Starting phenix.real_space_refine on Tue Jan 21 15:32:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfl_60064/01_2025/8zfl_60064.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 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 105 5.16 5 C 11140 2.51 5 N 2715 2.21 5 O 3110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17070 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "B" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "C" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3344 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.33, per 1000 atoms: 0.66 Number of scatterers: 17070 At special positions: 0 Unit cell: (106.144, 106.144, 156.648, 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 105 16.00 O 3110 8.00 N 2715 7.00 C 11140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 97 " " NAG B 601 " - " ASN B 97 " " NAG C 601 " - " ASN C 97 " " NAG D 601 " - " ASN D 97 " " NAG E 601 " - " ASN E 97 " " NAG G 1 " - " ASN A 228 " " NAG I 1 " - " ASN B 228 " " NAG K 1 " - " ASN C 228 " " NAG M 1 " - " ASN D 228 " " NAG O 1 " - " ASN E 228 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.1 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 43.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.910A pdb=" N GLU A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP A 96 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 344 through 359 removed outlier: 3.798A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 487 through 532 Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.909A pdb=" N GLU B 29 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP B 96 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.530A pdb=" N PHE B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 363 through 385 Processing helix chain 'B' and resid 487 through 532 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.911A pdb=" N GLU C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP C 96 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 363 through 385 Processing helix chain 'C' and resid 487 through 532 Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.910A pdb=" N GLU D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP D 96 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.798A pdb=" N ARG D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Proline residue: D 356 - end of helix Processing helix chain 'D' and resid 363 through 385 Processing helix chain 'D' and resid 487 through 532 Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.909A pdb=" N GLU E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.025A pdb=" N ASP E 96 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.655A pdb=" N PHE E 265 " --> pdb=" O ILE E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.531A pdb=" N PHE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 335 removed outlier: 3.736A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 344 through 359 removed outlier: 3.799A pdb=" N ARG E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Proline residue: E 356 - end of helix Processing helix chain 'E' and resid 363 through 385 Processing helix chain 'E' and resid 487 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.021A pdb=" N HIS A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 148 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 65 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 76 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE A 63 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 78 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR A 61 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 80 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN A 59 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG A 82 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER A 57 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL A 84 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR A 55 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 52 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE A 188 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 54 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.021A pdb=" N HIS A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 148 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 65 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 76 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE A 63 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 78 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR A 61 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 80 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN A 59 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG A 82 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER A 57 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL A 84 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR A 55 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 removed outlier: 4.487A pdb=" N SER A 177 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 212 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN A 239 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 210 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 148 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 65 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 76 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 63 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP B 78 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 61 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL B 80 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 59 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG B 82 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER B 57 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL B 84 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR B 55 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 52 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 188 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 54 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 148 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 