Starting phenix.real_space_refine on Sun May 3 12:15:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ley_63037/05_2026/9ley_63037.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.083 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8359 2.51 5 N 2074 2.21 5 O 2342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 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: 12830 Number of models: 1 Model: "" Number of chains: 17 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: "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: "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: "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: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'TC9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'TC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.65, per 1000 atoms: 0.28 Number of scatterers: 12830 At special positions: 0 Unit cell: (96.928, 100.656, 125.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2342 8.00 N 2074 7.00 C 8359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 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 B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.04 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=2.04 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=2.04 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 D 55 " " NAG G 1 " - " ASN D 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 A 55 " " NAG M 1 " - " ASN A 170 " " NAG N 1 " - " ASN E 55 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 551.4 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, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.656A 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 259 through 282 removed outlier: 3.997A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 322 removed outlier: 4.031A 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 'B' and resid 94 through 97 Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.655A 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: 4.398A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 removed outlier: 4.030A 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: 4.656A 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: 4.399A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 322 removed outlier: 4.031A 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 '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: 4.068A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 4.030A 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 '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: 4.379A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 322 removed outlier: 4.030A 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 'D' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.863A 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=AA2, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.623A 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: 4.463A 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: 5.291A 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: 7.185A pdb=" N SER D 90 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.340A 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: 8.057A pdb=" N VAL D 62 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 68 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 130 removed outlier: 6.810A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 128 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP B 91 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 74 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 86 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 68 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL B 66 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 90 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL B 64 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU B 92 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL B 62 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 68 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 111 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: 5.115A 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: 4.863A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL C 128 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.810A 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: 5.115A 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: 4.463A 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: 5.291A 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: 