Starting phenix.real_space_refine on Thu Sep 18 13:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfl_60064/09_2025/8zfl_60064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfl_60064/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zfl_60064/09_2025/8zfl_60064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfl_60064/09_2025/8zfl_60064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zfl_60064/09_2025/8zfl_60064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfl_60064/09_2025/8zfl_60064.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.72, per 1000 atoms: 0.28 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: 1.82 Conformation dependent library (CDL) restraints added in 883.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 3.07 Time building geometry restraints manager: 2.34 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: 0.03 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: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.160 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 274 TYR 0.008 0.001 TYR E 72 PHE 0.017 0.001 PHE C 332 TRP 0.012 0.001 TRP B 350 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00253 (17505) covalent geometry : angle 0.50863 (23815) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.20232 ( 10) hydrogen bonds : bond 0.24623 ( 885) hydrogen bonds : angle 6.20418 ( 2925) link_BETA1-4 : bond 0.00328 ( 10) link_BETA1-4 : angle 1.72006 ( 30) link_NAG-ASN : bond 0.00175 ( 10) link_NAG-ASN : angle 1.55992 ( 30) *********************** 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 : 0.707 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: 0.6287 time to fit residues: 271.7588 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 : 0.423 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.141148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102996 restraints weight = 18325.304| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.85 r_work: 0.2904 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17530 Z= 0.171 Angle : 0.700 11.185 23885 Z= 0.347 Chirality : 0.049 0.354 2800 Planarity : 0.005 0.038 2890 Dihedral : 7.240 56.138 2746 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.63 % Allowed : 17.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.18), residues: 2040 helix: 2.67 (0.17), residues: 835 sheet: 1.62 (0.24), residues: 470 loop : -0.64 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 382 TYR 0.015 0.002 TYR C 72 PHE 0.010 0.001 PHE E 312 TRP 0.013 0.002 TRP C 494 HIS 0.005 0.002 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00366 (17505) covalent geometry : angle 0.67725 (23815) SS BOND : bond 0.01785 ( 5) SS BOND : angle 4.41419 ( 10) hydrogen bonds : bond 0.07865 ( 885) hydrogen bonds : angle 3.98837 ( 2925) link_BETA1-4 : bond 0.00502 ( 10) link_BETA1-4 : angle 1.93636 ( 30) link_NAG-ASN : bond 0.01603 ( 10) link_NAG-ASN : angle 3.90323 ( 30) *********************** 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 326 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8320 (m) cc_final: 0.8055 (m) REVERT: A 247 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 266 THR cc_start: 0.8346 (m) cc_final: 0.7759 (p) REVERT: A 291 MET cc_start: 0.7405 (mtp) cc_final: 0.7056 (mtp) REVERT: A 489 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 493 ASP cc_start: 0.8000 (m-30) cc_final: 0.7697 (m-30) REVERT: A 514 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 47 ARG cc_start: 0.7779 (mpp-170) cc_final: 0.7447 (mpp-170) REVERT: B 266 THR cc_start: 0.8344 (m) cc_final: 0.7902 (p) REVERT: B 291 MET cc_start: 0.7329 (mtp) cc_final: 0.6968 (mtp) REVERT: B 349 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7808 (tppp) REVERT: B 353 ARG cc_start: 0.7759 (ptt180) cc_final: 0.7338 (ptt90) REVERT: C 23 ASP cc_start: 0.8009 (p0) cc_final: 0.7623 (p0) REVERT: C 40 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8831 (pttm) REVERT: C 47 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7480 (mpp-170) REVERT: C 227 VAL cc_start: 0.8153 (m) cc_final: 0.7902 (m) REVERT: C 288 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7734 (mmm) REVERT: C 291 MET cc_start: 0.7548 (mtp) cc_final: 0.7105 (mtp) REVERT: C 292 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6662 (mt) REVERT: C 489 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 514 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 291 MET cc_start: 0.7374 (mtp) cc_final: 0.6931 (mtp) REVERT: D 294 MET cc_start: 0.5363 (mmt) cc_final: 0.4124 (mmp) REVERT: D 353 ARG cc_start: 0.7624 (ptt180) cc_final: 0.7243 (ptt90) REVERT: D 489 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 493 ASP cc_start: 0.7986 (m-30) cc_final: 0.7741 (m-30) REVERT: D 514 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (p) REVERT: E 23 