0.20 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.018 0.001 TYR B 272 PHE 0.012 0.001 PHE A 220 TRP 0.018 0.001 TRP C 391 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00237 (13040) covalent geometry : angle 0.51359 (17850) SS BOND : bond 0.00336 ( 10) SS BOND : angle 1.00069 ( 20) hydrogen bonds : bond 0.04148 ( 665) hydrogen bonds : angle 3.99790 ( 2190) link_BETA1-4 : bond 0.00478 ( 20) link_BETA1-4 : angle 1.34417 ( 60) link_NAG-ASN : bond 0.00165 ( 10) link_NAG-ASN : angle 1.06014 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.05 seconds wall clock time: 75 minutes 22.26 seconds (4522.26 seconds total)