5.787A pdb=" N VAL C 66 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.185A 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: 3.709A 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 'A' and resid 107 through 111 removed outlier: 6.211A 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: 4.623A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.863A 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: 6.810A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.211A 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: 4.623A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 6.624A 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: 6.955A pdb=" N LEU A 86 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL A 68 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL A 66 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER A 90 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 5.340A 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: 8.058A 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=AB6, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AB7, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.211A 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: 4.623A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.065A 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: 6.451A pdb=" N THR E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.576A 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: 6.211A 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: 4.623A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR E 80 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.382A 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: 5.291A pdb=" N VAL E 68 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG E 88 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL E 66 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.185A 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: 8.736A 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 122 740 hydrogen bonds defined for protein. 2160 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: 2.18 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1967 1.31 - 1.44: 3689 1.44 - 1.56: 7401 1.56 - 1.69: 10 1.69 - 1.81: 75 Bond restraints: 13142 Sorted by residual: bond pdb=" C12 TC9 B 801 " pdb=" C17 TC9 B 801 " ideal model delta sigma weight residual 1.383 1.581 -0.198 2.00e-02 2.50e+03 9.76e+01 bond pdb=" C12 TC9 D 801 " pdb=" C17 TC9 D 801 " ideal model delta sigma weight residual 1.383 1.572 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C30 TC9 B 801 " pdb=" C35 TC9 B 801 " ideal model delta sigma weight residual 1.387 1.555 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C30 TC9 D 801 " pdb=" C35 TC9 D 801 " ideal model delta sigma weight residual 1.387 1.551 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" C16 TC9 B 801 " pdb=" C18 TC9 B 801 " ideal model delta sigma weight residual 1.513 1.672 -0.159 2.00e-02 2.50e+03 6.30e+01 ... (remaining 13137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 17478 2.64 - 5.28: 413 5.28 - 7.92: 92 7.92 - 10.56: 19 10.56 - 13.20: 2 Bond angle restraints: 18004 Sorted by residual: angle pdb=" N HIS B 276 " pdb=" CA HIS B 276 " pdb=" C HIS B 276 " ideal model delta sigma weight residual 112.68 102.47 10.21 1.33e+00 5.65e-01 5.89e+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 109.54 118.82 -9.28 1.37e+00 5.33e-01 4.58e+01 angle pdb=" N TRP D 391 " pdb=" CA TRP D 391 " pdb=" C TRP D 391 " ideal model delta sigma weight residual 109.54 118.79 -9.25 1.37e+00 5.33e-01 4.56e+01 angle pdb=" N TRP C 391 " pdb=" CA TRP C 391 " pdb=" C TRP C 391 " ideal model delta sigma weight residual 109.54 118.78 -9.24 1.37e+00 5.33e-01 4.55e+01 ... (remaining 17999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7907 35.94 - 71.88: 194 71.88 - 107.82: 95 107.82 - 143.75: 6 143.75 - 179.69: 5 Dihedral angle restraints: 8207 sinusoidal: 3597 harmonic: 4610 Sorted by residual: 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 93.00 156.92 -63.92 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS D 289 " pdb=" SG CYS D 289 " pdb=" SG CYS D 394 " pdb=" CB CYS D 394 " ideal model delta sinusoidal sigma weight residual 93.00 156.91 -63.91 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 394 " pdb=" CB CYS A 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 8204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.940: 2259 0.940 - 1.881: 0 1.881 - 2.821: 0 2.821 - 3.761: 0 3.761 - 4.701: 2 Chirality restraints: 2261 Sorted by residual: chirality pdb=" N1 TC9 D 801 " pdb=" C2 TC9 D 801 " pdb=" C43 TC9 D 801 " pdb=" C6 TC9 D 801 " both_signs ideal model delta sigma weight residual False 2.29 -2.42 4.70 2.00e-01 2.50e+01 5.53e+02 chirality pdb=" N1 TC9 B 801 " pdb=" C2 TC9 B 801 " pdb=" C43 TC9 B 801 " pdb=" C6 TC9 B 801 " both_signs ideal model delta sigma weight residual False 2.29 -2.39 4.67 2.00e-01 2.50e+01 5.46e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 ... (remaining 2258 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.198 2.00e-02 2.50e+03 1.68e-01 3.54e+02 pdb=" C7 NAG O 1 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.198 2.00e-02 2.50e+03 1.68e-01 3.53e+02 pdb=" C7 NAG K 1 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.274 2.00e-02 2.50e+03 pdb=" O7 NAG K 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 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.155 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1563 2.75 - 3.29: 12047 3.29 - 3.83: 21986 3.83 - 4.36: 25952 4.36 - 4.90: 45046 Nonbonded interactions: 106594 Sorted by model distance: 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 2.214 3.120 nonbonded pdb=" OD2 ASP D 142 " pdb=" ND1 HIS D 144 " model vdw 2.214 3.120 nonbonded pdb=" OD2 ASP E 142 " pdb=" ND1 HIS E 144 " model vdw 2.214 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 2.214 3.120 ... (remaining 106589 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' selection = (chain 'B' and resid 47 through 395) selection = chain 'C' selection = (chain 'D' and resid 47 through 395) 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: 2.720 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.300 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 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 : 0.008 0.198 13182 Z= 0.497 Angle : 1.035 13.205 18114 Z= 0.564 Chirality : 0.154 4.701 2261 Planarity : 0.010 0.168 2158 Dihedral : 19.348 179.693 5157 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1535 helix: 2.11 (0.22), residues: 490 sheet: 1.28 (0.25), residues: 465 loop : -0.38 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.016 0.002 TYR B 272 PHE 0.020 0.002 PHE C 72 TRP 0.011 0.001 TRP B 112 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00837 (13142) covalent geometry : angle 1.00979 (18004) SS BOND : bond 0.00996 ( 10) SS BOND : angle 4.03121 ( 20) hydrogen bonds : bond 0.14947 ( 662) hydrogen bonds : angle 6.61367 ( 2160) link_BETA1-4 : bond 0.00472 ( 20) link_BETA1-4 : angle 1.41300 ( 60) link_NAG-ASN : bond 0.01198 ( 10) link_NAG-ASN : angle 4.53611 ( 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 342 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.7371 (p-90) cc_final: 0.6886 (p-90) outliers start: 0 outliers final: 2 residues processed: 342 average time/residue: 0.5250 time to fit residues: 197.3644 Evaluate side-chains 179 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN D 156 ASN D 163 HIS D 215 GLN D 228 ASN D 382 GLN B 103 HIS C 73 ASN C 144 HIS C 156 ASN C 180 ASN C 215 GLN C 281 GLN C 382 GLN A 51 GLN A 73 ASN A 180 ASN A 190 HIS A 215 GLN A 228 ASN A 382 GLN E 180 ASN E 215 GLN E 221 GLN E 382 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136262 restraints weight = 13967.814| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.46 r_work: 0.3727 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13182 Z= 0.160 Angle : 0.694 10.614 18114 Z= 0.332 Chirality : 0.045 0.333 2261 Planarity : 0.005 0.039 2158 Dihedral : 15.634 172.488 2361 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.83 % Allowed : 12.42 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1535 helix: 2.68 (0.20), residues: 480 sheet: 1.17 (0.25), residues: 465 loop : -0.35 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 119 TYR 0.020 0.002 TYR D 272 PHE 0.015 0.002 PHE C 72 TRP 0.030 0.002 TRP A 391 HIS 0.008 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00362 (13142) covalent geometry : angle 0.68511 (18004) SS BOND : bond 0.00244 ( 10) SS BOND : angle 1.37055 ( 20) hydrogen bonds : bond 0.04843 ( 662) hydrogen bonds : angle 4.75642 ( 2160) link_BETA1-4 : bond 0.00708 ( 20) link_BETA1-4 : angle 1.81227 ( 60) link_NAG-ASN : bond 0.00218 ( 10) link_NAG-ASN : angle 1.25841 ( 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 256 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: D 113 GLU cc_start: 0.8857 (mp0) cc_final: 0.8579 (mp0) REVERT: D 144 HIS cc_start: 0.6915 (m90) cc_final: 0.6556 (m90) REVERT: D 390 MET cc_start: 0.7602 (mmt) cc_final: 0.7076 (mtp) REVERT: B 73 ASN cc_start: 0.8046 (m-40) cc_final: 0.7302 (t0) REVERT: B 112 TRP cc_start: 0.8018 (p-90) cc_final: 0.7668 (p-90) REVERT: B 167 ASP cc_start: 0.6992 (p0) cc_final: 0.6701 (p0) REVERT: B 186 GLU cc_start: 0.7928 (tt0) cc_final: 0.7597 (tt0) REVERT: C 63 ASP cc_start: 0.7954 (t0) cc_final: 0.7488 (m-30) REVERT: C 158 ASN cc_start: 0.7499 (p0) cc_final: 0.6856 (m-40) REVERT: C 225 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7093 (ttp-170) REVERT: E 81 MET cc_start: 0.7865 (ptt) cc_final: 0.7640 (ptt) REVERT: E 84 MET cc_start: 0.7543 (mtp) cc_final: 0.7333 (mtp) REVERT: E 154 GLU cc_start: 0.7779 (tt0) cc_final: 0.7439 (tt0) REVERT: E 390 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5720 (mpt) outliers start: 53 outliers final: 29 residues processed: 237 average time/residue: 0.4431 time to fit residues: 117.4392 Evaluate side-chains 204 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 390 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS C 156 ASN A 180 ASN E 158 ASN E 281 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.160640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136985 restraints weight = 14597.027| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.54 r_work: 0.3734 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13182 Z= 0.140 Angle : 0.619 12.847 18114 Z= 0.295 Chirality : 0.042 0.271 2261 Planarity : 0.004 0.055 2158 Dihedral : 11.051 167.150 2357 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.83 % Allowed : 15.38 % Favored : 80.79 % 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: 1.79 (0.22), residues: 1535 helix: 3.01 (0.21), residues: 480 sheet: 1.36 (0.25), residues: 420 loop : -0.40 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 78 TYR 0.018 0.002 TYR D 272 PHE 0.015 0.002 PHE B 164 TRP 0.015 0.001 TRP E 389 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00313 (13142) covalent geometry : angle 0.61133 (18004) SS BOND : bond 0.00444 ( 10) SS BOND : angle 0.73840 ( 20) hydrogen bonds : bond 0.04452 ( 662) hydrogen bonds : angle 4.47390 ( 2160) link_BETA1-4 : bond 0.00549 ( 20) link_BETA1-4 : angle 1.61322 ( 60) link_NAG-ASN : bond 0.00156 ( 10) link_NAG-ASN : angle 1.15840 ( 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: 53 poor density : 199 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 113 GLU cc_start: 0.8701 (mp0) cc_final: 0.8394 (mp0) REVERT: D 390 MET cc_start: 0.7594 (mmt) cc_final: 0.7067 (mtp) REVERT: B 73 ASN cc_start: 0.8070 (m-40) cc_final: 0.7300 (t0) REVERT: B 112 TRP cc_start: 0.8071 (p-90) cc_final: 0.7714 (p-90) REVERT: B 167 ASP cc_start: 0.7076 (p0) cc_final: 0.6766 (p0) REVERT: B 184 GLU cc_start: 0.8031 (pt0) cc_final: 0.7808 (pt0) REVERT: B 186 GLU cc_start: 0.8143 (tt0) cc_final: 0.7824 (tt0) REVERT: B 225 ARG cc_start: 0.7428 (mmm160) cc_final: 0.7182 (mmm-85) REVERT: B 260 GLU cc_start: 0.8295 (pm20) cc_final: 0.8074 (pm20) REVERT: B 271 SER cc_start: 0.8696 (t) cc_final: 0.8434 (p) REVERT: C 63 ASP cc_start: 0.7841 (t0) cc_final: 0.7323 (m-30) REVERT: C 96 LEU cc_start: 0.8390 (mt) cc_final: 0.8055 (mp) REVERT: C 158 ASN cc_start: 0.7356 (p0) cc_final: 0.6564 (m-40) REVERT: C 225 ARG cc_start: 0.7585 (mtp180) cc_final: 0.6748 (ttp-170) REVERT: C 227 LYS cc_start: 0.7944 (ptpt) cc_final: 0.7580 (ptpt) REVERT: A 98 TRP cc_start: 0.5291 (p90) cc_final: 0.5054 (p90) REVERT: A 201 GLU cc_start: 0.6865 (mp0) cc_final: 0.6623 (mp0) REVERT: A 246 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (tp) REVERT: A 248 ASP cc_start: 0.7836 (t0) cc_final: 0.7521 (m-30) REVERT: E 84 MET cc_start: 0.7501 (mtp) cc_final: 0.7297 (mtp) REVERT: E 186 GLU cc_start: 0.7097 (tt0) cc_final: 0.6868 (mt-10) REVERT: E 390 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5620 (mpt) outliers start: 53 outliers final: 32 residues processed: 233 average time/residue: 0.4844 time to fit residues: 125.0153 Evaluate side-chains 215 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 390 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 ASN B 144 HIS B 221 GLN C 144 HIS ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN E 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135951 restraints weight = 14705.326| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.54 r_work: 0.3707 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13182 Z= 0.152 Angle : 0.603 10.999 18114 Z= 0.292 Chirality : 0.042 0.313 2261 Planarity : 0.004 0.049 2158 Dihedral : 10.349 165.786 2357 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.91 % Allowed : 17.33 % Favored : 77.76 % 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: 1.64 (0.22), residues: 1535 helix: 