ASP cc_start: 0.7807 (p0) cc_final: 0.7594 (p0) REVERT: E 47 ARG cc_start: 0.7901 (mpp-170) cc_final: 0.7488 (mpp-170) REVERT: E 146 GLU cc_start: 0.8750 (tt0) cc_final: 0.8532 (tt0) REVERT: E 227 VAL cc_start: 0.8375 (m) cc_final: 0.8140 (m) REVERT: E 292 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6609 (mt) REVERT: E 353 ARG cc_start: 0.7549 (ptt180) cc_final: 0.7269 (ptt90) REVERT: E 493 ASP cc_start: 0.8091 (m-30) cc_final: 0.7848 (m-30) REVERT: E 514 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7911 (p) outliers start: 68 outliers final: 24 residues processed: 293 average time/residue: 0.5560 time to fit residues: 181.9755 Evaluate side-chains 270 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 514 SER 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 514 SER Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 168 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 overall best weight: 1.3004 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.137696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098089 restraints weight = 17377.832| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.99 r_work: 0.2878 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17530 Z= 0.173 Angle : 0.695 11.977 23885 Z= 0.344 Chirality : 0.049 0.334 2800 Planarity : 0.005 0.037 2890 Dihedral : 6.898 55.537 2740 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.89 % Allowed : 19.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.18), residues: 2040 helix: 3.10 (0.17), residues: 825 sheet: 1.57 (0.23), residues: 470 loop : -0.92 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 172 TYR 0.015 0.002 TYR B 245 PHE 0.010 0.001 PHE E 312 TRP 0.013 0.002 TRP C 494 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00389 (17505) covalent geometry : angle 0.67386 (23815) SS BOND : bond 0.00938 ( 5) SS BOND : angle 3.76673 ( 10) hydrogen bonds : bond 0.07408 ( 885) hydrogen bonds : angle 3.87645 ( 2925) link_BETA1-4 : bond 0.00506 ( 10) link_BETA1-4 : angle 1.94396 ( 30) link_NAG-ASN : bond 0.00484 ( 10) link_NAG-ASN : angle 3.91036 ( 30) *********************** 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 307 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 249 LEU cc_start: 0.7917 (mp) cc_final: 0.7205 (tp) REVERT: A 266 THR cc_start: 0.8480 (m) cc_final: 0.7938 (p) REVERT: A 291 MET cc_start: 0.7261 (mtp) cc_final: 0.6924 (mtp) REVERT: A 489 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 493 ASP cc_start: 0.7944 (m-30) cc_final: 0.7619 (m-30) REVERT: B 266 THR cc_start: 0.8490 (m) cc_final: 0.8033 (p) REVERT: B 291 MET cc_start: 0.7148 (mtp) cc_final: 0.6784 (mtp) REVERT: B 292 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6725 (mt) REVERT: B 349 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7742 (tppp) REVERT: B 493 ASP cc_start: 0.7988 (m-30) cc_final: 0.7747 (m-30) REVERT: C 23 ASP cc_start: 0.7929 (p0) cc_final: 0.7595 (p0) REVERT: C 40 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8873 (pttm) REVERT: C 47 ARG cc_start: 0.8035 (mpp-170) cc_final: 0.7519 (mtm180) REVERT: C 227 VAL cc_start: 0.8291 (m) cc_final: 0.7993 (m) REVERT: C 249 LEU cc_start: 0.7891 (mp) cc_final: 0.7226 (tp) REVERT: C 288 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7628 (mmm) REVERT: C 291 MET cc_start: 0.7267 (mtp) cc_final: 0.6868 (mtp) REVERT: C 292 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6505 (mt) REVERT: C 530 ASN cc_start: 0.7844 (t0) cc_final: 0.7637 (t0) REVERT: D 40 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8814 (pttm) REVERT: D 288 MET cc_start: 0.8063 (mtm) cc_final: 0.7758 (mmm) REVERT: D 291 MET cc_start: 0.7264 (mtp) cc_final: 0.6846 (mtp) REVERT: D 294 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.4270 (mmp) REVERT: D 353 ARG cc_start: 0.7674 (ptt180) cc_final: 0.7360 (ptt90) REVERT: D 489 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7034 (mt-10) REVERT: D 493 ASP cc_start: 0.7925 (m-30) cc_final: 0.7670 (m-30) REVERT: E 23 ASP cc_start: 0.7826 (p0) cc_final: 0.7607 (p0) REVERT: E 47 ARG cc_start: 0.7979 (mpp-170) cc_final: 0.7631 (mpp-170) REVERT: E 146 GLU cc_start: 0.8785 (tt0) cc_final: 0.8580 (tt0) REVERT: E 171 CYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6010 (m) REVERT: E 227 VAL cc_start: 0.8432 (m) cc_final: 0.8193 (m) REVERT: E 247 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8386 (mp) REVERT: E 288 MET cc_start: 0.7950 (mtm) cc_final: 0.7561 (mmm) REVERT: E 291 MET cc_start: 0.7207 (mtp) cc_final: 0.6798 (mtp) REVERT: E 292 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6504 (mt) REVERT: E 493 ASP cc_start: 0.8092 (m-30) cc_final: 0.7845 (m-30) outliers start: 73 outliers final: 31 residues processed: 275 average time/residue: 0.5433 time to fit residues: 167.1953 Evaluate side-chains 263 