Starting phenix.real_space_refine on Sun Jul 5 08:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzp_45073/07_2026/9bzp_45073.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14692 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 100 5.16 5 C 9705 2.51 5 N 2320 2.21 5 O 2675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14805 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} 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: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 104 Unusual residues: {' ZN': 1, 'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 118 Unusual residues: {' ZN': 1, 'PIO': 5, 'PX4': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 5} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {' ZN': 1, 'PIO': 5, 'PX4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 3} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 118 Unusual residues: {' ZN': 1, 'PIO': 5, 'PX4': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 5} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {' ZN': 1, 'PIO': 5, 'PX4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PX4:plan-1': 3, 'PIO:plan-2': 5} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.19 Number of scatterers: 14805 At special positions: 0 Unit cell: (100.3, 99.45, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 100 16.00 O 2675 8.00 N 2320 7.00 C 9705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.04 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-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 626.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 427 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 215 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 427 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 215 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 427 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 215 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 427 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 215 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 427 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 215 " 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 39.2% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.781A pdb=" N PHE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.319A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.887A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.755A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.586A pdb=" N ILE A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.743A pdb=" N ILE A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 419 " --> pdb=" O TRP A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.781A pdb=" N PHE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 4.318A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.886A pdb=" N SER B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.755A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.586A pdb=" N ILE B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 3.743A pdb=" N ILE B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 419 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.781A pdb=" N PHE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 4.318A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.887A pdb=" N SER C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.755A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.585A pdb=" N ILE C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.742A pdb=" N ILE C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 419 " --> pdb=" O TRP C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.781A pdb=" N PHE D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 4.318A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.887A pdb=" N SER D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.755A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.586A pdb=" N ILE D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix removed outlier: 3.742A pdb=" N ILE D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 419 " --> pdb=" O TRP D 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 removed outlier: 3.781A pdb=" N PHE E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 93 removed outlier: 4.319A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.887A pdb=" N SER E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.756A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.585A pdb=" N ILE E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix removed outlier: 3.742A