65 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN B 76 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 63 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP B 78 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 61 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL B 80 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN B 59 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG B 82 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER B 57 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL B 84 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR B 55 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 removed outlier: 4.488A pdb=" N SER B 177 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 212 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 239 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 210 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS C 131 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 148 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 65 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN C 76 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE C 63 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N TRP C 78 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR C 61 " --> pdb=" O TRP C 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL C 80 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN C 59 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG C 82 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER C 57 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL C 84 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE C 52 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE C 188 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 54 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS C 131 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 148 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 65 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN C 76 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE C 63 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N TRP C 78 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR C 61 " --> pdb=" O TRP C 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL C 80 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN C 59 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG C 82 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER C 57 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL C 84 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 115 removed outlier: 4.487A pdb=" N SER C 177 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 212 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 239 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 210 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 148 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 65 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 76 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 63 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP D 78 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR D 61 " --> pdb=" O TRP D 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL D 80 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN D 59 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG D 82 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER D 57 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL D 84 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR D 55 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 52 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE D 188 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 54 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.020A pdb=" N HIS D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 148 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 65 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 76 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 63 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP D 78 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR D 61 " --> pdb=" O TRP D 78 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL D 80 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN D 59 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG D 82 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER D 57 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL D 84 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N THR D 55 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 113 through 115 removed outlier: 4.489A pdb=" N SER D 177 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 212 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN D 239 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL D 210 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS E 131 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 148 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 65 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN E 76 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE E 63 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP E 78 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR E 61 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL E 80 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG E 82 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER E 57 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL E 84 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR E 55 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 52 " --> pdb=" O ASP E 186 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE E 188 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL E 54 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.019A pdb=" N HIS E 131 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 148 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 65 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN E 76 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE E 63 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP E 78 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR E 61 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL E 80 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ARG E 82 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER E 57 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL E 84 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR E 55 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 115 removed outlier: 4.488A pdb=" N SER E 177 " --> pdb=" O THR E 230 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY E 212 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN E 239 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL E 210 " --> pdb=" O GLN E 239 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2925 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: 5.51 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5135 1.34 - 1.46: 3931 1.46 - 1.58: 8259 1.58 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 17505 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 23280 1.49 - 2.97: 452 2.97 - 4.46: 53 4.46 - 5.94: 25 5.94 - 7.43: 5 Bond angle restraints: 23815 Sorted by residual: angle pdb=" N VAL E 295 " pdb=" CA VAL E 295 " pdb=" C VAL E 295 " ideal model delta sigma weight residual 112.17 104.74 7.43 9.50e-01 1.11e+00 6.11e+01 angle pdb=" N VAL B 295 " pdb=" CA VAL B 295 " pdb=" C VAL B 295 " ideal model delta sigma weight residual 112.17 104.79 7.38 9.50e-01 1.11e+00 6.04e+01 angle pdb=" N VAL D 295 " pdb=" CA VAL D 295 " pdb=" C VAL D 295 " ideal model delta sigma weight residual 112.17 104.82 7.35 9.50e-01 1.11e+00 5.98e+01 angle pdb=" N VAL A 295 " pdb=" CA VAL A 295 " pdb=" C VAL A 295 " ideal model delta sigma weight residual 112.17 104.83 7.34 9.50e-01 1.11e+00 5.97e+01 angle pdb=" N VAL C 295 " pdb=" CA VAL C 295 " pdb=" C VAL C 295 " ideal model delta sigma weight residual 112.17 104.84 7.33 9.50e-01 1.11e+00 5.95e+01 ... (remaining 23810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 9195 16.82 - 33.63: 1078 33.63 - 50.45: 337 50.45 - 67.27: 110 67.27 - 84.08: 10 Dihedral angle restraints: 10730 sinusoidal: 4625 harmonic: 6105 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.82 59.18 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.84 59.16 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS E 157 " pdb=" SG CYS E 157 " pdb=" SG CYS E 171 " pdb=" CB CYS E 171 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 10727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1921 0.037 - 0.075: 646 0.075 - 0.112: 185 0.112 - 0.149: 33 0.149 - 0.187: 15 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C2 NAG O 1 " pdb=" C1 NAG O 1 " pdb=" C3 NAG O 1 " pdb=" N2 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" N2 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" N2 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 2797 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 299 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO E 300 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 299 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO B 300 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 299 " -0.016 5.00e-02 4.00e+02 2.51e-02 1.00e+00 pdb=" N PRO C 300 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 300 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 300 " -0.014 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2636 2.77 - 3.30: 14670 3.30 - 3.83: 27043 3.83 - 4.37: 31867 4.37 - 4.90: 56358 Nonbonded interactions: 132574 Sorted by model distance: nonbonded pdb=" OD2 ASP B 181 " pdb=" OG SER B 183 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP A 181 " pdb=" OG SER A 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP D 181 " pdb=" OG SER D 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP C 181 " pdb=" OG SER C 183 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP E 181 " pdb=" OG SER E 183 " model vdw 2.238 3.040 ... (remaining 132569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.220 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: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 39.320 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.003 0.029 17505 Z= 0.165 Angle : 0.509 7.428 23815 Z= 0.293 Chirality : 0.042 0.187 2800 Planarity : 0.003 0.025 2890 Dihedral : 16.533 84.082 6755 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.69 % Allowed : 21.97 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2040 helix: 1.65 (0.17), residues: 785 sheet: 1.77 (0.25), residues: 445 loop : -0.89 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 350 HIS 0.004 0.001 HIS C 352 PHE 0.017 0.001 PHE C 332 TYR 0.008 0.001 TYR E 72 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 390 time to evaluate : 1.691 Fit side-chains REVERT: A 146 GLU cc_start: 0.8381 (tt0) cc_final: 0.8173 (tt0) REVERT: A 162 LYS cc_start: 0.8616 (tttt) cc_final: 0.8401 (ttmt) REVERT: A 227 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7599 (m) REVERT: A 249 LEU cc_start: 0.8051 (mt) cc_final: 0.7365 (tp) REVERT: A 266 THR cc_start: 0.8110 (m) cc_final: 0.7610 (p) REVERT: A 489 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 514 SER cc_start: 0.8470 (m) cc_final: 0.8077 (p) REVERT: B 227 VAL cc_start: 0.7699 (m) cc_final: 0.7376 (m) REVERT: B 249 LEU cc_start: 0.8091 (mt) cc_final: 0.7464 (tp) REVERT: B 266 THR cc_start: 0.8075 (m) cc_final: 0.7700 (p) REVERT: B 291 MET cc_start: 0.7564 (mtp) cc_final: 0.7025 (mtp) REVERT: B 349 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7585 (tppp) REVERT: B 489 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6688 (tt0) REVERT: B 514 SER cc_start: 0.8394 (m) cc_final: 0.8005 (t) REVERT: B 530 ASN cc_start: 0.7922 (t0) cc_final: 0.7691 (t0) REVERT: C 23 ASP cc_start: 0.7799 (p0) cc_final: 0.7399 (p0) REVERT: C 47 ARG cc_start: 0.7534 (mpp-170) cc_final: 0.7328 (mpp-170) REVERT: C 227 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7432 (m) REVERT: C 247 LEU cc_start: 0.8534 (tp) cc_final: 0.8313 (mt) REVERT: C 249 LEU cc_start: 0.7890 (mt) cc_final: 0.7312 (tp) REVERT: C 291 MET cc_start: 0.7674 (mtp) cc_final: 0.7087 (mtp) REVERT: C 489 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7251 (mt-10) REVERT: C 514 SER cc_start: 0.8400 (m) cc_final: 0.7968 (p) REVERT: D 146 GLU cc_start: 0.8419 (tt0) cc_final: 0.8154 (tt0) REVERT: D 227 VAL cc_start: 0.7760 (m) cc_final: 0.7303 (m) REVERT: D 245 TYR cc_start: 0.8775 (m-80) cc_final: 0.8466 (m-80) REVERT: D 249 LEU cc_start: 0.8121 (mt) cc_final: 0.7446 (tp) REVERT: D 291 MET cc_start: 0.7548 (mtp) cc_final: 0.7048 (mtp) REVERT: D 294 MET cc_start: 0.4592 (mmt) cc_final: 0.3339 (mmp) REVERT: D 311 LEU cc_start: 0.8260 (tp) cc_final: 0.8039 (tp) REVERT: D 489 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 493 ASP cc_start: 0.7714 (m-30) cc_final: 0.7433 (m-30) REVERT: D 514 SER cc_start: 0.8544 (m) cc_final: 0.8153 (p) REVERT: E 23 ASP cc_start: 0.7723 (p0) cc_final: 0.7509 (p0) REVERT: E 47 ARG cc_start: 0.7575 (mpp-170) cc_final: 0.7128 (mpp-170) REVERT: E 146 GLU cc_start: 0.8416 (tt0) cc_final: 0.8206 (tt0) REVERT: E 227 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7382 (m) REVERT: E 249 LEU cc_start: 0.7916 (mt) cc_final: 0.7361 (tp) REVERT: E 514 SER cc_start: 0.8375 (m) cc_final: 0.7886 (p) outliers start: 13 outliers final: 1 residues processed: 390 average time/residue: 1.3289 time to fit residues: 575.8613 Evaluate side-chains 237 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 70 GLN B 271 HIS B 361 GLN B 519 ASN C 70 GLN C 352 HIS C 530 ASN D 271 HIS D 352 HIS D 530 ASN E 70 GLN E 352 HIS E 530 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101774 restraints weight = 18228.358| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.72 r_work: 0.2914 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17505 Z= 0.252 Angle : 0.692 11.828 23815 Z= 0.349 Chirality : 0.049 0.266 2800 Planarity : 0.005 0.038 2890 Dihedral : 7.267 55.961 2746 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.52 % Allowed : 18.03 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2040 helix: 2.65 (0.17), residues: 835 sheet: 1.61 (0.24), residues: 470 loop : -0.68 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 494 HIS 0.006 0.002 HIS B 131 PHE 0.010 0.001 PHE E 312 TYR 0.015 0.002 TYR B 245 ARG 0.005 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8293 (m) cc_final: 0.8013 (m) REVERT: A 247 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 266 THR cc_start: 0.8371 (m) cc_final: 0.7855 (p) REVERT: A 291 MET cc_start: 0.7251 (mtp) cc_final: 0.6919 (mtp) REVERT: A 489 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7324 (mt-10) REVERT: A 493 ASP cc_start: 0.8016 (m-30) cc_final: 0.7724 (m-30) REVERT: A 514 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 47 ARG cc_start: 0.7804 (mpp-170) cc_final: 0.7482 (mpp-170) REVERT: B 266 THR cc_start: 0.8372 (m) cc_final: 0.7926 (p) REVERT: B 291 MET cc_start: 0.7345 (mtp) cc_final: 0.6965 (mtp) REVERT: B 349 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7829 (tppp) REVERT: B 353 ARG cc_start: 0.7762 (ptt180) cc_final: 0.7339 (ptt90) REVERT: C 23 ASP cc_start: 0.8018 (p0) cc_final: 0.7635 (p0) REVERT: C 40 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8823 (pttm) REVERT: C 47 ARG cc_start: 0.7932 (mpp-170) cc_final: 0.7486 (mpp-170) REVERT: C 227 VAL cc_start: 0.8126 (m) cc_final: 0.7863 (m) REVERT: C 288 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: C 291 MET cc_start: 0.7551 (mtp) cc_final: 0.7116 (mtp) REVERT: C 292 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6722 (mt) REVERT: C 489 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 514 SER cc_start: 0.8232 (m) cc_final: 0.7996 (p) REVERT: D 291 MET cc_start: 0.7386 (mtp) cc_final: 0.6883 (mtp) REVERT: D 294 MET cc_start: 0.5372 (mmp) cc_final: 0.4131 (mmp) REVERT: D 353 ARG cc_start: 0.7635 (ptt180) cc_final: 0.7242 (ptt90) REVERT: D 489 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7286 (mt-10) REVERT: D 493 ASP cc_start: 0.8016 (m-30) cc_final: 0.7775 (m-30) REVERT: D 514 SER cc_start: 0.8307 (m) cc_final: 0.8074 (p) REVERT: E 23 ASP cc_start: 0.7814 (p0) cc_final: 0.7602 (p0) REVERT: E 47 ARG cc_start: 0.7914 (mpp-170) cc_final: 0.7505 (mpp-170) REVERT: E 227 VAL cc_start: 0.8410 (m) cc_final: 0.8171 (m) REVERT: E 292 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6628 (mt) REVERT: E 353 ARG cc_start: 0.7559 (ptt180) cc_final: 0.7274 (ptt90) REVERT: E 493 ASP cc_start: 0.8112 (m-30) cc_final: 0.7871 (m-30) REVERT: E 514 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7931 (p) REVERT: E 529 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7596 (tt0) outliers start: 66 outliers final: 25 residues processed: 292 average time/residue: 1.3105 time to fit residues: 426.8836 Evaluate side-chains 263 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 116 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 55 optimal weight: 0.0010 chunk 166 optimal weight: 0.0040 chunk 111 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100568 restraints weight = 17320.768| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.02 r_work: 0.2914 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17505 Z= 0.174 Angle : 0.609 10.596 23815 Z= 0.305 Chirality : 0.047 0.348 2800 Planarity : 0.004 0.035 2890 Dihedral : 6.853 56.217 2740 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.93 % Allowed : 20.27 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.18), residues: 2040 helix: 3.30 (0.17), residues: 820 sheet: 1.77 (0.25), residues: 425 loop : -0.68 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 494 HIS 0.003 0.001 HIS B 271 PHE 0.009 0.001 PHE E 312 TYR 0.012 0.001 TYR B 72 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8774 (mpp) REVERT: A 227 VAL cc_start: 0.8289 (m) cc_final: 0.7985 (m) REVERT: A 249 LEU cc_start: 0.7720 (mp) cc_final: 0.6923 (tp) REVERT: A 266 THR cc_start: 0.8342 (m) cc_final: 0.7733 (p) REVERT: A 291 MET cc_start: 0.7169 (mtp) cc_final: 0.6854 (mtp) REVERT: A 294 MET cc_start: 0.4554 (mpm) cc_final: 0.4345 (tpp) REVERT: A 493 ASP cc_start: 0.7838 (m-30) cc_final: 0.7604 (m-30) REVERT: B 47 ARG cc_start: 0.7869 (mpp-170) cc_final: 0.7629 (mpp-170) REVERT: B 266 THR cc_start: 0.8350 (m) cc_final: 0.7918 (p) REVERT: B 291 MET cc_start: 0.7150 (mtp) cc_final: 0.6826 (mtp) REVERT: B 349 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7839 (tppp) REVERT: B 353 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7267 (ptt90) REVERT: B 493 ASP cc_start: 0.7966 (m-30) cc_final: 0.7748 (m-30) REVERT: C 23 ASP cc_start: 0.7944 (p0) cc_final: 0.7591 (p0) REVERT: C 47 ARG cc_start: 0.7896 (mpp-170) cc_final: 0.7332 (mtm180) REVERT: C 227 VAL cc_start: 0.8123 (m) cc_final: 0.7843 (m) REVERT: C 249 LEU cc_start: 0.7751 (mp) cc_final: 0.7030 (tp) REVERT: C 288 MET cc_start: 0.8051 (ttm) cc_final: 0.7637 (mmm) REVERT: C 291 MET cc_start: 0.7207 (mtp) cc_final: 0.6825 (mtp) REVERT: C 292 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6493 (mt) REVERT: C 493 ASP cc_start: 0.7876 (m-30) cc_final: 0.7594 (m-30) REVERT: D 40 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8813 (pttm) REVERT: D 288 MET cc_start: 0.8072 (mtm) cc_final: 0.7766 (mmm) REVERT: D 291 MET cc_start: 0.7283 (mtp) cc_final: 0.6859 (mtp) REVERT: D 294 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4241 (mmp) REVERT: D 353 ARG cc_start: 0.7631 (ptt180) cc_final: 0.7346 (ptt90) REVERT: E 23 ASP cc_start: 0.7826 (p0) cc_final: 0.7612 (p0) REVERT: E 47 ARG cc_start: 0.7835 (mpp-170) cc_final: 0.7409 (mpp-170) REVERT: E 102 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8728 (mpp) REVERT: E 227 VAL cc_start: 0.8404 (m) cc_final: 0.8161 (m) REVERT: E 247 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8372 (mp) REVERT: E 288 MET cc_start: 0.7901 (mtm) cc_final: 0.7634 (mmm) REVERT: E 291 MET cc_start: 0.7124 (mtp) cc_final: 0.6710 (mtp) REVERT: E 292 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6486 (mt) REVERT: E 493 ASP cc_start: 0.8025 (m-30) cc_final: 0.7751 (m-30) outliers start: 55 outliers final: 11 residues processed: 269 average time/residue: 1.2131 time to fit residues: 367.3302 Evaluate side-chains 243 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 14 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 271 HIS B 361 GLN C 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104803 restraints weight = 18243.493| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.76 r_work: 0.2897 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17505 Z= 0.203 Angle : 0.628 9.785 23815 Z= 0.313 Chirality : 0.046 0.306 2800 Planarity : 0.004 0.038 2890 Dihedral : 6.630 56.413 2740 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.27 % Allowed : 19.25 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 2040 helix: 3.30 (0.17), residues: 825 sheet: 1.56 (0.24), residues: 470 loop : -0.81 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 494 HIS 0.005 0.001 HIS E 131 PHE 0.011 0.001 PHE E 312 TYR 0.013 0.001 TYR C 72 ARG 0.003 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8130 (mpp-170) cc_final: 0.7876 (mtm180) REVERT: A 104 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8464 (mtm180) REVERT: A 266 THR cc_start: 0.8498 (m) cc_final: 0.7992 (p) REVERT: A 291 MET cc_start: 0.7207 (mtp) cc_final: 0.6831 (mtp) REVERT: A 308 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 493 ASP cc_start: 0.8067 (m-30) cc_final: 0.7753 (m-30) REVERT: B 291 MET cc_start: 0.7112 (mtp) cc_final: 0.6794 (mtp) REVERT: B 308 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 349 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7814 (tppp) REVERT: B 493 ASP cc_start: 0.8141 (m-30) cc_final: 0.7891 (m-30) REVERT: B 516 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7620 (mp) REVERT: C 23 ASP cc_start: 0.7905 (p0) cc_final: 0.7534 (p0) REVERT: C 47 ARG cc_start: 0.8085 (mpp-170) cc_final: 0.7515 (mtm180) REVERT: C 104 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8378 (mtm180) REVERT: C 227 VAL cc_start: 0.8330 (m) cc_final: 0.8030 (m) REVERT: C 288 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7729 (mmm) REVERT: C 291 MET cc_start: 0.7193 (mtp) cc_final: 0.6786 (mtp) REVERT: C 292 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6405 (mt) REVERT: C 493 ASP cc_start: 0.8034 (m-30) cc_final: 0.7766 (m-30) REVERT: D 40 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8821 (pttm) REVERT: D 288 MET cc_start: 0.8123 (mtm) cc_final: 0.7798 (mmm) REVERT: D 291 MET cc_start: 0.7215 (mtp) cc_final: 0.6888 (mtp) REVERT: D 294 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4407 (mmp) REVERT: D 308 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8072 (mt) REVERT: D 353 ARG cc_start: 0.7698 (ptt180) cc_final: 0.7407 (ptt90) REVERT: D 383 MET cc_start: 0.2478 (OUTLIER) cc_final: 0.1328 (mmt) REVERT: E 23 ASP cc_start: 0.7821 (p0) cc_final: 0.7606 (p0) REVERT: E 47 ARG cc_start: 0.8004 (mpp-170) cc_final: 0.7645 (mpp-170) REVERT: E 102 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8824 (mpp) REVERT: E 227 VAL cc_start: 0.8460 (m) cc_final: 0.8194 (m) REVERT: E 247 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8435 (mp) REVERT: E 291 MET cc_start: 0.7030 (mtp) cc_final: 0.6655 (mtp) REVERT: E 292 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6526 (mt) REVERT: E 493 ASP cc_start: 0.8198 (m-30) cc_final: 0.7929 (m-30) outliers start: 80 outliers final: 30 residues processed: 276 average time/residue: 1.2049 time to fit residues: 374.5725 Evaluate side-chains 255 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 520 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 519 ASN B 271 HIS C 352 HIS D 519 ASN E 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106366 restraints weight = 18431.984| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.74 r_work: 0.2936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17505 Z= 0.160 Angle : 0.583 9.648 23815 Z= 0.290 Chirality : 0.046 0.304 2800 Planarity : 0.004 0.036 2890 Dihedral : 6.518 56.771 2740 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.57 % Allowed : 19.95 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.19), residues: 2040 helix: 3.42 (0.17), residues: 825 sheet: 1.78 (0.25), residues: 425 loop : -0.74 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.011 0.001 TYR B 72 ARG 0.003 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8059 (mpp-170) cc_final: 0.7852 (mtm180) REVERT: A 102 