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 516 ILE Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain 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 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 516 ILE 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 171 CYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104641 restraints weight = 18322.970| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.79 r_work: 0.2897 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2372 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= 0.129 Angle : 0.618 9.725 23885 Z= 0.304 Chirality : 0.046 0.313 2800 Planarity : 0.004 0.038 2890 Dihedral : 6.642 56.987 2740 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.68 % Allowed : 19.84 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.18), residues: 2040 helix: 3.32 (0.17), residues: 825 sheet: 1.79 (0.25), residues: 425 loop : -0.81 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 104 TYR 0.011 0.001 TYR C 72 PHE 0.010 0.001 PHE E 312 TRP 0.011 0.001 TRP B 494 HIS 0.003 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00270 (17505) covalent geometry : angle 0.59755 (23815) SS BOND : bond 0.01058 ( 5) SS BOND : angle 3.48681 ( 10) hydrogen bonds : bond 0.06082 ( 885) hydrogen bonds : angle 3.63709 ( 2925) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.89900 ( 30) link_NAG-ASN : bond 0.00399 ( 10) link_NAG-ASN : angle 3.55889 ( 30) *********************** 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 301 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8118 (mpp-170) cc_final: 0.7905 (mtm180) REVERT: A 102 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8871 (mpp) REVERT: A 266 THR cc_start: 0.8515 (m) cc_final: 0.8003 (p) REVERT: A 288 MET cc_start: 0.7979 (mmm) cc_final: 0.7696 (mmm) REVERT: A 291 MET cc_start: 0.7217 (mtp) cc_final: 0.6890 (mtp) REVERT: B 102 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8842 (mpp) REVERT: B 203 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 291 MET cc_start: 0.7058 (mtp) cc_final: 0.6740 (mtp) REVERT: B 308 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 349 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7841 (tppp) REVERT: B 493 ASP cc_start: 0.8138 (m-30) cc_final: 0.7876 (m-30) REVERT: C 23 ASP cc_start: 0.7918 (p0) cc_final: 0.7532 (p0) REVERT: C 40 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8866 (pttm) REVERT: C 47 ARG cc_start: 0.8085 (mpp-170) cc_final: 0.7524 (mtm180) REVERT: C 104 ARG cc_start: 0.8609 (mtm110) cc_final: 0.8370 (mtm180) REVERT: C 227 VAL cc_start: 0.8317 (m) cc_final: 0.8021 (m) REVERT: C 288 MET cc_start: 0.8137 (ttm) cc_final: 0.7733 (mmm) REVERT: C 291 MET cc_start: 0.7190 (mtp) cc_final: 0.6821 (mtp) REVERT: C 493 ASP cc_start: 0.8023 (m-30) cc_final: 0.7746 (m-30) REVERT: D 40 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8812 (pttm) REVERT: D 203 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8296 (mp) REVERT: D 288 MET cc_start: 0.8104 (mtm) cc_final: 0.7827 (mmm) REVERT: D 291 MET cc_start: 0.7186 (mtp) cc_final: 0.6850 (mtp) REVERT: D 294 MET cc_start: 0.5474 (OUTLIER) cc_final: 0.4465 (mmp) REVERT: D 308 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8056 (mt) REVERT: D 346 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7260 (ptpt) REVERT: D 353 ARG cc_start: 0.7789 (ptt180) cc_final: 0.7506 (ptt90) REVERT: D 383 MET cc_start: 0.2452 (OUTLIER) cc_final: 0.1319 (mmt) REVERT: E 23 ASP cc_start: 0.7791 (p0) cc_final: 0.7549 (p0) REVERT: E 47 ARG cc_start: 0.8052 (mpp-170) cc_final: 0.7592 (mpp-170) REVERT: E 102 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8817 (mpp) REVERT: E 146 GLU cc_start: 0.8776 (tt0) cc_final: 0.8572 (tt0) REVERT: E 203 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8367 (mp) REVERT: E 227 VAL cc_start: 0.8449 (m) cc_final: 0.8176 (m) REVERT: E 291 MET cc_start: 0.6958 (mtp) cc_final: 0.6549 (mtm) REVERT: E 292 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6500 (mt) REVERT: E 493 ASP cc_start: 0.8235 (m-30) cc_final: 0.7971 (m-30) outliers start: 69 outliers final: 15 residues processed: 275 average time/residue: 0.5533 time to fit residues: 170.8104 Evaluate side-chains 250 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 A residue 170 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 40 LYS 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 D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 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 102 MET Chi-restraints excluded: chain E residue 203 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 202 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 271 HIS B 519 ASN C 519 ASN D 37 ASN D 519 ASN E 519 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.099210 restraints weight = 17315.268| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.00 r_work: 0.2882 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17530 Z= 0.166 Angle : 0.678 9.829 23885 Z= 0.333 Chirality : 0.047 0.285 2800 Planarity : 0.004 0.040 2890 Dihedral : 6.607 56.017 2740 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.37 % Allowed : 19.15 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.18), residues: 2040 helix: 3.36 (0.17), residues: 805 sheet: 1.56 (0.23), residues: 470 loop : -0.93 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 104 TYR 0.013 0.001 TYR C 72 PHE 0.012 0.001 PHE E 312 TRP 0.015 0.002 TRP D 494 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00371 (17505) covalent geometry : angle 0.66020 (23815) SS BOND : bond 0.01863 ( 5) SS BOND : angle 2.97302 ( 10) hydrogen bonds : bond 0.06868 ( 885) hydrogen bonds : angle 3.74971 ( 2925) link_BETA1-4 : bond 0.00489 ( 10) link_BETA1-4 : angle 2.11288 ( 30) link_NAG-ASN : bond 0.00375 ( 10) link_NAG-ASN : angle 3.48398 ( 30) *********************** 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 308 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 226 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.7815 (mp) cc_final: 0.7068 (tp) REVERT: A 266 THR cc_start: 0.8535 (m) cc_final: 0.7972 (p) REVERT: A 288 MET cc_start: 0.7930 (mmm) cc_final: 0.7693 (mmm) REVERT: A 291 MET cc_start: 0.7258 (mtp) cc_final: 0.6839 (mtp) REVERT: A 493 ASP cc_start: 0.7960 (m-30) cc_final: 0.7660 (m-30) REVERT: B 203 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 291 MET cc_start: 0.7078 (mtp) cc_final: 0.6744 (mtp) REVERT: B 308 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8148 (mt) REVERT: B 349 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7747 (tppp) REVERT: B 493 ASP cc_start: 0.7967 (m-30) cc_final: 0.7734 (m-30) REVERT: B 516 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 23 ASP cc_start: 0.7845 (p0) cc_final: 0.7485 (p0) REVERT: C 40 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8804 (pttm) REVERT: C 47 ARG cc_start: 0.8112 (mpp-170) cc_final: 0.7628 (mtm180) REVERT: C 104 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8253 (mtm180) REVERT: C 148 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8797 (tp) REVERT: C 227 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8017 (m) REVERT: C 288 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7642 (mmm) REVERT: C 291 MET cc_start: 0.7237 (mtp) cc_final: 0.6751 (mtp) REVERT: D 40 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8838 (pttm) REVERT: D 203 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8206 (mp) REVERT: D 288 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (mmm) REVERT: D 291 MET cc_start: 0.7180 (mtp) cc_final: 0.6855 (mtp) REVERT: D 294 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.4270 (mmp) REVERT: D 308 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8075 (mt) REVERT: D 353 ARG cc_start: 0.7664 (ptt180) cc_final: 0.7349 (ptt90) REVERT: D 383 MET cc_start: 0.2374 (OUTLIER) cc_final: 0.1286 (mmt) REVERT: E 23 ASP cc_start: 0.7736 (p0) cc_final: 0.7471 (p0) REVERT: E 47 ARG cc_start: 0.8139 (mpp-170) cc_final: 0.7714 (mpp-170) REVERT: E 102 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8751 (mpp) REVERT: E 146 GLU cc_start: 0.8761 (tt0) cc_final: 0.8546 (tt0) REVERT: E 203 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8299 (mp) REVERT: E 227 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (m) REVERT: E 291 MET cc_start: 0.7111 (mtp) cc_final: 0.6664 (mtm) REVERT: E 292 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6313 (mt) REVERT: E 493 ASP cc_start: 0.8073 (m-30) cc_final: 0.7826 (m-30) outliers start: 82 outliers final: 36 residues processed: 277 average time/residue: 0.5855 time to fit residues: 181.2808 Evaluate side-chains 271 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL 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 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 148 LEU 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 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 131 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098964 restraints weight = 17333.236| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.96 r_work: 0.2870 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17530 Z= 0.130 Angle : 0.622 9.633 23885 Z= 0.306 Chirality : 0.047 0.296 2800 Planarity : 0.004 0.040 2890 Dihedral : 6.525 55.774 2740 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.52 % Allowed : 19.79 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.19), residues: 2040 helix: 3.48 (0.17), residues: 805 sheet: 1.76 (0.25), residues: 425 loop : -0.83 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 240 TYR 0.011 0.001 TYR C 72 PHE 0.010 0.001 PHE E 312 