pdb=" N ILE E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS E 419 " --> pdb=" O TRP E 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.260A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.579A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 200 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS A 198 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 196 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.260A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.579A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 200 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 198 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 211 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 196 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.261A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.579A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 198 " --> pdb=" O CYS C 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.261A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.579A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 200 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 198 " --> pdb=" O CYS D 209 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.260A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.579A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.247A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 200 " --> pdb=" O PHE E 207 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS E 198 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E 211 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 196 " --> pdb=" O GLU E 211 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2963 1.33 - 1.46: 3827 1.46 - 1.58: 7915 1.58 - 1.71: 235 1.71 - 1.83: 165 Bond restraints: 15105 Sorted by residual: bond pdb=" C23 PX4 D 507 " pdb=" O7 PX4 D 507 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C23 PX4 B 510 " pdb=" O7 PX4 B 510 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C23 PX4 D 510 " pdb=" O7 PX4 D 510 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C23 PX4 B 507 " pdb=" O7 PX4 B 507 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C23 PX4 D 512 " pdb=" O7 PX4 D 512 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.73e+01 ... (remaining 15100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19193 1.93 - 3.85: 830 3.85 - 5.78: 232 5.78 - 7.70: 31 7.70 - 9.63: 34 Bond angle restraints: 20320 Sorted by residual: angle pdb=" N LYS C 419 " pdb=" CA LYS C 419 " pdb=" C LYS C 419 " ideal model delta sigma weight residual 113.41 105.66 7.75 1.22e+00 6.72e-01 4.04e+01 angle pdb=" N LYS B 419 " pdb=" CA LYS B 419 " pdb=" C LYS B 419 " ideal model delta sigma weight residual 113.41 105.67 7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N LYS A 419 " pdb=" CA LYS A 419 " pdb=" C LYS A 419 " ideal model delta sigma weight residual 113.41 105.68 7.73 1.22e+00 6.72e-01 4.01e+01 angle pdb=" N LYS D 419 " pdb=" CA LYS D 419 " pdb=" C LYS D 419 " ideal model delta sigma weight residual 113.41 105.70 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N LYS E 419 " pdb=" CA LYS E 419 " pdb=" C LYS E 419 " ideal model delta sigma weight residual 113.41 105.72 7.69 1.22e+00 6.72e-01 3.97e+01 ... (remaining 20315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8389 17.35 - 34.71: 623 34.71 - 52.06: 128 52.06 - 69.41: 30 69.41 - 86.77: 15 Dihedral angle restraints: 9185 sinusoidal: 4050 harmonic: 5135 Sorted by residual: dihedral pdb=" CA GLU A 110 " pdb=" C GLU A 110 " pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU E 110 " pdb=" C GLU E 110 " pdb=" N VAL E 111 " pdb=" CA VAL E 111 " ideal model delta harmonic sigma weight residual -180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU C 110 " pdb=" C GLU C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1900 0.065 - 0.130: 282 0.130 - 0.196: 53 0.196 - 0.261: 5 0.261 - 0.326: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA ILE D 420 " pdb=" N ILE D 420 " pdb=" C ILE D 420 " pdb=" CB ILE D 420 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ILE C 420 " pdb=" N ILE C 420 " pdb=" C ILE C 420 " pdb=" CB ILE C 420 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ILE E 420 " pdb=" N ILE E 420 " pdb=" C ILE E 420 " pdb=" CB ILE E 420 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2242 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 86 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO B 87 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 86 " 0.080 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO C 87 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO E 87 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " -0.065 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 301 2.70 - 3.25: 13551 3.25 - 3.80: 21792 3.80 - 4.35: 29292 4.35 - 4.90: 49331 Nonbonded interactions: 114267 Sorted by model distance: nonbonded pdb=" OD2 ASP E 194 " pdb="ZN ZN E 502 " model vdw 2.152 2.230 nonbonded pdb=" OD2 ASP D 194 " pdb="ZN ZN D 502 " model vdw 2.152 2.230 nonbonded pdb=" OD2 ASP A 194 " pdb="ZN ZN A 502 " model vdw 2.152 2.230 nonbonded pdb=" OD2 ASP C 194 " pdb="ZN ZN C 502 " model vdw 2.152 2.230 nonbonded pdb=" OD2 ASP B 194 " pdb="ZN ZN B 502 " model vdw 2.152 2.230 ... (remaining 114262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 502 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'B' and (resid 8 through 502 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'C' and (resid 8 through 502 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'D' and (resid 8 through 502 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)))) selection = (chain 'E' and (resid 8 through 502 or resid 506)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.013 0.255 15130 Z= 0.636 Angle : 1.016 9.626 20360 Z= 0.505 Chirality : 0.052 0.326 2245 Planarity : 0.008 0.122 2520 Dihedral : 13.341 86.767 5830 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1710 helix: 0.91 (0.21), residues: 600 sheet: 0.85 (0.25), residues: 390 loop : -0.91 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 29 TYR 0.015 0.001 TYR E 301 PHE 0.014 0.001 PHE C 407 TRP 0.030 0.002 TRP C 415 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.62 (15105) covalent geometry : angle 1.01293 / 0.50 (20320) SS BOND : bond 0.00671 / 0.36 ( 5) SS BOND : angle 3.94936 / 2.06 ( 10) hydrogen bonds : bond 0.19825 / 13.03 ( 675) hydrogen bonds : angle 6.77497 / 4.75 ( 2385) metal coordination : bond 0.17981 / 9.95 ( 10) link_BETA1-4 : bond 0.00201 / 0.11 ( 5) link_BETA1-4 : angle 0.94604 / 0.57 ( 15) link_NAG-ASN : bond 0.00033 / 0.02 ( 5) link_NAG-ASN : angle 0.86971 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.379 Fit side-chains REVERT: A 121 PHE cc_start: 0.7616 (m-10) cc_final: 0.7234 (m-10) REVERT: B 121 PHE cc_start: 0.7686 (m-10) cc_final: 0.7398 (m-10) REVERT: C 121 PHE cc_start: 0.7731 (m-10) cc_final: 0.7470 (m-10) REVERT: C 163 MET cc_start: 0.7911 (mmt) cc_final: 0.7609 (mmm) REVERT: D 121 PHE cc_start: 0.7505 (m-10) cc_final: 0.7198 (m-80) REVERT: E 121 PHE cc_start: 0.7600 (m-10) cc_final: 0.7297 (m-10) outliers start: 0 outliers final: 2 residues processed: 148 average time/residue: 0.4268 time to fit residues: 71.5181 Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN C 144 ASN D 144 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077567 restraints weight = 29553.664| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.30 r_work: 0.3075 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15130 Z= 0.126 Angle : 0.575 6.328 20360 Z= 0.295 Chirality : 0.042 0.138 2245 Planarity : 0.005 0.064 2520 Dihedral : 9.784 60.236 2434 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.34 % Allowed : 7.96 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1710 helix: 2.03 (0.21), residues: 575 sheet: 1.45 (0.25), residues: 380 loop : -0.37 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.015 0.001 TYR A 301 PHE 0.014 0.001 PHE D 13 TRP 0.011 0.001 TRP E 68 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (15105) covalent geometry : angle 0.57219 / 0.29 (20320) SS BOND : bond 0.00325 / 0.17 ( 5) SS BOND : angle 2.09335 / 1.09 ( 10) hydrogen bonds : bond 0.05407 / 3.61 ( 675) hydrogen bonds : angle 4.95471 / 3.49 ( 2385) metal coordination : bond 0.01692 / 0.95 ( 10) link_BETA1-4 : bond 0.00467 / 0.25 ( 5) link_BETA1-4 : angle 1.49359 / 0.97 ( 15) link_NAG-ASN : bond 0.00025 / 0.01 ( 5) link_NAG-ASN : angle 0.59536 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.575 Fit side-chains REVERT: A 8 MET cc_start: 0.6134 (pp-130) cc_final: 0.5803 (ppp) REVERT: A 121 PHE cc_start: 0.8195 (m-10) cc_final: 0.7741 (m-10) REVERT: B 121 PHE cc_start: 0.8268 (m-10) cc_final: 0.7926 (m-10) REVERT: C 121 PHE cc_start: 0.8270 (m-10) cc_final: 0.7897 (m-10) REVERT: C 186 GLN cc_start: 0.8145 (tt0) cc_final: 0.7874 (tt0) REVERT: D 121 PHE cc_start: 0.8061 (m-10) cc_final: 0.7694 (m-10) REVERT: D 227 MET cc_start: 0.7935 (mtt) cc_final: 0.7721 (mtt) REVERT: E 121 PHE cc_start: 0.8163 (m-10) cc_final: 0.7838 (m-10) outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 