3.00 (0.21), residues: 480 sheet: 1.08 (0.25), residues: 420 loop : -0.44 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 368 TYR 0.018 0.002 TYR D 272 PHE 0.026 0.002 PHE D 164 TRP 0.012 0.001 TRP E 389 HIS 0.007 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00356 (13142) covalent geometry : angle 0.59738 (18004) SS BOND : bond 0.00263 ( 10) SS BOND : angle 0.69229 ( 20) hydrogen bonds : bond 0.04404 ( 662) hydrogen bonds : angle 4.40037 ( 2160) link_BETA1-4 : bond 0.00448 ( 20) link_BETA1-4 : angle 1.42547 ( 60) link_NAG-ASN : bond 0.00144 ( 10) link_NAG-ASN : angle 1.16452 ( 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 270 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: D 113 GLU cc_start: 0.8701 (mp0) cc_final: 0.8347 (mp0) REVERT: B 112 TRP cc_start: 0.8083 (p-90) cc_final: 0.7714 (p-90) REVERT: B 184 GLU cc_start: 0.7897 (pt0) cc_final: 0.7678 (pt0) REVERT: B 225 ARG cc_start: 0.7473 (mmm160) cc_final: 0.7227 (mmm-85) REVERT: B 271 SER cc_start: 0.8746 (t) cc_final: 0.8489 (p) REVERT: C 63 ASP cc_start: 0.7848 (t0) cc_final: 0.7324 (m-30) REVERT: C 96 LEU cc_start: 0.8372 (mt) cc_final: 0.8020 (mp) REVERT: C 158 ASN cc_start: 0.7438 (p0) cc_final: 0.6605 (m-40) REVERT: C 225 ARG cc_start: 0.7570 (mtp180) cc_final: 0.6831 (ttp-110) REVERT: C 248 ASP cc_start: 0.7343 (t70) cc_final: 0.7105 (t70) REVERT: A 98 TRP cc_start: 0.5449 (p90) cc_final: 0.5115 (p90) REVERT: A 246 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 248 ASP cc_start: 0.7857 (t0) cc_final: 0.7529 (m-30) REVERT: E 186 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: E 260 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7425 (mt-10) REVERT: E 310 GLU cc_start: 0.7553 (tp30) cc_final: 0.7142 (mm-30) outliers start: 68 outliers final: 37 residues processed: 243 average time/residue: 0.4427 time to fit residues: 120.2764 Evaluate side-chains 222 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 63 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123784 restraints weight = 15401.730| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.61 r_work: 0.3563 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 13182 Z= 0.312 Angle : 0.796 11.342 18114 Z= 0.386 Chirality : 0.048 0.244 2261 Planarity : 0.005 0.048 2158 Dihedral : 10.802 165.337 2357 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.70 % Allowed : 18.48 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1535 helix: 2.08 (0.21), residues: 480 sheet: 0.41 (0.25), residues: 430 loop : -0.69 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 78 TYR 0.023 0.003 TYR D 272 PHE 0.037 0.003 PHE D 164 TRP 0.022 0.002 TRP B 389 HIS 0.009 0.002 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00757 (13142) covalent geometry : angle 0.78961 (18004) SS BOND : bond 0.00569 ( 10) SS BOND : angle 1.06671 ( 20) hydrogen bonds : bond 0.05410 ( 662) hydrogen bonds : angle 4.90693 ( 2160) link_BETA1-4 : bond 0.00548 ( 20) link_BETA1-4 : angle 1.54139 ( 60) link_NAG-ASN : bond 0.00453 ( 10) link_NAG-ASN : angle 1.73652 ( 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 278 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: D 75 ASP cc_start: 0.8099 (t0) cc_final: 0.7687 (t0) REVERT: D 113 GLU cc_start: 0.8615 (mp0) cc_final: 0.8393 (mp0) REVERT: D 123 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8563 (mm) REVERT: D 260 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: B 112 TRP cc_start: 0.8499 (p-90) cc_final: 0.8068 (p-90) REVERT: B 113 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8337 (tp30) REVERT: B 153 THR cc_start: 0.9088 (p) cc_final: 0.8816 (t) REVERT: C 96 LEU cc_start: 0.8375 (mt) cc_final: 0.7978 (mp) REVERT: C 142 ASP cc_start: 0.6292 (p0) cc_final: 0.5543 (m-30) REVERT: C 158 ASN cc_start: 0.7592 (p0) cc_final: 0.6691 (m-40) REVERT: C 160 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7206 (mp0) REVERT: C 225 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7121 (ttp-110) REVERT: C 232 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7668 (ttmm) REVERT: A 140 ASP cc_start: 0.7943 (m-30) cc_final: 0.7437 (t0) REVERT: A 142 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 201 GLU cc_start: 0.7118 (mp0) cc_final: 0.6843 (mp0) REVERT: A 233 SER cc_start: 0.7453 (m) cc_final: 0.7212 (p) REVERT: E 81 MET cc_start: 0.8206 (ptm) cc_final: 0.7725 (ptt) REVERT: E 186 GLU cc_start: 0.7333 (tt0) cc_final: 0.7094 (mt-10) outliers start: 79 outliers final: 47 residues processed: 261 average time/residue: 0.4468 time to fit residues: 129.9258 Evaluate side-chains 236 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 