TRP 0.012 0.001 TRP D 494 HIS 0.003 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00275 (17505) covalent geometry : angle 0.60454 (23815) SS BOND : bond 0.00902 ( 5) SS BOND : angle 2.71898 ( 10) hydrogen bonds : bond 0.05971 ( 885) hydrogen bonds : angle 3.61351 ( 2925) link_BETA1-4 : bond 0.00468 ( 10) link_BETA1-4 : angle 2.02581 ( 30) link_NAG-ASN : bond 0.00420 ( 10) link_NAG-ASN : angle 3.37827 ( 30) *********************** 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 291 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8807 (mpp) REVERT: A 291 MET cc_start: 0.7312 (mtp) cc_final: 0.6958 (mtp) REVERT: A 493 ASP cc_start: 0.7947 (m-30) cc_final: 0.7611 (m-30) REVERT: B 203 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 291 MET cc_start: 0.7071 (mtp) cc_final: 0.6691 (mtp) REVERT: B 349 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7716 (tppp) REVERT: B 493 ASP cc_start: 0.8020 (m-30) cc_final: 0.7733 (m-30) REVERT: B 516 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7390 (mp) REVERT: C 40 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8821 (pttm) REVERT: C 47 ARG cc_start: 0.8140 (mpp-170) cc_final: 0.7633 (mtm180) REVERT: C 203 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8271 (mp) REVERT: C 227 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 288 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: C 291 MET cc_start: 0.7208 (mtp) cc_final: 0.6785 (mtp) REVERT: C 493 ASP cc_start: 0.7901 (m-30) cc_final: 0.7637 (m-30) REVERT: D 36 GLU cc_start: 0.8143 (tt0) cc_final: 0.7774 (mt-10) REVERT: D 40 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8830 (pttm) REVERT: D 203 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (mp) REVERT: D 288 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: D 291 MET cc_start: 0.7135 (mtp) cc_final: 0.6743 (mtp) REVERT: D 294 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4410 (tmm) REVERT: D 308 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7986 (mt) REVERT: D 383 MET cc_start: 0.2554 (OUTLIER) cc_final: 0.1504 (mmt) REVERT: E 23 ASP cc_start: 0.7760 (p0) cc_final: 0.7446 (p0) REVERT: E 47 ARG cc_start: 0.8114 (mpp-170) cc_final: 0.7685 (mpp-170) REVERT: E 102 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8764 (mpp) REVERT: E 146 GLU cc_start: 0.8805 (tt0) cc_final: 0.8590 (tt0) REVERT: E 203 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8317 (mp) REVERT: E 227 VAL cc_start: 0.8395 (m) cc_final: 0.8136 (m) REVERT: E 291 MET cc_start: 0.7076 (mtp) cc_final: 0.6722 (mtp) REVERT: E 292 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6241 (mt) REVERT: E 493 ASP cc_start: 0.8039 (m-30) cc_final: 0.7762 (m-30) outliers start: 66 outliers final: 22 residues processed: 269 average time/residue: 0.5773 time to fit residues: 174.5377 Evaluate side-chains 259 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 294 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 40 LYS 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 288 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 18 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 519 ASN B 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099019 restraints weight = 17272.984| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.88 r_work: 0.2879 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17530 Z= 0.143 Angle : 0.653 17.038 23885 Z= 0.319 Chirality : 0.047 0.313 2800 Planarity : 0.004 0.040 2890 Dihedral : 6.494 55.396 2740 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.68 % Allowed : 19.47 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.19), residues: 2040 helix: 3.31 (0.17), residues: 825 sheet: 1.54 (0.24), residues: 470 loop : -0.75 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.015 0.001 TYR E 229 PHE 0.011 0.001 PHE E 312 TRP 0.011 0.001 TRP D 494 HIS 0.004 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00313 (17505) covalent geometry : angle 0.63658 (23815) SS BOND : bond 0.01044 ( 5) SS BOND : angle 2.80140 ( 10) hydrogen bonds : bond 0.06088 ( 885) hydrogen bonds : angle 3.62093 ( 2925) link_BETA1-4 : bond 0.00466 ( 10) link_BETA1-4 : angle 2.08726 ( 30) link_NAG-ASN : bond 0.00398 ( 10) link_NAG-ASN : angle 3.25550 ( 30) *********************** 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 298 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7828 (mmm) cc_final: 0.7477 (mmm) REVERT: A 291 MET cc_start: 0.7271 (mtp) cc_final: 0.6882 (mtp) REVERT: A 493 ASP cc_start: 0.7918 (m-30) cc_final: 0.7591 (m-30) REVERT: B 203 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 249 LEU cc_start: 0.7819 (mt) cc_final: 0.7425 (mt) REVERT: B 291 MET cc_start: 0.6980 (mtp) cc_final: 0.6590 (mtp) REVERT: B 349 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7847 (tppp) REVERT: B 493 ASP cc_start: 