Starting phenix.real_space_refine on Sun May 18 13:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfl_60064/05_2025/8zfl_60064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfl_60064/05_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_60064/05_2025/8zfl_60064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfl_60064/05_2025/8zfl_60064.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfl_60064/05_2025/8zfl_60064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfl_60064/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.20, per 1000 atoms: 0.60 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: 3.85 Conformation dependent library (CDL) restraints added in 1.9 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: 1.63 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: 5.31 Time building geometry restraints manager: 4.56 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: 5.820 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.490 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.450 ------------------------------------------------------------------------------- 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 17530 Z= 0.130 Angle : 0.515 7.428 23885 Z= 0.294 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 10) link_NAG-ASN : angle 1.55992 ( 30) link_BETA1-4 : bond 0.00328 ( 10) link_BETA1-4 : angle 1.72006 ( 30) hydrogen bonds : bond 0.24623 ( 885) hydrogen bonds : angle 6.20418 ( 2925) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.20232 ( 10) covalent geometry : bond 0.00253 (17505) covalent geometry : angle 0.50863 (23815) *********************** 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 : 1.950 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: 1.2374 time to fit residues: 537.3522 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 : 2.100 ------------------------------------------------------------------------------- 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: 0.6980 chunk 119 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102687 restraints weight = 18238.091| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.83 r_work: 0.2903 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17530 Z= 0.174 Angle : 0.702 12.152 23885 Z= 0.349 Chirality : 0.049 0.262 2800 Planarity : 0.005 0.037 2890 Dihedral : 7.247 56.069 2746 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.31 % Allowed : 18.24 % 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: 1.86 (0.18), residues: 2040 helix: 2.63 (0.17), residues: 840 sheet: 1.63 (0.24), residues: 470 loop : -0.78 (0.21), residues: 730 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 0.011 0.001 PHE E 312 TYR 0.015 0.002 TYR C 72 ARG 0.004 0.001 ARG A 382 Details of bonding type rmsd link_NAG-ASN : bond 0.00992 ( 10) link_NAG-ASN : angle 3.89643 ( 30) link_BETA1-4 : bond 0.00486 ( 10) link_BETA1-4 : angle 1.88017 ( 30) hydrogen bonds : bond 0.08145 ( 885) hydrogen bonds : angle 4.03904 ( 2925) SS BOND : bond 0.01368 ( 5) SS BOND : angle 4.37354 ( 10) covalent geometry : bond 0.00377 (17505) covalent geometry : angle 0.67982 (23815) *********************** 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 320 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8322 (m) cc_final: 0.8053 (m) REVERT: A 247 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 266 THR cc_start: 0.8349 (m) cc_final: 0.7835 (p) REVERT: A 291 MET cc_start: 0.7299 (mtp) cc_final: 0.6967 (mtp) REVERT: A 489 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 493 ASP cc_start: 0.8003 (m-30) cc_final: 0.7712 (m-30) REVERT: A 514 SER cc_start: 0.8375 (m) cc_final: 0.8128 (p) REVERT: B 47 ARG cc_start: 0.7788 (mpp-170) cc_final: 0.7458 (mpp-170) REVERT: B 266 THR cc_start: 0.8350 (m) cc_final: 0.7908 (p) REVERT: B 291 MET cc_start: 0.7349 (mtp) cc_final: 0.6968 (mtp) REVERT: B 349 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7808 (tppp) REVERT: B 353 ARG cc_start: 0.7742 (ptt180) cc_final: 0.7260 (ptt90) REVERT: B 514 SER cc_start: 0.8215 (m) cc_final: 0.8011 (p) REVERT: B 530 ASN cc_start: 0.7998 (t0) cc_final: 0.7786 (t0) REVERT: C 23 ASP cc_start: 0.8015 (p0) cc_final: 0.7628 (p0) REVERT: C 40 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8824 (pttm) REVERT: C 47 ARG cc_start: 0.7890 (mpp-170) cc_final: 0.7489 (mpp-170) REVERT: C 227 VAL cc_start: 0.8151 (m) cc_final: 0.7899 (m) REVERT: C 288 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: C 291 MET cc_start: 0.7543 (mtp) cc_final: 0.7106 (mtp) REVERT: C 292 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6720 (mt) REVERT: C 489 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 514 SER cc_start: 0.8223 (m) cc_final: 0.7983 (p) REVERT: D 291 MET cc_start: 0.7385 (mtp) cc_final: 0.6899 (mtp) REVERT: D 294 MET cc_start: 0.5339 (mmp) cc_final: 0.4115 (mmp) REVERT: D 353 ARG cc_start: 0.7619 (ptt180) cc_final: 0.7216 (ptt90) REVERT: D 489 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7260 (mt-10) REVERT: D 493 ASP