0.4854 time to fit residues: 70.5479 Evaluate side-chains 131 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 162 optimal weight: 0.0270 chunk 134 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 171 GLN A 186 GLN C 144 ASN D 144 ASN D 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072256 restraints weight = 29626.566| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.25 r_work: 0.2981 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15130 Z= 0.149 Angle : 0.559 7.371 20360 Z= 0.289 Chirality : 0.042 0.132 2245 Planarity : 0.004 0.052 2520 Dihedral : 8.363 58.090 2430 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.42 % Allowed : 8.09 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1710 helix: 2.19 (0.21), residues: 580 sheet: 1.58 (0.25), residues: 380 loop : -0.41 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.020 0.002 TYR A 301 PHE 0.012 0.001 PHE C 13 TRP 0.012 0.001 TRP D 68 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15105) covalent geometry : angle 0.55594 / 0.29 (20320) SS BOND : bond 0.00330 / 0.18 ( 5) SS BOND : angle 1.87244 / 0.97 ( 10) hydrogen bonds : bond 0.05301 / 3.54 ( 675) hydrogen bonds : angle 4.63443 / 3.26 ( 2385) metal coordination : bond 0.00420 / 0.24 ( 10) link_BETA1-4 : bond 0.00237 / 0.13 ( 5) link_BETA1-4 : angle 1.44091 / 0.96 ( 15) link_NAG-ASN : bond 0.00243 / 0.13 ( 5) link_NAG-ASN : angle 0.83954 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.576 Fit side-chains REVERT: A 121 PHE cc_start: 0.8238 (m-10) cc_final: 0.7855 (m-10) REVERT: A 171 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: A 220 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8335 (ttp) REVERT: B 121 PHE cc_start: 0.8290 (m-10) cc_final: 0.7939 (m-10) REVERT: C 121 PHE cc_start: 0.8285 (m-10) cc_final: 0.7908 (m-10) REVERT: D 56 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7560 (mpt) REVERT: D 121 PHE cc_start: 0.8141 (m-10) cc_final: 0.7745 (m-10) REVERT: E 121 PHE cc_start: 0.8202 (m-10) cc_final: 0.7857 (m-10) outliers start: 38 outliers final: 14 residues processed: 140 average time/residue: 0.4512 time to fit residues: 70.8086 Evaluate side-chains 131 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072546 restraints weight = 29903.859| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.27 r_work: 0.2996 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15130 Z= 0.138 Angle : 0.617 15.486 20360 Z= 0.309 Chirality : 0.042 0.146 2245 Planarity : 0.004 0.042 2520 Dihedral : 7.908 59.262 2430 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.29 % Allowed : 9.43 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1710 helix: 2.31 (0.22), residues: 580 sheet: 1.29 (0.25), residues: 425 loop : -0.24 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.018 0.001 TYR A 301 PHE 0.014 0.001 PHE D 99 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15105) covalent geometry : angle 0.59506 / 0.30 (20320) SS BOND : bond 0.01213 / 0.64 ( 5) SS BOND : angle 7.23998 / 3.75 ( 10) hydrogen bonds : bond 0.04772 / 3.20 ( 675) hydrogen bonds : angle 4.36441 / 2.98 ( 2385) metal coordination : bond 0.00137 / 0.08 ( 10) link_BETA1-4 : bond 0.00321 / 0.17 ( 5) link_BETA1-4 : angle 1.36040 / 0.89 ( 15) link_NAG-ASN : bond 0.00087 / 0.05 ( 5) link_NAG-ASN : angle 0.61132 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.539 Fit side-chains REVERT: A 8 MET cc_start: 0.6213 (pp-130) cc_final: 0.5947 (ppp) REVERT: A 78 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.7045 (t80) REVERT: A 121 PHE cc_start: 0.8230 (m-10) cc_final: 0.7863 (m-10) REVERT: A 220 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (ttp) REVERT: B 121 PHE cc_start: 0.8297 (m-10) cc_final: 0.7953 (m-10) REVERT: C 78 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: C 121 PHE cc_start: 0.8290 (m-10) cc_final: 0.7944 (m-10) REVERT: D 56 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7671 (mpt) REVERT: D 121 PHE cc_start: 0.8210 (m-10) cc_final: 0.7812 (m-10) REVERT: E 121 PHE cc_start: 0.8207 (m-10) cc_final: 0.7865 (m-10) outliers start: 36 outliers final: 16 residues processed: 130 average time/residue: 0.4876 time to fit residues: 70.6179 Evaluate side-chains 136 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 138 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN D 171 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071035 restraints weight = 29712.736| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.25 r_work: 0.2957 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15130 Z= 0.153 