0.7968 (m-30) cc_final: 0.7689 (m-30) REVERT: C 40 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8804 (pttm) REVERT: C 47 ARG cc_start: 0.8114 (mpp-170) cc_final: 0.7639 (mtm180) REVERT: C 148 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 227 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 288 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: C 291 MET cc_start: 0.7201 (mtp) cc_final: 0.6779 (mtp) REVERT: C 294 MET cc_start: 0.5891 (tmm) cc_final: 0.5645 (tmm) REVERT: C 493 ASP cc_start: 0.7884 (m-30) cc_final: 0.7602 (m-30) REVERT: C 513 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: D 36 GLU cc_start: 0.8131 (tt0) cc_final: 0.7810 (mt-10) REVERT: D 40 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8831 (pttm) REVERT: D 203 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8188 (mp) REVERT: D 288 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: D 291 MET cc_start: 0.7086 (mtp) cc_final: 0.6810 (mtp) REVERT: D 294 MET cc_start: 0.5127 (OUTLIER) cc_final: 0.4538 (ttp) REVERT: D 308 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (mt) REVERT: D 383 MET cc_start: 0.2418 (OUTLIER) cc_final: 0.1385 (mmt) REVERT: E 23 ASP cc_start: 0.7734 (p0) cc_final: 0.7392 (p0) REVERT: E 47 ARG cc_start: 0.8146 (mpp-170) cc_final: 0.7709 (mpp-170) REVERT: E 102 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: E 146 GLU cc_start: 0.8779 (tt0) cc_final: 0.8562 (tt0) REVERT: E 203 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8285 (mp) REVERT: E 227 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8103 (m) REVERT: E 291 MET cc_start: 0.6942 (mtp) cc_final: 0.6614 (mtp) REVERT: E 493 ASP cc_start: 0.8039 (m-30) cc_final: 0.7770 (m-30) outliers start: 69 outliers final: 35 residues processed: 268 average time/residue: 0.5624 time to fit residues: 169.3757 Evaluate side-chains 272 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL 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 203 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 193 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 358 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 516 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS C 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099881 restraints weight = 17501.939| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.92 r_work: 0.2882 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2773 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= 0.125 Angle : 0.617 10.520 23885 Z= 0.301 Chirality : 0.046 0.282 2800 Planarity : 0.004 0.038 2890 Dihedral : 6.441 55.762 2740 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.31 % Allowed : 20.05 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 2040 helix: 3.41 (0.17), residues: 825 sheet: 1.71 (0.25), residues: 425 loop : -0.73 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 172 TYR 0.012 0.001 TYR C 72 PHE 0.010 0.001 PHE B 312 TRP 0.010 0.001 TRP D 494 HIS 0.003 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00264 (17505) covalent geometry : angle 0.60022 (23815) SS BOND : bond 0.00885 ( 5) SS BOND : angle 2.75294 ( 10) hydrogen bonds : bond 0.05667 ( 885) hydrogen bonds : angle 3.54378 ( 2925) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 2.04466 ( 30) link_NAG-ASN : bond 0.00417 ( 10) link_NAG-ASN : angle 3.14882 ( 30) *********************** 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 292 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8786 (mpp) REVERT: A 227 VAL cc_start: 0.8415 (m) cc_final: 0.8159 (m) REVERT: A 288 MET cc_start: 0.7796 (mmm) cc_final: 0.7420 (mmm) REVERT: A 291 MET cc_start: 0.7203 (mtp) cc_final: 0.6828 (mtp) REVERT: A 493 ASP cc_start: 0.7893 (m-30) cc_final: 0.7556 (m-30) REVERT: B 102 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8747 (mpp) REVERT: B 203 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8314 (mp) REVERT: B 291 MET cc_start: 0.7182 (mtp) cc_final: 0.6774 (mtp) REVERT: B 349 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8092 (ptmm) REVERT: B 493 ASP cc_start: 0.7963 (m-30) cc_final: 0.7676 (m-30) REVERT: C 40 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8860 (pttm) REVERT: C 47 ARG cc_start: 0.8100 (mpp-170) cc_final: 0.7623 (mtm180) REVERT: C 203 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 227 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8038 (m) REVERT: C 288 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7582 (mmm) REVERT: C 291 MET cc_start: 0.7139 (mtp) cc_final: 0.6752 (mtp) REVERT: C 493 ASP cc_start: 0.7875 (m-30) cc_final: 0.7614 (m-30) REVERT: C 513 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: D 36 GLU cc_start: 0.8108 (tt0) cc_final: 0.7788 (mt-10) REVERT: D 40 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8811 (pttm) REVERT: D 203 