cc_start: 0.7995 (m-30) cc_final: 0.7750 (m-30) REVERT: D 514 SER cc_start: 0.8306 (m) cc_final: 0.8063 (p) REVERT: E 23 ASP cc_start: 0.7817 (p0) cc_final: 0.7609 (p0) REVERT: E 47 ARG cc_start: 0.7907 (mpp-170) cc_final: 0.7494 (mpp-170) REVERT: E 146 GLU cc_start: 0.8731 (tt0) cc_final: 0.8529 (tt0) REVERT: E 227 VAL cc_start: 0.8373 (m) cc_final: 0.8136 (m) REVERT: E 292 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6625 (mt) REVERT: E 353 ARG cc_start: 0.7531 (ptt180) cc_final: 0.7239 (ptt90) REVERT: E 493 ASP cc_start: 0.8097 (m-30) cc_final: 0.7856 (m-30) REVERT: E 514 SER cc_start: 0.8230 (m) cc_final: 0.7918 (p) REVERT: E 529 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7597 (tt0) outliers start: 62 outliers final: 25 residues processed: 293 average time/residue: 1.3081 time to fit residues: 427.4987 Evaluate side-chains 264 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 55 optimal weight: 0.0770 chunk 166 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 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 B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101041 restraints weight = 17332.469| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.01 r_work: 0.2922 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17530 Z= 0.129 Angle : 0.625 10.798 23885 Z= 0.308 Chirality : 0.046 0.352 2800 Planarity : 0.004 0.035 2890 Dihedral : 6.843 56.297 2740 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 19.95 % Favored : 76.91 % 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: 2.31 (0.19), residues: 2040 helix: 3.33 (0.17), residues: 820 sheet: 1.77 (0.25), residues: 425 loop : -0.65 (0.21), residues: 795 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 0.009 0.001 PHE E 312 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 10) link_NAG-ASN : angle 3.86698 ( 30) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 1.72486 ( 30) hydrogen bonds : bond 0.06492 ( 885) hydrogen bonds : angle 3.73995 ( 2925) SS BOND : bond 0.00922 ( 5) SS BOND : angle 3.76679 ( 10) covalent geometry : bond 0.00259 (17505) covalent geometry : angle 0.60282 (23815) *********************** 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 299 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8756 (mpp) REVERT: A 227 VAL cc_start: 0.8274 (m) cc_final: 0.7973 (m) REVERT: A 249 LEU cc_start: 0.7670 (mp) cc_final: 0.6867 (tp) REVERT: A 266 THR cc_start: 0.8313 (m) cc_final: 0.7713 (p) REVERT: A 291 MET cc_start: 0.7174 (mtp) cc_final: 0.6853 (mtp) REVERT: A 294 MET cc_start: 0.4550 (mpm) cc_final: 0.4327 (tpp) REVERT: A 493 ASP cc_start: 0.7804 (m-30) cc_final: 0.7575 (m-30) REVERT: B 47 ARG cc_start: 0.7833 (mpp-170) cc_final: 0.7578 (mpp-170) REVERT: B 266 THR cc_start: 0.8329 (m) cc_final: 0.7899 (p) REVERT: B 291 MET cc_start: 0.7172 (mtp) cc_final: 0.6831 (mtp) REVERT: B 349 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7829 (tppp) REVERT: B 353 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7250 (ptt90) REVERT: B 493 ASP cc_start: 0.7946 (m-30) cc_final: 0.7731 (m-30) REVERT: C 23 ASP cc_start: 0.7959 (p0) cc_final: 0.7601 (p0) REVERT: C 47 ARG cc_start: 0.7863 (mpp-170) cc_final: 0.7330 (mtm180) REVERT: C 227 VAL cc_start: 0.8114 (m) cc_final: 0.7834 (m) REVERT: C 249 LEU cc_start: 0.7717 (mp) cc_final: 0.6963 (tp) REVERT: C 288 MET cc_start: 0.8035 (ttm) cc_final: 0.7615 (mmm) REVERT: C 291 MET cc_start: 0.7214 (mtp) cc_final: 0.6838 (mtp) REVERT: C 292 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6489 (mt) REVERT: C 493 ASP cc_start: 0.7853 (m-30) cc_final: 0.7580 (m-30) REVERT: D 40 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8815 (pttm) REVERT: D 288 MET cc_start: 0.8025 (mtm) cc_final: 0.7769 (mmm) REVERT: D 291 MET cc_start: 0.7266 (mtp) cc_final: 0.6834 (mtp) REVERT: D 294 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4171 (mmp) REVERT: D 353 ARG cc_start: 0.7610 (ptt180) cc_final: 0.7323 (ptt90) REVERT: E 23 ASP cc_start: 0.7832 (p0) cc_final: 0.7596 (p0) REVERT: E 47 ARG cc_start: 0.7829 (mpp-170) cc_final: 0.7399 (mpp-170) REVERT: E 102 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8715 (mpp) REVERT: E 146 GLU cc_start: 0.8749 (tt0) cc_final: 0.8549 (tt0) REVERT: E 227 VAL cc_start: 0.8387 (m) cc_final: 0.8135 (m) REVERT: E 247 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8338 (mp) REVERT: E 288 MET cc_start: 0.7887 (mtm) cc_final: 0.7506 (mmm) REVERT: E 291 MET cc_start: 0.7134 (mtp) cc_final: 0.6730 (mtp) REVERT: E 292 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6488 (mt) REVERT: E 493 ASP cc_start: 0.7999 (m-30) cc_final: 0.7724 (m-30) outliers start: 59 outliers final: 11 residues processed: 275 average time/residue: 1.1374 time to fit residues: 352.3608 Evaluate side-chains 249 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 227 VAL 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 266 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 266 THR 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: 