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8873 (mpp) REVERT: A 227 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8148 (m) REVERT: A 249 LEU cc_start: 0.7783 (mp) cc_final: 0.7050 (tp) REVERT: A 288 MET cc_start: 0.7822 (mmm) cc_final: 0.7474 (mmm) REVERT: A 291 MET cc_start: 0.7168 (mtp) cc_final: 0.6852 (mtp) REVERT: A 493 ASP cc_start: 0.8019 (m-30) cc_final: 0.7801 (m-30) REVERT: B 203 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 291 MET cc_start: 0.7008 (mtp) cc_final: 0.6667 (mtp) REVERT: B 349 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7971 (tppp) REVERT: B 493 ASP cc_start: 0.8119 (m-30) cc_final: 0.7864 (m-30) REVERT: C 23 ASP cc_start: 0.7931 (p0) cc_final: 0.7553 (p0) REVERT: C 47 ARG cc_start: 0.8081 (mpp-170) cc_final: 0.7502 (mtm180) REVERT: C 227 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8032 (m) REVERT: C 288 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7718 (mmm) REVERT: C 291 MET cc_start: 0.7040 (mtp) cc_final: 0.6601 (mtp) REVERT: C 493 ASP cc_start: 0.8015 (m-30) cc_final: 0.7675 (m-30) REVERT: D 40 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8806 (pttm) REVERT: D 203 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8285 (mp) REVERT: D 291 MET cc_start: 0.7033 (mtp) cc_final: 0.6661 (mtp) REVERT: D 294 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.4473 (mmp) REVERT: D 308 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 353 ARG cc_start: 0.7765 (ptt180) cc_final: 0.7489 (ptt90) REVERT: D 383 MET cc_start: 0.2455 (OUTLIER) cc_final: 0.1408 (mmt) REVERT: E 23 ASP cc_start: 0.7788 (p0) cc_final: 0.7536 (p0) REVERT: E 47 ARG cc_start: 0.7991 (mpp-170) cc_final: 0.7637 (mpp-170) REVERT: E 102 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8789 (mpp) REVERT: E 203 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8368 (mp) REVERT: E 227 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8190 (m) REVERT: E 247 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (mt) REVERT: E 291 MET cc_start: 0.6976 (mtp) cc_final: 0.6559 (mtp) REVERT: E 292 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6455 (mt) REVERT: E 493 ASP cc_start: 0.8105 (m-30) cc_final: 0.7816 (m-30) outliers start: 67 outliers final: 13 residues processed: 277 average time/residue: 1.1779 time to fit residues: 367.5663 Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 104 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 182 optimal weight: 0.0670 chunk 170 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 271 HIS C 352 HIS D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102978 restraints weight = 17565.486| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.88 r_work: 0.2907 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17505 Z= 0.147 Angle : 0.571 9.657 23815 Z= 0.282 Chirality : 0.046 0.311 2800 Planarity : 0.004 0.035 2890 Dihedral : 6.413 56.717 2740 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.47 % Allowed : 19.79 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2040 helix: 3.52 (0.17), residues: 825 sheet: 1.76 (0.25), residues: 420 loop : -0.72 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.011 0.001 TYR B 72 ARG 0.001 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8080 (mpp-170) cc_final: 0.7833 (mpp-170) REVERT: A 102 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8819 (mpp) REVERT: A 227 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8148 (m) REVERT: A 288 MET cc_start: 0.7876 (mmm) cc_final: 0.7527 (mmm) REVERT: A 291 MET cc_start: 0.7152 (mtp) cc_final: 0.6825 (mtp) REVERT: A 493 ASP cc_start: 0.7959 (m-30) cc_final: 0.7622 (m-30) REVERT: B 291 MET cc_start: 0.6852 (mtp) cc_final: 0.6591 (mtp) REVERT: B 349 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7917 (tppp) REVERT: C 23 ASP cc_start: 0.7874 (p0) cc_final: 0.7509 (p0) REVERT: C 47 ARG cc_start: 0.8049 (mpp-170) cc_final: 0.7490 (mtm180) REVERT: C 227 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.7997 (m) REVERT: C 288 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: C 291 MET cc_start: 0.7048 (mtp) cc_final: 0.6622 (mtp) REVERT: C 493 ASP cc_start: 0.7982 (m-30) cc_final: 0.7635 (m-30) REVERT: D 36 GLU cc_start: 0.8161 (tt0) cc_final: 0.7874 (mt-10) REVERT: D 40 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (pttm) REVERT: D 203 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8254 (mp) REVERT: D 291 MET cc_start: 0.7032 (mtp) cc_final: 0.6761 (mtp) REVERT: D 294 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.4291 (mmp) REVERT: D 353 ARG cc_start: 0.7785 (ptt180) cc_final: 0.7515 (ptt90) REVERT: D 383 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1281 (mmt) REVERT: E 23 ASP cc_start: 0.7763 (p0) cc_final: 0.7448 (p0) REVERT: E 47 ARG cc_start: 0.7966 (mpp-170) cc_final: 0.7502 (mpp-170) REVERT: E 102 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8753 (mpp) REVERT: E 227 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (m) REVERT: E 291 MET cc_start: 0.7093 (mtp) cc_final: 0.6764 (mtp) REVERT: E 292 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6323 (mt) REVERT: E 493 ASP cc_start: 0.8037 (m-30) cc_final: 0.7746 (m-30) outliers start: 65 outliers final: 17 residues processed: 272 average time/residue: 1.2181 time to fit residues: 371.9882 Evaluate side-chains 254 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 158 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 189 optimal weight: 0.1980 chunk 148 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS E 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101783 restraints weight = 17402.489| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.95 r_work: 0.2907 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17505 Z= 0.167 Angle : 0.593 9.941 23815 Z= 0.293 Chirality : 0.046 0.277 2800 Planarity : 0.004 0.038 2890 Dihedral : 6.380 55.542 2740 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.20 % Allowed : 20.00 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2040 helix: 3.51 (0.17), residues: 825 sheet: 1.71 (0.25), residues: 425 loop : -0.68 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 494 HIS 