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8181 (mp) REVERT: D 288 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7722 (mmm) REVERT: D 291 MET cc_start: 0.7045 (mtp) cc_final: 0.6784 (mtp) REVERT: D 308 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (mt) REVERT: D 383 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.1383 (mmt) REVERT: E 23 ASP cc_start: 0.7682 (p0) cc_final: 0.7329 (p0) REVERT: E 47 ARG cc_start: 0.8158 (mpp-170) cc_final: 0.7805 (mpp-170) REVERT: E 102 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8728 (mpp) REVERT: E 146 GLU cc_start: 0.8783 (tt0) cc_final: 0.8567 (tt0) REVERT: E 203 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8266 (mp) REVERT: E 227 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8113 (m) REVERT: E 288 MET cc_start: 0.7963 (mtm) cc_final: 0.7392 (mmm) REVERT: E 291 MET cc_start: 0.6926 (mtp) cc_final: 0.6598 (mtp) REVERT: E 292 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6301 (mt) REVERT: E 493 ASP cc_start: 0.7970 (m-30) cc_final: 0.7707 (m-30) outliers start: 62 outliers final: 23 residues processed: 263 average time/residue: 0.5436 time to fit residues: 160.6655 Evaluate side-chains 264 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 513 PHE 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 266 THR Chi-restraints excluded: chain C residue 40 LYS 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 288 MET Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 519 ASN D 37 ASN E 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096001 restraints weight = 17328.772| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.73 r_work: 0.2834 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17530 Z= 0.203 Angle : 0.732 10.068 23885 Z= 0.361 Chirality : 0.050 0.320 2800 Planarity : 0.004 0.039 2890 Dihedral : 6.625 54.260 2740 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.15 % Allowed : 19.79 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.18), residues: 2040 helix: 3.23 (0.17), residues: 805 sheet: 1.63 (0.24), residues: 465 loop : -0.96 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.016 0.002 TYR E 229 PHE 0.012 0.001 PHE B 312 TRP 0.012 0.002 TRP D 494 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00479 (17505) covalent geometry : angle 0.71661 (23815) SS BOND : bond 0.01582 ( 5) SS BOND : angle 3.37834 ( 10) hydrogen bonds : bond 0.07278 ( 885) hydrogen bonds : angle 3.79067 ( 2925) link_BETA1-4 : bond 0.00525 ( 10) link_BETA1-4 : angle 2.35691 ( 30) link_NAG-ASN : bond 0.00331 ( 10) link_NAG-ASN : angle 3.03845 ( 30) *********************** 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 283 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7948 (mmm) cc_final: 0.7599 (mmm) REVERT: A 291 MET cc_start: 0.7434 (mtp) cc_final: 0.6997 (mtp) REVERT: A 489 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7387 (mt-10) REVERT: A 493 ASP cc_start: 0.8046 (m-30) cc_final: 0.7731 (m-30) REVERT: B 203 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 291 MET cc_start: 0.7314 (mtp) cc_final: 0.6946 (mtp) REVERT: B 349 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8146 (ptmm) REVERT: C 40 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8839 (pttm) REVERT: C 47 ARG cc_start: 0.8208 (mpp-170) cc_final: 0.7751 (mtm180) REVERT: C 288 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: C 291 MET cc_start: 0.7334 (mtp) cc_final: 0.6856 (mtp) REVERT: D 36 GLU cc_start: 0.8194 (tt0) cc_final: 0.7841 (mt-10) REVERT: D 203 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 247 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 288 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7773 (mmm) REVERT: D 291 MET cc_start: 0.7311 (mtp) cc_final: 0.6946 (mtp) REVERT: D 308 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8144 (mt) REVERT: D 493 ASP cc_start: 0.7692 (m-30) cc_final: 0.7403 (m-30) REVERT: E 47 ARG cc_start: 0.8239 (mpp-170) cc_final: 0.7908 (mpp-170) REVERT: E 146 GLU cc_start: 0.8815 (tt0) cc_final: 0.8599 (tt0) REVERT: E 203 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (mp) REVERT: E 291 MET cc_start: 0.7083 (mtp) cc_final: 0.6711 (mtp) outliers start: 59 outliers final: 34 residues processed: 255 average time/residue: 0.5748 time to fit residues: 163.9483 Evaluate side-chains 257 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 40 LYS 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 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 358 VAL 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 236 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 157 optimal weight: 0.0060 chunk 51 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS D 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098704 restraints weight = 