0.8980 chunk 4 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 110 optimal weight: 0.0020 chunk 153 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 overall best weight: 0.4286 ------------------------------------------------------------------------------- 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 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103617 restraints weight = 17512.276| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.06 r_work: 0.2946 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17530 Z= 0.110 Angle : 0.580 9.714 23885 Z= 0.283 Chirality : 0.045 0.314 2800 Planarity : 0.004 0.037 2890 Dihedral : 6.516 57.136 2740 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.52 % Allowed : 19.84 % Favored : 76.64 % 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: 2.46 (0.19), residues: 2040 helix: 3.53 (0.17), residues: 820 sheet: 1.77 (0.26), residues: 420 loop : -0.59 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 494 HIS 0.003 0.001 HIS B 271 PHE 0.009 0.001 PHE D 312 TYR 0.011 0.001 TYR B 72 ARG 0.002 0.000 ARG E 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 10) link_NAG-ASN : angle 3.42682 ( 30) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 1.73432 ( 30) hydrogen bonds : bond 0.05310 ( 885) hydrogen bonds : angle 3.49769 ( 2925) SS BOND : bond 0.00806 ( 5) SS BOND : angle 2.93962 ( 10) covalent geometry : bond 0.00217 (17505) covalent geometry : angle 0.56161 (23815) *********************** 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 305 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8813 (mpp) REVERT: A 288 MET cc_start: 0.7826 (mmm) cc_final: 0.7157 (mmm) REVERT: A 291 MET cc_start: 0.7063 (mtp) cc_final: 0.6697 (mtp) REVERT: A 493 ASP cc_start: 0.7850 (m-30) cc_final: 0.7549 (m-30) REVERT: B 47 ARG cc_start: 0.7858 (mpp-170) cc_final: 0.7628 (mpp-170) REVERT: B 102 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8796 (mpp) REVERT: B 291 MET cc_start: 0.6978 (mtp) cc_final: 0.6682 (mtp) REVERT: B 349 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7864 (tppp) REVERT: B 362 MET cc_start: 0.8772 (ttm) cc_final: 0.8561 (ttm) REVERT: C 23 ASP cc_start: 0.7892 (p0) cc_final: 0.7523 (p0) REVERT: C 47 ARG cc_start: 0.7901 (mpp-170) cc_final: 0.7285 (mtm180) REVERT: C 102 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8739 (mpp) REVERT: C 227 VAL cc_start: 0.8121 (m) cc_final: 0.7814 (m) REVERT: C 288 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7598 (mmm) REVERT: C 291 MET cc_start: 0.7046 (mtp) cc_final: 0.6671 (mtp) REVERT: C 292 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6338 (mt) REVERT: C 493 ASP cc_start: 0.7849 (m-30) cc_final: 0.7483 (m-30) REVERT: D 40 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8842 (pttm) REVERT: D 288 MET cc_start: 0.8028 (mtm) cc_final: 0.7764 (mmm) REVERT: D 291 MET cc_start: 0.7097 (mtp) cc_final: 0.6798 (mtp) REVERT: D 294 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4218 (mmp) REVERT: D 353 ARG cc_start: 0.7660 (ptt180) cc_final: 0.7398 (ptt90) REVERT: D 383 MET cc_start: 0.2415 (OUTLIER) cc_final: 0.1406 (mmt) REVERT: E 23 ASP cc_start: 0.7812 (p0) cc_final: 0.7562 (p0) REVERT: E 47 ARG cc_start: 0.7817 (mpp-170) cc_final: 0.7377 (mpp-170) REVERT: E 102 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8734 (mpp) REVERT: E 146 GLU cc_start: 0.8774 (tt0) cc_final: 0.8567 (tt0) REVERT: E 227 VAL cc_start: 0.8416 (m) cc_final: 0.8171 (m) REVERT: E 288 MET cc_start: 0.7924 (mtm) cc_final: 0.7561 (mmm) REVERT: E 291 MET cc_start: 0.6930 (mtp) cc_final: 0.6534 (mtp) REVERT: E 292 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6476 (mt) REVERT: E 493 ASP cc_start: 0.7922 (m-30) cc_final: 0.7603 (m-30) outliers start: 66 outliers final: 14 residues processed: 283 average time/residue: 1.0980 time to fit residues: 351.2061 Evaluate side-chains 247 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 97 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 383 MET 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 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 286 LEU Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 72 optimal weight: 0.0670 chunk 49 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- 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 B 530 ASN C 352 HIS E 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104968 restraints weight = 17679.454| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.99 r_work: 0.2943 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17530 Z= 0.104 Angle : 0.568 9.827 23885 Z= 0.275 Chirality : 0.045 0.308 2800 Planarity : 0.003 0.035 2890 Dihedral : 6.405 56.242 2740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.09 % Allowed : 20.27 % Favored : 76.64 % 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: 2.55 (0.19), residues: 2040 helix: 3.65 (0.17), residues: 820 sheet: 1.70 (0.26), residues: 420 loop : -0.52 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 494 HIS 0.003 