ASN B 144 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 290 ASN B 382 GLN C 144 HIS ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132750 restraints weight = 14838.036| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.54 r_work: 0.3685 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13182 Z= 0.134 Angle : 0.600 11.375 18114 Z= 0.291 Chirality : 0.041 0.291 2261 Planarity : 0.004 0.036 2158 Dihedral : 10.366 164.292 2357 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.97 % Allowed : 21.30 % Favored : 74.73 % 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: 1.18 (0.22), residues: 1535 helix: 2.82 (0.22), residues: 480 sheet: 0.54 (0.25), residues: 420 loop : -0.65 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 78 TYR 0.029 0.002 TYR A 176 PHE 0.022 0.002 PHE D 164 TRP 0.017 0.001 TRP E 91 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00303 (13142) covalent geometry : angle 0.59420 (18004) SS BOND : bond 0.00274 ( 10) SS BOND : angle 0.61769 ( 20) hydrogen bonds : bond 0.04456 ( 662) hydrogen bonds : angle 4.55740 ( 2160) link_BETA1-4 : bond 0.00479 ( 20) link_BETA1-4 : angle 1.39354 ( 60) link_NAG-ASN : bond 0.00105 ( 10) link_NAG-ASN : angle 1.22413 ( 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 243 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.466 Fit side-chains REVERT: D 113 GLU cc_start: 0.8629 (mp0) cc_final: 0.8405 (mp0) REVERT: D 302 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 112 TRP cc_start: 0.8307 (p-90) cc_final: 0.7795 (p-90) REVERT: B 153 THR cc_start: 0.9097 (p) cc_final: 0.8817 (t) REVERT: B 320 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5991 (mpt90) REVERT: C 96 LEU cc_start: 0.8284 (mt) cc_final: 0.7967 (mp) REVERT: C 142 ASP cc_start: 0.6120 (p0) cc_final: 0.5522 (m-30) REVERT: C 158 ASN cc_start: 0.7450 (p0) cc_final: 0.6544 (m-40) REVERT: C 225 ARG cc_start: 0.7649 (mtp180) cc_final: 0.6976 (ttp-110) REVERT: A 98 TRP cc_start: 0.5519 (p90) cc_final: 0.5257 (p90) REVERT: A 142 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: A 274 VAL cc_start: 0.7445 (t) cc_final: 0.7176 (t) REVERT: E 186 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7043 (mt-10) outliers start: 55 outliers final: 31 residues processed: 221 average time/residue: 0.4929 time to fit residues: 120.5738 Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain B residue 81 MET 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 320 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 136 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.155926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132720 restraints weight = 14886.408| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.53 r_work: 0.3653 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13182 Z= 0.122 Angle : 0.584 10.394 18114 Z= 0.283 Chirality : 0.040 0.264 2261 Planarity : 0.004 0.076 2158 Dihedral : 10.142 163.032 2357 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.19 % Allowed : 21.37 % Favored : 74.44 % 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: 1.34 (0.22), residues: 1535 helix: 3.10 (0.22), residues: 480 sheet: 0.52 (0.25), residues: 420 loop : -0.61 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 78 TYR 0.038 0.002 TYR A 176 PHE 0.025 0.002 PHE D 164 TRP 0.022 0.001 TRP E 91 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00273 (13142) covalent geometry : angle 0.57823 (18004) SS BOND : bond 0.00247 ( 10) SS BOND : angle 0.48157 ( 20) hydrogen bonds : bond 0.04188 ( 662) hydrogen bonds : angle 4.37134 ( 2160) link_BETA1-4 : bond 0.00499 ( 20) link_BETA1-4 : angle 1.36059 ( 60) link_NAG-ASN : bond 0.00104 ( 10) link_NAG-ASN : angle 1.20463 ( 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 246 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: D 78 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.8001 (ttp80) REVERT: D 113 GLU cc_start: 0.8664 (mp0) cc_final: 0.8428 (mp0) REVERT: D 302 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7993 (mm) REVERT: B 112 TRP cc_start: 0.8179 (p-90) cc_final: 0.7744 (p-90) REVERT: B 153 THR cc_start: 0.9125 (p) cc_final: 0.8868 (t) REVERT: C 63 ASP cc_start: 0.7901 (t0) cc_final: 0.7457 (m-30) REVERT: C 96 LEU cc_start: 0.8311 (mt) cc_final: 0.7912 (mp) REVERT: C 142 ASP cc_start: 0.6127 (p0) cc_final: 0.5693 (m-30) REVERT: C 158 ASN cc_start: 0.7472 (p0) cc_final: 0.6536 (m-40) REVERT: C 160 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7138 (mp0) REVERT: C 225 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7032 (ttp-170) REVERT: A 98 TRP