17355.685| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.92 r_work: 0.2865 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2869 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= 0.137 Angle : 0.647 10.175 23885 Z= 0.317 Chirality : 0.047 0.282 2800 Planarity : 0.004 0.039 2890 Dihedral : 6.557 55.985 2740 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.51 % Allowed : 20.59 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 2040 helix: 3.40 (0.17), residues: 805 sheet: 1.55 (0.24), residues: 470 loop : -0.84 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.014 0.001 TYR E 229 PHE 0.010 0.001 PHE B 312 TRP 0.010 0.001 TRP B 494 HIS 0.004 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00297 (17505) covalent geometry : angle 0.63085 (23815) SS BOND : bond 0.00926 ( 5) SS BOND : angle 3.04329 ( 10) hydrogen bonds : bond 0.06131 ( 885) hydrogen bonds : angle 3.63016 ( 2925) link_BETA1-4 : bond 0.00471 ( 10) link_BETA1-4 : angle 2.14402 ( 30) link_NAG-ASN : bond 0.00411 ( 10) link_NAG-ASN : angle 3.08957 ( 30) ********************** 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 268 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8458 (m) cc_final: 0.8226 (m) REVERT: A 288 MET cc_start: 0.7880 (mmm) cc_final: 0.7505 (mmm) REVERT: A 291 MET cc_start: 0.7363 (mtp) cc_final: 0.6970 (mtp) REVERT: A 493 ASP cc_start: 0.7968 (m-30) cc_final: 0.7612 (m-30) REVERT: B 203 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 291 MET cc_start: 0.7307 (mtp) cc_final: 0.6939 (mtp) REVERT: B 349 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8102 (ptmm) REVERT: B 383 MET cc_start: 0.2410 (mmp) cc_final: 0.1434 (ptt) REVERT: B 493 ASP cc_start: 0.8014 (m-30) cc_final: 0.7755 (m-30) REVERT: C 40 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8802 (pttm) REVERT: C 47 ARG cc_start: 0.8107 (mpp-170) cc_final: 0.7655 (mtm180) REVERT: C 227 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8085 (m) REVERT: C 288 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: C 291 MET cc_start: 0.7240 (mtp) cc_final: 0.6787 (mtp) REVERT: C 493 ASP cc_start: 0.7948 (m-30) cc_final: 0.7707 (m-30) REVERT: D 36 GLU cc_start: 0.8147 (tt0) cc_final: 0.7811 (mt-10) REVERT: D 40 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8821 (pttm) REVERT: D 203 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (mp) REVERT: D 288 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7728 (mmm) REVERT: D 291 MET cc_start: 0.7264 (mtp) cc_final: 0.6899 (mtp) REVERT: D 294 MET cc_start: 0.5844 (tmm) cc_final: 0.5509 (tmm) REVERT: D 308 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7980 (mt) REVERT: E 47 ARG cc_start: 0.8137 (mpp-170) cc_final: 0.7758 (mpp-170) REVERT: E 102 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8792 (mpp) REVERT: E 146 GLU cc_start: 0.8817 (tt0) cc_final: 0.8605 (tt0) REVERT: E 203 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (mp) REVERT: E 227 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8177 (m) REVERT: E 291 MET cc_start: 0.7027 (mtp) cc_final: 0.6675 (mtp) REVERT: E 493 ASP cc_start: 0.8093 (m-30) cc_final: 0.7832 (m-30) outliers start: 47 outliers final: 26 residues processed: 246 average time/residue: 0.5849 time to fit residues: 160.6060 Evaluate side-chains 254 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 40 LYS 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 236 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 358 VAL 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 288 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 271 HIS D 37 ASN E 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099654 restraints weight = 17410.559| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.93 r_work: 0.2886 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2898 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= 0.138 Angle : 0.645 9.625 23885 Z= 0.316 Chirality : 0.047 0.260 2800 Planarity : 0.004 0.040 2890 Dihedral : 6.506 55.309 2740 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 20.53 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 2040 helix: 3.44 (0.17), residues: 805 sheet: 1.53 (0.24), residues: 470 loop : -0.83 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.012 0.001 TYR C 72 PHE 0.012 0.001 PHE B 312 TRP 0.012 0.001 TRP B 494 HIS 0.004 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00300 (17505) covalent geometry : angle 0.63096 (23815) SS BOND : bond 0.00969 ( 5) SS BOND : angle 2.76562 ( 10) hydrogen bonds : bond 0.06067 ( 885) hydrogen bonds : angle 3.61104 ( 2925) link_BETA1-4 : bond 0.00507 ( 10) link_BETA1-4 : angle 2.14168 ( 30) link_NAG-ASN : bond 0.00397 ( 10) link_NAG-ASN : angle 2.91117 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6729.05 seconds wall clock time: 115 minutes 6.95 seconds (6906.95 seconds total)