0.001 HIS B 271 PHE 0.009 0.001 PHE D 312 TYR 0.012 0.001 TYR C 72 ARG 0.004 0.000 ARG D 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 10) link_NAG-ASN : angle 3.31395 ( 30) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.72409 ( 30) hydrogen bonds : bond 0.04902 ( 885) hydrogen bonds : angle 3.40472 ( 2925) SS BOND : bond 0.00833 ( 5) SS BOND : angle 2.35180 ( 10) covalent geometry : bond 0.00205 (17505) covalent geometry : angle 0.55090 (23815) *********************** 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 287 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 229 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8816 (mpp) REVERT: A 227 VAL cc_start: 0.8351 (m) cc_final: 0.8062 (m) REVERT: A 288 MET cc_start: 0.7879 (mmm) cc_final: 0.7406 (mmm) REVERT: A 291 MET cc_start: 0.7110 (mtp) cc_final: 0.6822 (mtp) REVERT: A 493 ASP cc_start: 0.7883 (m-30) cc_final: 0.7613 (m-30) REVERT: B 47 ARG cc_start: 0.7910 (mpp-170) cc_final: 0.7684 (mpp-170) REVERT: B 288 MET cc_start: 0.8011 (mtm) cc_final: 0.7717 (mmm) REVERT: B 291 MET cc_start: 0.6956 (mtp) cc_final: 0.6620 (mtp) REVERT: B 349 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7879 (tppp) REVERT: B 362 MET cc_start: 0.8724 (ttm) cc_final: 0.8519 (ttm) REVERT: C 23 ASP cc_start: 0.7885 (p0) cc_final: 0.7464 (p0) REVERT: C 47 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7267 (mtm180) REVERT: C 227 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7840 (m) REVERT: C 288 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7649 (mmm) REVERT: C 291 MET cc_start: 0.6991 (mtp) cc_final: 0.6574 (mtp) REVERT: D 40 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8843 (pttm) REVERT: D 203 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 291 MET cc_start: 0.6980 (mtp) cc_final: 0.6629 (mtp) REVERT: D 294 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4744 (tpp) REVERT: D 353 ARG cc_start: 0.7767 (ptt180) cc_final: 0.7445 (ptt90) REVERT: D 383 MET cc_start: 0.2245 (OUTLIER) cc_final: 0.1230 (mmt) REVERT: E 23 ASP cc_start: 0.7750 (p0) cc_final: 0.7467 (p0) REVERT: E 47 ARG cc_start: 0.7813 (mpp-170) cc_final: 0.7438 (mpp-170) REVERT: E 102 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8747 (mpp) REVERT: E 146 GLU cc_start: 0.8785 (tt0) cc_final: 0.8578 (tt0) REVERT: E 227 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8036 (m) REVERT: E 291 MET cc_start: 0.7055 (mtp) cc_final: 0.6658 (mtp) REVERT: E 292 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6486 (mt) REVERT: E 493 ASP cc_start: 0.7964 (m-30) cc_final: 0.7676 (m-30) outliers start: 58 outliers final: 12 residues processed: 267 average time/residue: 1.1147 time to fit residues: 335.8593 Evaluate side-chains 248 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 B residue 97 ASN Chi-restraints excluded: chain B residue 170 THR 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 236 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 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 227 VAL 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: 0.8980 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 530 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 = 0.3570 r_free = 0.3570 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099897 restraints weight = 17440.888| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.93 r_work: 0.2879 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17530 Z= 0.154 Angle : 0.657 9.808 23885 Z= 0.324 Chirality : 0.048 0.288 2800 Planarity : 0.004 0.037 2890 Dihedral : 6.469 56.333 2740 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.95 % Allowed : 18.88 % Favored : 77.17 % 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: 2.30 (0.19), residues: 2040 helix: 3.39 (0.17), residues: 825 sheet: 1.47 (0.24), residues: 470 loop : -0.71 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 494 HIS 0.005 0.001 HIS A 131 PHE 0.013 0.001 PHE E 312 TYR 0.014 0.002 TYR C 72 ARG 0.002 0.000 ARG C 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 3.12242 ( 30) link_BETA1-4 : bond 0.00493 ( 10) link_BETA1-4 : angle 1.98583 ( 30) hydrogen bonds : bond 0.06414 ( 885) hydrogen bonds : angle 3.63038 ( 2925) SS BOND : bond 0.01316 ( 5) SS BOND : angle 2.59910 ( 10) covalent geometry : bond 0.00342 (17505) covalent geometry : angle 0.64242 (23815) *********************** 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 309 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 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: 0.8099 (mpp-170) cc_final: 0.7883 (mtm180) REVERT: A 227 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8227 (m) REVERT: A 249 LEU cc_start: 0.7856 (mp) cc_final: 0.7108 (tp) REVERT: A 291 MET cc_start: 0.7310 (mtp) cc_final: 0.6934 (mtp) REVERT: A 493 ASP cc_start: 0.8037 (m-30) cc_final: 0.7722 (m-30) REVERT: A 516 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7448 (mp) REVERT: B 148 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8766 (tp) REVERT: B 203 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 249 LEU cc_start: 0.7832 (mt) cc_final: 0.7448 (mt) REVERT: B 291 MET cc_start: 0.7005 (mtp) cc_final: 0.6711 (mtp) REVERT: B 349 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7763 (tppp) REVERT: B 493 ASP cc_start: 0.8084 (m-30) cc_final: 0.7853 (m-30) REVERT: C 23 ASP cc_start: 0.7831 (p0) cc_final: 0.7426 (p0) REVERT: C 47 ARG cc_start: 0.8034 (mpp-170) cc_final: 0.7466 (mtm180) REVERT: C 203 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 227 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8053 (m) REVERT: C 288 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7698 (mmm) REVERT: C 291 MET cc_start: 0.7111 (mtp) cc_final: 0.6713 (mtp) REVERT: D 40 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (pttm) REVERT: D 47 ARG cc_start: 0.8058 (mpp-170) cc_final: 0.7856 (mpp-170) REVERT: D 203 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8293 (mp) REVERT: D 288 MET cc_start: 0.8068 (mmm) cc_final: 0.7862 (mmm) REVERT: D 291 MET cc_start: 0.7078 (mtp) cc_final: 0.6797 (mtp) REVERT: D 294 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4529 (tpp) REVERT: D 353 ARG cc_start: 0.7734 (ptt180) cc_final: 0.7450 (ptt90) REVERT: D 383 MET cc_start: 0.2432 (OUTLIER) cc_final: 0.1408 (mmt) REVERT: E 23 ASP cc_start: 0.7740 (p0) cc_final: 0.7465 (p0) REVERT: E 47 ARG cc_start: 0.7969 (mpp-170) cc_final: 0.7637 (mpp-170) REVERT: E 146 GLU cc_start: 0.8793 (tt0) cc_final: 0.8585 (tt0) REVERT: E 227 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (m) REVERT: E 288 MET cc_start: 0.7876 (mmm) cc_final: 0.7596 (mmm) REVERT: E 291 MET cc_start: 0.7142 (mtp) cc_final: 0.6784 (mtp) REVERT: E 292 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6287 (mt) REVERT: E 493 ASP cc_start: 0.8140 (m-30) cc_final: 0.7905 (m-30) outliers start: 74 outliers final: 29 residues processed: 279 average time/residue: 1.1390 time to fit residues: 357.7531 Evaluate side-chains 267 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 266 THR 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 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 193 THR Chi-restraints excluded: chain C residue 203 LEU 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 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 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 346 LYS 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 170 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL 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 516 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 158 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 189 optimal weight: 0.1980 chunk 148 optimal weight: 0.0010 chunk 181 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 530 ASN E 361 GLN E 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104548 restraints weight = 17540.037| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.00 r_work: 0.2956 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17530 Z= 0.106 Angle : 0.571 9.831 23885 Z= 0.278 Chirality : 0.045 0.294 2800 Planarity : 0.003 0.033 2890 Dihedral : 6.369 56.637 2740 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.29 % Allowed : 20.91 % 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: 2.56 (0.19), residues: 2040 helix: 3.66 (0.17), residues: 820 sheet: 1.69 (0.26), residues: 420 loop : -0.50 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 83 HIS 0.003 0.000 HIS A 271 PHE 0.012 0.001 PHE A 293 TYR 0.014 0.001 TYR E 229 ARG 0.001 0.000 ARG C 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 10) link_NAG-ASN : angle 3.14496 ( 30) link_BETA1-4 : bond 0.00482 ( 10) link_BETA1-4 : angle 1.79359 ( 30) hydrogen bonds : bond 0.04885 ( 885) hydrogen bonds : angle 3.40240 ( 2925) SS BOND : bond 0.00916 ( 5) SS BOND : angle 2.46144 ( 10) covalent geometry : bond 0.00206 (17505) covalent geometry : angle 0.55458 (23815) *********************** 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 279 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7968 (mpp-170) cc_final: 0.7743 (mtm180) REVERT: A 102 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8780 (mpp) REVERT: A 227 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8131 (m) REVERT: A 247 LEU cc_start: 0.8871 (tp) cc_final: 0.8665 (mt) REVERT: A 288 MET cc_start: 0.7864 (mmm) cc_final: 0.7512 (mmm) REVERT: A 291 MET cc_start: 0.7060 (mtp) cc_final: 0.6753 (mtp) REVERT: A 493 ASP cc_start: 0.7844 (m-30) cc_final: 0.7511 (m-30) REVERT: B 102 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8739 (mpp) REVERT: B 288 MET cc_start: 0.7989 (mtm) cc_final: 0.7744 (mmm) REVERT: B 291 MET cc_start: 0.6807 (mtp) cc_final: 0.6544 (mtp) REVERT: B 349 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7864 (tppp) REVERT: C 47 ARG cc_start: 0.7989 (mpp-170) cc_final: 0.7402 (mtm180) REVERT: C 227 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7937 (m) REVERT: C 288 MET cc_start: 0.8001 (ttm) cc_final: 0.7649 (mmm) REVERT: C 291 MET cc_start: 0.6918 (mtp) cc_final: 0.6509 (mtp) REVERT: C 513 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: D 36 GLU cc_start: 0.8019 (tt0) cc_final: 0.7764 (mt-10) REVERT: D 203 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8233 (mp) REVERT: D 288 MET cc_start: 0.7971 (mmm) cc_final: 0.7764 (mmm) REVERT: D 291 MET cc_start: 0.6842 (mtp) cc_final: 0.6598 (mtp) REVERT: D 346 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7280 (ptpt) REVERT: D 349 LYS cc_start: 0.8183 (tttt) cc_final: 0.7498 (tppp) REVERT: D 353 ARG cc_start: 0.7719 (ptt180) cc_final: 0.7310 (ptt90) REVERT: D 383 MET cc_start: 0.2453 (OUTLIER) cc_final: 0.1424 (mmt) REVERT: E 23 ASP cc_start: 0.7733 (p0) cc_final: 0.7450 (p0) REVERT: E 47 ARG cc_start: 0.7881 (mpp-170) cc_final: 0.7425 (mpp-170) REVERT: E 102 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8723 (mpp) REVERT: E 146 GLU cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0) REVERT: E 227 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8083 (m) REVERT: E 288 MET cc_start: 0.7801 (mmm) cc_final: 0.7587 (mmm) REVERT: E 291 MET cc_start: 0.7053 (mtp) cc_final: 0.6752 (mtp) REVERT: E 292 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6364 (mt) REVERT: E 493 ASP cc_start: 0.7932 (m-30) cc_final: 0.7616 (m-30) outliers start: 43 outliers final: 14 residues processed: 258 average time/residue: 1.1436 time to fit residues: 331.5004 Evaluate side-chains 256 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 102 MET 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 193 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 346 LYS 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 227 VAL Chi-restraints excluded: chain E residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 ASN B 271 HIS B 352 HIS B 530 ASN D 37 ASN E 361 GLN E 530 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102281 restraints weight = 17427.294| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.12 r_work: 0.2918 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17530 Z= 0.121 Angle : 0.610 11.712 23885 Z= 0.295 Chirality : 0.046 0.268 2800 Planarity : 0.004 0.031 2890 Dihedral : 6.335 55.562 2740 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.72 % Allowed : 20.53 % 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: 2.47 (0.19), residues: 2040 helix: 3.56 (0.17), residues: 825 sheet: 1.63 (0.25), residues: 425 loop : -0.56 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.003 0.001 HIS B 131 PHE 0.010 0.001 PHE E 312 TYR 0.012 0.001 TYR C 72 ARG 0.001 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 10) link_NAG-ASN : angle 2.92360 ( 30) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 1.88641 ( 30) hydrogen bonds : bond 0.05321 ( 885) hydrogen bonds : angle 3.43070 ( 2925) SS BOND : bond 0.00846 ( 5) SS BOND : angle 2.27349 ( 10) covalent geometry : bond 0.00256 (17505) covalent geometry : angle 0.59641 (23815) *********************** 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 281 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8043 (mpp-170) cc_final: 0.7833 (mtm180) REVERT: A 102 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8797 (mpp) REVERT: A 227 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 288 MET cc_start: 0.7861 (mmm) cc_final: 0.7477 (mmm) REVERT: A 291 MET cc_start: 0.7115 (mtp) cc_final: 0.6790 (mtp) REVERT: A 493 ASP cc_start: 0.7904 (m-30) cc_final: 0.7564 (m-30) REVERT: A 516 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7273 (mp) REVERT: B 102 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8777 (mpp) REVERT: B 203 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 291 MET cc_start: 0.6811 (mtp) cc_final: 0.6498 (mtp) REVERT: B 349 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8081 (ptmm) REVERT: C 47 ARG cc_start: 0.8012 (mpp-170) cc_final: 0.7430 (mtm180) REVERT: C 227 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8009 (m) REVERT: C 288 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: C 291 MET cc_start: 0.7049 (mtp) cc_final: 0.6549 (mtp) REVERT: C 513 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: D 36 GLU cc_start: 0.8130 (tt0) cc_final: 0.7803 (mt-10) REVERT: D 203 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 291 MET cc_start: 0.6864 (mtp) cc_final: 0.6632 (mtp) REVERT: D 294 MET cc_start: 0.5048 (OUTLIER) cc_final: 0.4577 (tmm) REVERT: D 349 LYS cc_start: 0.8234 (tttt) cc_final: 0.7514 (tppp) REVERT: D 353 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7403 (ptt90) REVERT: D 383 MET cc_start: 0.2474 (OUTLIER) cc_final: 0.1436 (mmt) REVERT: E 23 ASP cc_start: 0.7707 (p0) cc_final: 0.7383 (p0) REVERT: E 47 ARG cc_start: 0.7932 (mpp-170) cc_final: 0.7586 (mpp-170) REVERT: E 102 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8777 (mpp) REVERT: E 146 GLU cc_start: 0.8779 (tt0) cc_final: 0.8570 (tt0) REVERT: E 227 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8109 (m) REVERT: E 288 MET cc_start: 0.7881 (mmm) cc_final: 