Angle : 0.596 13.696 20360 Z= 0.302 Chirality : 0.042 0.135 2245 Planarity : 0.004 0.038 2520 Dihedral : 7.438 59.519 2430 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.06 % Allowed : 10.38 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1710 helix: 2.33 (0.21), residues: 580 sheet: 1.38 (0.26), residues: 400 loop : -0.35 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.019 0.001 TYR B 301 PHE 0.013 0.001 PHE D 99 TRP 0.009 0.001 TRP A 68 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15105) covalent geometry : angle 0.58064 / 0.29 (20320) SS BOND : bond 0.00751 / 0.41 ( 5) SS BOND : angle 5.95403 / 3.09 ( 10) hydrogen bonds : bond 0.04865 / 3.26 ( 675) hydrogen bonds : angle 4.36056 / 2.97 ( 2385) metal coordination : bond 0.00138 / 0.09 ( 10) link_BETA1-4 : bond 0.00258 / 0.14 ( 5) link_BETA1-4 : angle 1.30743 / 0.87 ( 15) link_NAG-ASN : bond 0.00212 / 0.11 ( 5) link_NAG-ASN : angle 0.76587 / 0.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.394 Fit side-chains REVERT: A 8 MET cc_start: 0.6213 (pp-130) cc_final: 0.5937 (ppp) REVERT: A 78 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.7049 (t80) REVERT: A 121 PHE cc_start: 0.8243 (m-10) cc_final: 0.7927 (m-10) REVERT: B 8 MET cc_start: 0.7072 (ppp) cc_final: 0.6803 (pmm) REVERT: B 121 PHE cc_start: 0.8284 (m-10) cc_final: 0.7956 (m-10) REVERT: C 78 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: C 121 PHE cc_start: 0.8331 (m-10) cc_final: 0.7992 (m-10) REVERT: D 56 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7701 (mpt) REVERT: D 121 PHE cc_start: 0.8209 (m-10) cc_final: 0.7833 (m-10) REVERT: E 121 PHE cc_start: 0.8197 (m-10) cc_final: 0.7860 (m-10) outliers start: 48 outliers final: 22 residues processed: 141 average time/residue: 0.4755 time to fit residues: 74.5470 Evaluate side-chains 137 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 130 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN D 171 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070708 restraints weight = 29795.873| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.24 r_work: 0.2952 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15130 Z= 0.152 Angle : 0.588 13.398 20360 Z= 0.296 Chirality : 0.042 0.137 2245 Planarity : 0.003 0.033 2520 Dihedral : 7.245 58.752 2430 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.93 % Allowed : 11.27 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1710 helix: 2.36 (0.21), residues: 580 sheet: 1.25 (0.26), residues: 410 loop : -0.34 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.019 0.001 TYR B 301 PHE 0.013 0.001 PHE A 99 TRP 0.009 0.001 TRP A 68 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15105) covalent geometry : angle 0.57513 / 0.29 (20320) SS BOND : bond 0.00559 / 0.31 ( 5) SS BOND : angle 5.34345 / 2.79 ( 10) hydrogen bonds : bond 0.04810 / 3.23 ( 675) hydrogen bonds : angle 4.31650 / 2.94 ( 2385) metal coordination : bond 0.00141 / 0.09 ( 10) link_BETA1-4 : bond 0.00290 / 0.16 ( 5) link_BETA1-4 : angle 1.25983 / 0.83 ( 15) link_NAG-ASN : bond 0.00160 / 0.08 ( 5) link_NAG-ASN : angle 0.71215 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.553 Fit side-chains REVERT: A 121 PHE cc_start: 0.8263 (m-10) cc_final: 0.7912 (m-10) REVERT: B 8 MET cc_start: 0.7001 (ppp) cc_final: 0.6727 (pmm) REVERT: B 121 PHE cc_start: 0.8275 (m-10) cc_final: 0.7970 (m-10) REVERT: C 78 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: C 121 PHE cc_start: 0.8313 (m-10) cc_final: 0.7969 (m-10) REVERT: D 56 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7722 (mpt) REVERT: D 121 PHE cc_start: 0.8207 (m-10) cc_final: 0.7830 (m-10) REVERT: E 8 MET cc_start: 0.7058 (ppp) cc_final: 0.6679 (pmm) REVERT: E 121 PHE cc_start: 0.8180 (m-10) cc_final: 0.7858 (m-10) outliers start: 46 outliers final: 28 residues processed: 136 average time/residue: 0.4847 time to fit residues: 73.4706 Evaluate side-chains 141 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN C 177 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072715 restraints weight = 29434.138| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.25 r_work: 0.2997 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15130 Z= 0.107 Angle : 0.544 12.271 20360 Z= 0.272 Chirality : 0.041 0.146 2245 Planarity : 0.003 0.034 2520 Dihedral : 6.446 58.248 2430 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.80 % Allowed : 11.91 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1710 helix: 2.39 (0.21), residues: 580 sheet: 1.13 (0.25), residues: 425 loop : -0.15 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.018 0.001 TYR D 301 PHE 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP A 68 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15105) covalent geometry : angle 0.53294 / 0.27 (20320) SS BOND : bond 0.00493 / 0.27 ( 5) SS BOND : angle 4.72775 / 2.48 ( 10) hydrogen bonds : bond 0.04018 / 2.70 ( 675) hydrogen bonds : angle 4.04934 / 2.76 ( 2385) metal coordination : bond 0.00053 / 0.03 ( 10) link_BETA1-4 : bond 0.00370 / 0.20 ( 5) link_BETA1-4 : angle 1.22179 / 0.80 ( 15) link_NAG-ASN : bond 0.00123 / 0.07 ( 5) link_NAG-ASN : angle 0.42146 / 0.