cc_start: 0.5513 (p90) cc_final: 0.5247 (p90) REVERT: E 186 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7006 (mt-10) outliers start: 58 outliers final: 33 residues processed: 225 average time/residue: 0.4339 time to fit residues: 109.2699 Evaluate side-chains 219 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 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 306 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 ASN B 144 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 290 ASN C 136 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.150118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126608 restraints weight = 15208.972| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.58 r_work: 0.3571 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13182 Z= 0.289 Angle : 0.750 14.627 18114 Z= 0.364 Chirality : 0.046 0.239 2261 Planarity : 0.005 0.039 2158 Dihedral : 10.469 163.716 2357 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.48 % Allowed : 21.59 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1535 helix: 2.37 (0.21), residues: 480 sheet: 0.17 (0.25), residues: 430 loop : -0.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.036 0.003 TYR A 176 PHE 0.052 0.003 PHE D 164 TRP 0.028 0.002 TRP E 91 HIS 0.006 0.002 HIS E 168 Details of bonding type rmsd covalent geometry : bond 0.00698 (13142) covalent geometry : angle 0.74256 (18004) SS BOND : bond 0.00591 ( 10) SS BOND : angle 1.50366 ( 20) hydrogen bonds : bond 0.05133 ( 662) hydrogen bonds : angle 4.76771 ( 2160) link_BETA1-4 : bond 0.00492 ( 20) link_BETA1-4 : angle 1.46468 ( 60) link_NAG-ASN : bond 0.00418 ( 10) link_NAG-ASN : angle 1.62409 ( 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 249 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.471 Fit side-chains REVERT: D 75 ASP cc_start: 0.8142 (t0) cc_final: 0.7760 (t70) REVERT: D 78 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7702 (ttp80) REVERT: D 113 GLU cc_start: 0.8543 (mp0) cc_final: 0.8320 (mp0) REVERT: D 260 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: D 302 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7922 (mm) REVERT: D 390 MET cc_start: 0.7515 (mmt) cc_final: 0.7308 (mmm) REVERT: B 112 TRP cc_start: 0.8428 (p-90) cc_final: 0.7965 (p-90) REVERT: B 113 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8323 (tp30) REVERT: B 144 HIS cc_start: 0.7119 (m-70) cc_final: 0.6023 (t-170) REVERT: B 153 THR cc_start: 0.9144 (p) cc_final: 0.8820 (t) REVERT: C 63 ASP cc_start: 0.7966 (t0) cc_final: 0.7477 (m-30) REVERT: C 96 LEU cc_start: 0.8368 (mt) cc_final: 0.7996 (mp) REVERT: C 142 ASP cc_start: 0.6197 (p0) cc_final: 0.5834 (m-30) REVERT: C 158 ASN cc_start: 0.7486 (p0) cc_final: 0.6502 (m-40) REVERT: C 160 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7087 (mp0) REVERT: C 225 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7129 (ttp-170) REVERT: C 227 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7538 (ptpt) REVERT: C 232 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7563 (ttmm) REVERT: A 201 GLU cc_start: 0.6975 (mp0) cc_final: 0.6688 (mp0) REVERT: A 233 SER cc_start: 0.7393 (m) cc_final: 0.7127 (p) REVERT: E 186 GLU cc_start: 0.7281 (tt0) cc_final: 0.7026 (mt-10) outliers start: 62 outliers final: 41 residues processed: 231 average time/residue: 0.4735 time to fit residues: 121.3348 Evaluate side-chains 218 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 281 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130854 restraints weight = 15013.022| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.59 r_work: 0.3648 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13182 Z= 0.136 Angle : 0.621 10.541 18114 Z= 0.301 Chirality : 0.041 0.269 2261 Planarity : 0.004 0.077 2158 Dihedral : 10.250 163.178 2357 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.90 % Allowed : 23.03 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1535 helix: 2.89 (0.22), residues: 480 sheet: 0.32 (0.26), residues: 420 loop : -0.70 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 78 TYR 0.034 0.002 TYR A 176 PHE 0.028 0.002 PHE A 370 TRP 0.030 0.001 TRP E 91 HIS 0.003 0.001 HIS E 168 Details of bonding type rmsd covalent geometry : bond 0.00305 (13142) covalent geometry : angle 0.61374 (18004) SS BOND : bond 0.00454 ( 10) SS BOND : angle 1.54974 ( 20) hydrogen bonds : bond 0.04452 ( 662) hydrogen bonds : angle 4.52548 ( 2160) link_BETA1-4 : bond 0.00483 ( 20) link_BETA1-4 : angle 1.38010 ( 60) link_NAG-ASN : bond 0.00173 ( 10) link_NAG-ASN : angle 1.26961 ( 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 