0.7664 (mmm) REVERT: E 291 MET cc_start: 0.7093 (mtp) cc_final: 0.6806 (mtp) REVERT: E 292 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6412 (mt) REVERT: E 493 ASP cc_start: 0.8017 (m-30) cc_final: 0.7747 (m-30) outliers start: 51 outliers final: 18 residues processed: 257 average time/residue: 1.1415 time to fit residues: 330.0740 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 : 1.740 ------------------------------------------------------------------------------- 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 520 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 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 C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE 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 294 MET 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 227 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: 0.9980 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.0770 chunk 189 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103505 restraints weight = 17603.329| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.98 r_work: 0.2912 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17530 Z= 0.110 Angle : 0.588 10.030 23885 Z= 0.285 Chirality : 0.046 0.275 2800 Planarity : 0.003 0.030 2890 Dihedral : 6.317 55.845 2740 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.19 % Allowed : 20.85 % Favored : 76.96 % 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: 2.58 (0.19), residues: 2040 helix: 3.65 (0.17), residues: 820 sheet: 1.70 (0.26), residues: 420 loop : -0.45 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 526 HIS 0.003 0.001 HIS B 271 PHE 0.009 0.001 PHE E 312 TYR 0.015 0.001 TYR E 229 ARG 0.001 0.000 ARG E 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 10) link_NAG-ASN : angle 2.84672 ( 30) link_BETA1-4 : bond 0.00463 ( 10) link_BETA1-4 : angle 1.84975 ( 30) hydrogen bonds : bond 0.05033 ( 885) hydrogen bonds : angle 3.38546 ( 2925) SS BOND : bond 0.00655 ( 5) SS BOND : angle 2.56475 ( 10) covalent geometry : bond 0.00224 (17505) covalent geometry : angle 0.57428 (23815) *********************** 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 275 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8061 (mpp-170) cc_final: 0.7857 (mtm180) REVERT: A 102 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8801 (mpp) REVERT: A 227 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8240 (m) REVERT: A 288 MET cc_start: 0.7887 (mmm) cc_final: 0.7485 (mmm) REVERT: A 291 MET cc_start: 0.7077 (mtp) cc_final: 0.6772 (mtp) REVERT: A 493 ASP cc_start: 0.7952 (m-30) cc_final: 0.7639 (m-30) REVERT: B 203 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 291 MET cc_start: 0.6968 (mtp) cc_final: 0.6679 (mtp) REVERT: B 349 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8092 (ptmm) REVERT: C 47 ARG cc_start: 0.8026 (mpp-170) cc_final: 0.7451 (mtm180) REVERT: C 227 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8034 (m) REVERT: C 288 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7728 (mmm) REVERT: C 291 MET cc_start: 0.7156 (mtp) cc_final: 0.6692 (mtp) REVERT: C 513 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: D 36 GLU cc_start: 0.8086 (tt0) cc_final: 0.7844 (mt-10) REVERT: D 203 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 288 MET cc_start: 0.7834 (mmm) cc_final: 0.7538 (mmm) REVERT: D 291 MET cc_start: 0.6850 (mtp) cc_final: 0.6621 (mtp) REVERT: D 294 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4866 (ttp) REVERT: D 349 LYS cc_start: 0.8260 (tttt) cc_final: 0.7524 (tppp) REVERT: D 353 ARG cc_start: 0.7771 (ptt180) cc_final: 0.7432 (ptt90) REVERT: D 383 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.1414 (mmt) REVERT: E 47 ARG cc_start: 0.7949 (mpp-170) cc_final: 0.7596 (mpp-170) REVERT: E 102 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8765 (mpp) REVERT: E 146 GLU cc_start: 0.8817 (tt0) cc_final: 0.8612 (tt0) REVERT: E 227 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8120 (m) REVERT: E 288 MET cc_start: 0.7896 (mmm) cc_final: 0.7668 (mmm) REVERT: E 291 MET cc_start: 0.7037 (mtp) cc_final: 0.6763 (mtp) REVERT: E 292 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6361 (mt) REVERT: E 493 ASP cc_start: 0.8042 (m-30) cc_final: 0.7750 (m-30) outliers start: 41 outliers final: 16 residues processed: 252 average time/residue: 1.1960 time to fit residues: 339.7445 Evaluate side-chains 256 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU 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 193 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 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 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 106 ASP 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 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 110 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 144 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 114 optimal weight: 0.0040 chunk 164 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 