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.538 Fit side-chains REVERT: A 121 PHE cc_start: 0.8233 (m-10) cc_final: 0.7906 (m-10) REVERT: B 121 PHE cc_start: 0.8263 (m-10) cc_final: 0.7926 (m-10) REVERT: B 171 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8261 (mm-40) REVERT: C 78 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: C 121 PHE cc_start: 0.8293 (m-10) cc_final: 0.7959 (m-10) REVERT: D 8 MET cc_start: 0.6509 (pmm) cc_final: 0.6281 (pmm) REVERT: D 103 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: D 121 PHE cc_start: 0.8200 (m-10) cc_final: 0.7846 (m-10) REVERT: E 121 PHE cc_start: 0.8198 (m-10) cc_final: 0.7870 (m-10) outliers start: 44 outliers final: 26 residues processed: 142 average time/residue: 0.4779 time to fit residues: 75.9977 Evaluate side-chains 148 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 153 optimal weight: 0.0370 chunk 162 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN C 177 GLN D 171 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072097 restraints weight = 29561.646| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.25 r_work: 0.2983 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15130 Z= 0.122 Angle : 0.557 12.408 20360 Z= 0.277 Chirality : 0.041 0.139 2245 Planarity : 0.003 0.035 2520 Dihedral : 6.323 57.724 2430 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.68 % Allowed : 12.61 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1710 helix: 2.41 (0.21), residues: 580 sheet: 1.24 (0.26), residues: 405 loop : -0.27 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.019 0.001 TYR D 301 PHE 0.012 0.001 PHE D 99 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15105) covalent geometry : angle 0.54672 / 0.27 (20320) SS BOND : bond 0.00467 / 0.26 ( 5) SS BOND : angle 4.69441 / 2.46 ( 10) hydrogen bonds : bond 0.04152 / 2.79 ( 675) hydrogen bonds : angle 4.04754 / 2.76 ( 2385) metal coordination : bond 0.00105 / 0.07 ( 10) link_BETA1-4 : bond 0.00319 / 0.17 ( 5) link_BETA1-4 : angle 1.22266 / 0.80 ( 15) link_NAG-ASN : bond 0.00020 / 0.01 ( 5) link_NAG-ASN : angle 0.57434 / 0.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.576 Fit side-chains REVERT: A 121 PHE cc_start: 0.8276 (m-10) cc_final: 0.7925 (m-10) REVERT: B 121 PHE cc_start: 0.8304 (m-10) cc_final: 0.7970 (m-10) REVERT: B 171 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 78 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: C 121 PHE cc_start: 0.8289 (m-10) cc_final: 0.7949 (m-10) REVERT: D 8 MET cc_start: 0.6525 (pmm) cc_final: 0.6313 (pmm) REVERT: D 121 PHE cc_start: 0.8216 (m-10) cc_final: 0.7862 (m-10) REVERT: E 8 MET cc_start: 0.7102 (ppp) cc_final: 0.6601 (pmm) REVERT: E 121 PHE cc_start: 0.8195 (m-10) cc_final: 0.7864 (m-10) outliers start: 42 outliers final: 26 residues processed: 138 average time/residue: 0.4681 time to fit residues: 72.0385 Evaluate side-chains 145 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN C 171 GLN C 177 GLN D 171 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071835 restraints weight = 29683.201| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.23 r_work: 0.2978 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15130 Z= 0.122 Angle : 0.567 12.069 20360 Z= 0.281 Chirality : 0.041 0.139 2245 Planarity : 0.003 0.036 2520 Dihedral : 6.118 57.759 2430 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.48 % Allowed : 12.80 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1710 helix: 2.42 (0.21), residues: 580 sheet: 1.19 (0.26), residues: 405 loop : -0.25 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.019 0.001 TYR D 301 PHE 0.013 0.001 PHE D 99 TRP 0.008 0.001 TRP A 68 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (15105) covalent geometry : angle 0.55710 / 0.28 (20320) SS BOND : bond 0.00454 / 0.25 ( 5) SS BOND : angle 4.60043 / 2.41 ( 10) hydrogen bonds : bond 0.04204 / 2.82 ( 675) hydrogen bonds : angle 4.04303 / 2.76 ( 2385) metal coordination : bond 