225 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.525 Fit side-chains REVERT: D 78 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: D 113 GLU cc_start: 0.8603 (mp0) cc_final: 0.8384 (mp0) REVERT: D 302 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7887 (mm) REVERT: B 112 TRP cc_start: 0.8236 (p-90) cc_final: 0.7720 (p-90) REVERT: B 144 HIS cc_start: 0.7331 (m-70) cc_final: 0.5936 (t-170) REVERT: B 153 THR cc_start: 0.9053 (p) cc_final: 0.8722 (t) REVERT: C 63 ASP cc_start: 0.7747 (t0) cc_final: 0.7321 (m-30) REVERT: C 96 LEU cc_start: 0.8269 (mt) cc_final: 0.7887 (mp) REVERT: C 142 ASP cc_start: 0.6012 (p0) cc_final: 0.5785 (m-30) REVERT: C 158 ASN cc_start: 0.7434 (p0) cc_final: 0.6542 (m-40) REVERT: C 225 ARG cc_start: 0.7472 (mtp180) cc_final: 0.6880 (ttp-170) REVERT: A 233 SER cc_start: 0.7234 (m) cc_final: 0.6976 (p) REVERT: E 186 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6865 (mt-10) outliers start: 54 outliers final: 37 residues processed: 206 average time/residue: 0.4351 time to fit residues: 100.7023 Evaluate side-chains 210 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 ASN C 136 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130857 restraints weight = 14925.058| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.59 r_work: 0.3652 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13182 Z= 0.145 Angle : 0.617 10.892 18114 Z= 0.299 Chirality : 0.041 0.253 2261 Planarity : 0.004 0.041 2158 Dihedral : 10.134 162.817 2357 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.25 % Allowed : 23.61 % Favored : 73.14 % 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: 1.17 (0.22), residues: 1535 helix: 2.97 (0.22), residues: 480 sheet: 0.29 (0.26), residues: 420 loop : -0.61 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.031 0.002 TYR A 176 PHE 0.035 0.002 PHE D 164 TRP 0.037 0.001 TRP E 91 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00334 (13142) covalent geometry : angle 0.61008 (18004) SS BOND : bond 0.00269 ( 10) SS BOND : angle 1.17173 ( 20) hydrogen bonds : bond 0.04388 ( 662) hydrogen bonds : angle 4.44929 ( 2160) link_BETA1-4 : bond 0.00486 ( 20) link_BETA1-4 : angle 1.36181 ( 60) link_NAG-ASN : bond 0.00151 ( 10) link_NAG-ASN : angle 1.29496 ( 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 221 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: D 113 GLU cc_start: 0.8612 (mp0) cc_final: 0.8389 (mp0) REVERT: D 302 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7860 (mm) REVERT: B 112 TRP cc_start: 0.8212 (p-90) cc_final: 0.7782 (p-90) REVERT: B 144 HIS cc_start: 0.7353 (m-70) cc_final: 0.6022 (t-170) REVERT: B 153 THR cc_start: 0.9087 (p) cc_final: 0.8797 (t) REVERT: C 63 ASP cc_start: 0.7769 (t0) cc_final: 0.7337 (m-30) REVERT: C 96 LEU cc_start: 0.8207 (mt) cc_final: 0.7993 (mp) REVERT: C 158 ASN cc_start: 0.7435 (p0) cc_final: 0.6558 (m-40) REVERT: C 227 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7338 (ptpt) REVERT: A 233 SER cc_start: 0.7187 (m) cc_final: 0.6955 (p) REVERT: E 186 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6871 (mt-10) outliers start: 45 outliers final: 34 residues processed: 203 average time/residue: 0.4631 time to fit residues: 104.7071 Evaluate side-chains 203 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 0.0670 chunk 98 optimal weight: 0.8980 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134077 restraints weight = 14769.953| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.61 r_work: 0.3711 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13182 Z= 0.115 Angle : 0.597 12.806 18114 Z= 0.286 Chirality : 0.040 0.281 2261 Planarity : 0.004 0.060 2158 Dihedral : 9.981 162.074 2357 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 23.97 % Favored : 72.71 % 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: 1.36 (0.22), residues: 1535 helix: 3.19 (0.22), residues: 480 sheet: 0.37 (0.26), residues: 420 loop : -0.52 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 78 TYR 0.027 0.001 TYR A 176 PHE 0.025 0.001 PHE A 370 TRP 0.029 0.001 TRP E 91 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00253 (13142) covalent geometry : angle 0.59094 (18004) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.86911 ( 20) hydrogen bonds : bond 0.04131 ( 662) hydrogen bonds : angle 4.32605 ( 2160) link_BETA1-4 : bond 0.00487 ( 20) link_BETA1-4 : angle 1.33487 ( 60) link_NAG-ASN : bond 0.00129 ( 10) link_NAG-ASN : angle 1.14210 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4660.36 seconds wall clock time: 80 minutes 7.87 seconds (4807.87 seconds total)