0.003 0.001 HIS A 271 PHE 0.011 0.001 PHE E 312 TYR 0.016 0.001 TYR E 229 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8114 (mpp-170) cc_final: 0.7875 (mpp-170) REVERT: A 102 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8792 (mpp) REVERT: A 227 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 288 MET cc_start: 0.7871 (mmm) cc_final: 0.7537 (mmm) REVERT: A 291 MET cc_start: 0.7197 (mtp) cc_final: 0.6878 (mtp) REVERT: A 493 ASP cc_start: 0.7906 (m-30) cc_final: 0.7588 (m-30) REVERT: A 516 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7314 (mp) REVERT: B 148 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8769 (tp) REVERT: B 203 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 291 MET cc_start: 0.6869 (mtp) cc_final: 0.6530 (mtp) REVERT: B 349 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8104 (ptmm) REVERT: C 47 ARG cc_start: 0.8059 (mpp-170) cc_final: 0.7553 (mtm180) REVERT: C 148 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8789 (tp) REVERT: C 227 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8012 (m) REVERT: C 288 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7808 (mmm) REVERT: C 291 MET cc_start: 0.7112 (mtp) cc_final: 0.6717 (mtp) REVERT: C 493 ASP cc_start: 0.7941 (m-30) cc_final: 0.7588 (m-30) REVERT: C 513 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: D 36 GLU cc_start: 0.8134 (tt0) cc_final: 0.7809 (mt-10) REVERT: D 40 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8851 (pttm) REVERT: D 203 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 288 MET cc_start: 0.7974 (mmm) cc_final: 0.7605 (mmm) REVERT: D 291 MET cc_start: 0.6926 (mtp) cc_final: 0.6692 (mtp) REVERT: D 294 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4884 (tmm) REVERT: D 353 ARG cc_start: 0.7770 (ptt180) cc_final: 0.7459 (ptt90) REVERT: D 383 MET cc_start: 0.2444 (OUTLIER) cc_final: 0.1395 (mmt) REVERT: E 23 ASP cc_start: 0.7747 (p0) cc_final: 0.7426 (p0) REVERT: E 47 ARG cc_start: 0.7983 (mpp-170) cc_final: 0.7642 (mpp-170) REVERT: E 102 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8741 (mpp) REVERT: E 227 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (m) REVERT: E 288 MET cc_start: 0.7903 (mmm) cc_final: 0.7614 (mmm) REVERT: E 291 MET cc_start: 0.7116 (mtp) cc_final: 0.6772 (mtp) REVERT: E 292 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6359 (mt) REVERT: E 493 ASP cc_start: 0.8014 (m-30) cc_final: 0.7732 (m-30) outliers start: 60 outliers final: 26 residues processed: 261 average time/residue: 1.1942 time to fit residues: 350.4596 Evaluate side-chains 265 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 520 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 271 HIS E 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102214 restraints weight = 17473.406| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.98 r_work: 0.2918 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17505 Z= 0.165 Angle : 0.589 9.790 23815 Z= 0.292 Chirality : 0.046 0.273 2800 Planarity : 0.004 0.032 2890 Dihedral : 6.367 55.614 2740 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.99 % Allowed : 20.16 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.19), residues: 2040 helix: 3.52 (0.17), residues: 825 sheet: 1.69 (0.25), residues: 425 loop : -0.66 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE E 312 TYR 0.013 0.001 TYR C 72 ARG 0.001 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8770 (mpp) REVERT: A 227 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8229 (m) REVERT: A 288 MET cc_start: 0.7896 (mmm) cc_final: 0.7521 (mmm) REVERT: A 291 MET cc_start: 0.7262 (mtp) cc_final: 0.6952 (mtp) REVERT: A 493 ASP cc_start: 0.7901 (m-30) cc_final: 0.7556 (m-30) REVERT: A 516 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 148 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8765 (tp) REVERT: B 203 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 291 MET cc_start: 0.7083 (mtp) cc_final: 0.6805 (mtp) REVERT: B 349 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8128 (ptmm) REVERT: C 47 ARG cc_start: 0.8050 (mpp-170) cc_final: 0.7564 (mtm180) REVERT: C 227 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8051 (m) REVERT: C 288 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: C 291 MET cc_start: 0.7043 (mtp) cc_final: 0.6671 (mtp) REVERT: C 493 ASP cc_start: 0.7945 (m-30) cc_final: 0.7616 (m-30) REVERT: C 513 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: D 36 GLU cc_start: 0.8096 (tt0) cc_final: 0.7842 (mt-10) REVERT: D 40 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8834 (pttm) REVERT: D 203 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (mp) REVERT: D 288 MET cc_start: 0.7961 (mmm) cc_final: 0.7575 (mmm) REVERT: D 291 MET cc_start: 0.6828 (mtp) cc_final: 0.6606 (mtp) REVERT: D 353 ARG cc_start: 0.7772 (ptt180) cc_final: 0.7492 (ptt90) REVERT: D 383 MET cc_start: 0.2432 (OUTLIER) cc_final: 0.1403 (mmt) REVERT: E 23 ASP cc_start: 0.7736 (p0) cc_final: 0.7400 (p0) REVERT: E 47 ARG cc_start: 0.8029 (mpp-170) cc_final: 0.7696 (mpp-170) REVERT: E 102 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8705 (mpp) REVERT: E 227 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8094 (m) REVERT: E 288 MET cc_start: 0.7860 (mmm) cc_final: 0.7605 (mmm) REVERT: E 291 MET cc_start: 0.7079 (mtp) cc_final: 0.6746 (mtp) REVERT: E 292 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6298 (mt) REVERT: E 493 ASP cc_start: 0.7995 (m-30) cc_final: 0.7737 (m-30) outliers start: 56 outliers final: 22 residues processed: 262 average time/residue: 1.2168 time to fit residues: 358.0809 Evaluate side-chains 262 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 189 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099990 restraints weight = 17431.803| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.01 r_work: 0.2883 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17505 Z= 0.195 Angle : 0.626 9.697 23815 Z= 0.310 Chirality : 0.047 0.255 2800 Planarity : 0.004 0.033 2890 Dihedral : 6.410 55.237 2740 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.72 % Allowed : 20.43 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 