ASN B 271 HIS B 530 ASN C 271 HIS E 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105017 restraints weight = 17636.009| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.07 r_work: 0.2958 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17530 Z= 0.102 Angle : 0.572 10.839 23885 Z= 0.275 Chirality : 0.045 0.276 2800 Planarity : 0.003 0.031 2890 Dihedral : 6.261 55.949 2740 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.60 % Allowed : 21.55 % 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: 2.69 (0.19), residues: 2040 helix: 3.75 (0.17), residues: 820 sheet: 1.70 (0.26), residues: 420 loop : -0.38 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.003 0.001 HIS B 271 PHE 0.008 0.001 PHE E 312 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG C 382 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 10) link_NAG-ASN : angle 2.73770 ( 30) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 1.79623 ( 30) hydrogen bonds : bond 0.04536 ( 885) hydrogen bonds : angle 3.30191 ( 2925) SS BOND : bond 0.00479 ( 5) SS BOND : angle 2.16193 ( 10) covalent geometry : bond 0.00202 (17505) covalent geometry : angle 0.55966 (23815) ********************** 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 270 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7999 (mpp-170) cc_final: 0.7794 (mtm180) REVERT: A 102 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8774 (mpp) REVERT: A 227 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 288 MET cc_start: 0.7822 (mmm) cc_final: 0.7415 (mmm) REVERT: A 291 MET cc_start: 0.6976 (mtp) cc_final: 0.6695 (mtp) REVERT: A 493 ASP cc_start: 0.7813 (m-30) cc_final: 0.7549 (m-30) REVERT: B 203 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 291 MET cc_start: 0.6924 (mtp) cc_final: 0.6611 (mtp) REVERT: B 349 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8062 (ptmm) REVERT: B 513 PHE cc_start: 0.7919 (m-80) cc_final: 0.7698 (m-80) REVERT: C 47 ARG cc_start: 0.7942 (mpp-170) cc_final: 0.7386 (mtm180) REVERT: C 227 VAL cc_start: 0.8302 (m) cc_final: 0.7976 (m) REVERT: C 288 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7877 (mmm) REVERT: C 291 MET cc_start: 0.7116 (mtp) cc_final: 0.6679 (mtp) REVERT: C 513 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: D 36 GLU cc_start: 0.8006 (tt0) cc_final: 0.7784 (mt-10) REVERT: D 288 MET cc_start: 0.7864 (mmm) cc_final: 0.7607 (mmm) REVERT: D 294 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4992 (ttp) REVERT: D 349 LYS cc_start: 0.8228 (tttt) cc_final: 0.7787 (ptmm) REVERT: D 353 ARG cc_start: 0.7769 (ptt180) cc_final: 0.7430 (ptt90) REVERT: D 383 MET cc_start: 0.2344 (OUTLIER) cc_final: 0.1374 (mmt) REVERT: E 47 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7502 (mpp-170) REVERT: E 146 GLU cc_start: 0.8760 (tt0) cc_final: 0.8550 (tt0) REVERT: E 227 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8101 (m) REVERT: E 288 MET cc_start: 0.7856 (mmm) cc_final: 0.7592 (mmm) REVERT: E 291 MET cc_start: 0.6888 (mtp) cc_final: 0.6645 (mtp) REVERT: E 292 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6381 (mt) REVERT: E 493 ASP cc_start: 0.7857 (m-30) cc_final: 0.7558 (m-30) outliers start: 30 outliers final: 12 residues processed: 252 average time/residue: 1.1135 time to fit residues: 316.1943 Evaluate side-chains 252 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 193 THR Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR 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 97 ASN Chi-restraints excluded: chain E residue 106 ASP 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: 5.9990 chunk 25 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 530 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 = 0.3596 r_free = 0.3596 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101540 restraints weight = 17452.499| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.92 r_work: 0.2921 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17530 Z= 0.124 Angle : 0.617 10.572 23885 Z= 0.299 Chirality : 0.046 0.252 2800 Planarity : 0.004 0.032 2890 Dihedral : 6.308 55.378 2740 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.49 % Allowed : 21.97 % Favored : 76.53 % 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: 2.49 (0.19), residues: 2040 helix: 3.56 (0.17), residues: 825 sheet: 1.64 (0.25), residues: 425 loop : -0.51 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 90 HIS 0.003 0.001 HIS B 271 PHE 0.011 0.001 PHE A 312 TYR 0.013 0.001 TYR C 72 ARG 0.001 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 2.53583 ( 30) link_BETA1-4 : bond 0.00498 ( 10) link_BETA1-4 : angle 1.90975 ( 30) hydrogen bonds : bond 0.05435 ( 885) hydrogen bonds : angle 3.43005 ( 2925) SS BOND : bond 0.00873 ( 5) SS BOND : angle 2.32135 ( 10) covalent geometry : bond 0.00263 (17505) covalent geometry : angle 0.60525 (23815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12900.02 seconds wall clock time: 222 minutes 35.27 seconds (13355.27 seconds total)