0.00106 / 0.07 ( 10) link_BETA1-4 : bond 0.00294 / 0.16 ( 5) link_BETA1-4 : angle 1.18149 / 0.78 ( 15) link_NAG-ASN : bond 0.00049 / 0.03 ( 5) link_NAG-ASN : angle 0.60549 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.363 Fit side-chains REVERT: A 121 PHE cc_start: 0.8320 (m-10) cc_final: 0.7976 (m-10) REVERT: B 121 PHE cc_start: 0.8320 (m-10) cc_final: 0.7992 (m-10) REVERT: B 171 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8279 (mm-40) REVERT: C 8 MET cc_start: 0.7019 (ppp) cc_final: 0.6641 (ptp) REVERT: C 78 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: C 121 PHE cc_start: 0.8303 (m-10) cc_final: 0.7966 (m-10) REVERT: D 121 PHE cc_start: 0.8224 (m-10) cc_final: 0.7880 (m-10) REVERT: E 8 MET cc_start: 0.7066 (ppp) cc_final: 0.6582 (pmm) REVERT: E 121 PHE cc_start: 0.8207 (m-10) cc_final: 0.7896 (m-10) outliers start: 39 outliers final: 24 residues processed: 142 average time/residue: 0.4699 time to fit residues: 74.5379 Evaluate side-chains 147 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 1 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN C 177 GLN D 171 GLN D 177 GLN E 171 GLN E 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.070012 restraints weight = 30812.374| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.35 r_work: 0.2921 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15130 Z= 0.173 Angle : 0.604 12.330 20360 Z= 0.304 Chirality : 0.042 0.149 2245 Planarity : 0.004 0.035 2520 Dihedral : 6.441 57.952 2430 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.23 % Allowed : 13.12 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1710 helix: 2.40 (0.22), residues: 580 sheet: 0.96 (0.25), residues: 425 loop : -0.29 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.020 0.001 TYR B 301 PHE 0.015 0.001 PHE D 99 TRP 0.009 0.001 TRP C 170 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (15105) covalent geometry : angle 0.59360 / 0.30 (20320) SS BOND : bond 0.00449 / 0.25 ( 5) SS BOND : angle 4.80210 / 2.51 ( 10) hydrogen bonds : bond 0.04922 / 3.31 ( 675) hydrogen bonds : angle 4.27289 / 2.92 ( 2385) metal coordination : bond 0.00180 / 0.11 ( 10) link_BETA1-4 : bond 0.00245 / 0.13 ( 5) link_BETA1-4 : angle 1.16177 / 0.77 ( 15) link_NAG-ASN : bond 0.00304 / 0.16 ( 5) link_NAG-ASN : angle 0.89088 / 0.55 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.597 Fit side-chains REVERT: A 121 PHE cc_start: 0.8326 (m-10) cc_final: 0.7976 (m-10) REVERT: B 121 PHE cc_start: 0.8354 (m-10) cc_final: 0.7982 (m-10) REVERT: B 171 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8314 (mm-40) REVERT: C 8 MET cc_start: 0.6772 (ppp) cc_final: 0.6390 (ptp) REVERT: C 78 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: C 121 PHE cc_start: 0.8278 (m-10) cc_final: 0.7938 (m-10) REVERT: D 121 PHE cc_start: 0.8233 (m-10) cc_final: 0.7889 (m-10) REVERT: E 8 MET cc_start: 0.6973 (ppp) cc_final: 0.6609 (pmm) REVERT: E 121 PHE cc_start: 0.8213 (m-10) cc_final: 0.7895 (m-10) outliers start: 35 outliers final: 24 residues processed: 131 average time/residue: 0.4963 time to fit residues: 72.5807 Evaluate side-chains 140 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 114 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN C 177 GLN D 171 GLN D 177 GLN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.070725 restraints weight = 30495.789| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.28 r_work: 0.2957 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15130 Z= 0.120 Angle : 0.573 12.008 20360 Z= 0.286 Chirality : 0.041 0.142 2245 Planarity : 0.003 0.036 2520 Dihedral : 6.156 57.369 2430 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.10 % Allowed : 13.38 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1710 helix: 2.42 (0.21), residues: 580 sheet: 1.02 (0.26), residues: 425 loop : -0.18 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.019 0.001 TYR B 301 PHE 0.013 0.001 PHE D 99 TRP 0.008 0.001 TRP A 68 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (15105) covalent geometry : angle 0.56430 / 0.28 (20320) SS BOND : bond 0.00453 / 0.25 ( 5) SS BOND : angle 4.47476 / 2.35 ( 10) hydrogen bonds : bond 0.04360 / 2.93 ( 675) hydrogen bonds : angle 4.12366 / 2.81 ( 2385) metal coordination : bond 0.00097 / 0.06 ( 10) link_BETA1-4 : bond 0.00283 / 0.15 ( 5) link_BETA1-4 : angle 1.14345 / 0.75 ( 15) link_NAG-ASN : bond 0.00026 / 0.01 ( 5) link_NAG-ASN : angle 0.58271 / 0.35 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.30 seconds wall clock time: 72 minutes 21.94 seconds (4341.94 seconds total)