2040 helix: 3.42 (0.17), residues: 825 sheet: 1.52 (0.24), residues: 470 loop : -0.68 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 494 HIS 0.004 0.001 HIS B 131 PHE 0.011 0.001 PHE E 312 TYR 0.015 0.001 TYR E 229 ARG 0.001 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8261 (m) REVERT: A 288 MET cc_start: 0.7892 (mmm) cc_final: 0.7511 (mmm) REVERT: A 291 MET cc_start: 0.7333 (mtp) cc_final: 0.6966 (mtp) REVERT: A 493 ASP cc_start: 0.8015 (m-30) cc_final: 0.7721 (m-30) REVERT: A 516 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 148 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8772 (tp) REVERT: B 203 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 291 MET cc_start: 0.7021 (mtp) cc_final: 0.6721 (mtp) REVERT: B 349 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8146 (ptmm) REVERT: B 493 ASP cc_start: 0.8024 (m-30) cc_final: 0.7765 (m-30) REVERT: C 47 ARG cc_start: 0.8127 (mpp-170) cc_final: 0.7627 (mtm180) REVERT: C 227 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8109 (m) REVERT: C 288 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: C 291 MET cc_start: 0.7223 (mtp) cc_final: 0.6837 (mtp) REVERT: C 493 ASP cc_start: 0.8006 (m-30) cc_final: 0.7774 (m-30) REVERT: C 513 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: D 36 GLU cc_start: 0.8193 (tt0) cc_final: 0.7900 (mt-10) REVERT: D 40 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8841 (pttm) REVERT: D 203 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (mp) REVERT: D 288 MET cc_start: 0.8113 (mmm) cc_final: 0.7739 (mmm) REVERT: D 291 MET cc_start: 0.7164 (mtp) cc_final: 0.6897 (mtp) REVERT: D 383 MET cc_start: 0.2402 (OUTLIER) cc_final: 0.1404 (mmt) REVERT: E 47 ARG cc_start: 0.8067 (mpp-170) cc_final: 0.7733 (mpp-170) REVERT: E 102 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8757 (mpp) REVERT: E 288 MET cc_start: 0.7945 (mmm) cc_final: 0.7667 (mmm) REVERT: E 291 MET cc_start: 0.7163 (mtp) cc_final: 0.6817 (mtp) REVERT: E 292 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6206 (mt) REVERT: E 493 ASP cc_start: 0.8126 (m-30) cc_final: 0.7879 (m-30) outliers start: 51 outliers final: 21 residues processed: 257 average time/residue: 1.2092 time to fit residues: 349.8449 Evaluate side-chains 253 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 200 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101702 restraints weight = 17481.300| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.85 r_work: 0.2885 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17505 Z= 0.164 Angle : 0.595 9.655 23815 Z= 0.294 Chirality : 0.046 0.268 2800 Planarity : 0.004 0.033 2890 Dihedral : 6.397 55.870 2740 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.03 % Allowed : 21.17 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2040 helix: 3.49 (0.17), residues: 825 sheet: 1.70 (0.25), residues: 425 loop : -0.66 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 494 HIS 0.003 0.001 HIS B 271 PHE 0.010 0.001 PHE B 312 TYR 0.013 0.001 TYR E 229 ARG 0.001 0.000 ARG C 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8829 (mpp) REVERT: A 227 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 288 MET cc_start: 0.7956 (mmm) cc_final: 0.7577 (mmm) REVERT: A 291 MET cc_start: 0.7294 (mtp) cc_final: 0.6959 (mtp) REVERT: A 516 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7291 (mp) REVERT: B 102 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8809 (mpp) REVERT: B 203 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8414 (mp) REVERT: B 291 MET cc_start: 0.6997 (mtp) cc_final: 0.6701 (mtp) REVERT: B 349 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8187 (ptmm) REVERT: B 383 MET cc_start: 0.2475 (mmp) cc_final: 0.1519 (ptt) REVERT: B 493 ASP cc_start: 0.8062 (m-30) cc_final: 0.7798 (m-30) REVERT: C 47 ARG cc_start: 0.8107 (mpp-170) cc_final: 0.7599 (mtm180) REVERT: C 227 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8112 (m) REVERT: C 288 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7703 (mmm) REVERT: C 291 MET cc_start: 0.7229 (mtp) cc_final: 0.6850 (mtp) REVERT: C 493 ASP cc_start: 0.8029 (m-30) cc_final: 0.7766 (m-30) REVERT: C 513 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: D 36 GLU cc_start: 0.8178 (tt0) cc_final: 0.7963 (mt-10) REVERT: D 40 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8839 (pttm) REVERT: D 203 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8308 (mp) REVERT: D 288 MET cc_start: 0.8092 (mmm) cc_final: 0.7794 (mmm) REVERT: D 291 MET cc_start: 0.7143 (mtp) cc_final: 0.6875 (mtp) REVERT: D 383 MET cc_start: 0.2321 (OUTLIER) cc_final: 0.1329 (mmt) REVERT: E 47 ARG cc_start: 0.8078 (mpp-170) cc_final: 0.7719 (mpp-170) REVERT: E 102 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8745 (mpp) REVERT: E 288 MET cc_start: 0.7914 (mmm) cc_final: 0.7653 (mmm) REVERT: E 291 MET cc_start: 0.7107 (mtp) cc_final: 0.6775 (mtp) REVERT: E 292 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6289 (mt) REVERT: E 294 MET cc_start: 0.5734 (tmm) cc_final: 0.5506 (tmm) REVERT: E 493 ASP cc_start: 0.8093 (m-30) cc_final: 0.7836 (m-30) outliers start: 38 outliers final: 19 residues processed: 249 average time/residue: 1.2139 time to fit residues: 339.6541 Evaluate side-chains 257 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099820 restraints weight = 17433.448| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.88 r_work: 0.2886 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17505 Z= 0.183 Angle : 0.616 9.794 23815 Z= 0.305 Chirality : 0.046 0.259 2800 Planarity : 0.004 0.034 2890 Dihedral : 6.412 55.289 2740 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.29 % Allowed : 21.17 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.19), residues: 2040 helix: 3.45 (0.17), residues: 825 sheet: 1.70 (0.25), residues: 425 loop : -0.68 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 494 HIS 0.004 0.001 HIS A 271 PHE 0.011 0.001 PHE E 312 TYR 0.013 0.001 TYR C 72 ARG 0.001 0.000 ARG C 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13059.14 seconds wall clock time: 232 minutes 16.55 seconds (13936.55 seconds total)