Starting phenix.real_space_refine on Sun Jul 5 03:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bvh_44933/07_2026/9bvh_44933.map" } resolution = 2.58 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= 0.003 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 13390 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9665 2.51 5 N 2285 2.21 5 O 2630 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: 14680 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} 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: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'CLR': 1, 'PIO': 4, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PIO:plan-2': 3, 'PIO:plan-1': 1, 'PX4:plan-2': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'CLR': 1, 'PIO': 4, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-2': 3, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'CLR': 1, 'PIO': 4, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-2': 3, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'CLR': 1, 'PIO': 4, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PX4:plan-2': 4, 'PIO:plan-2': 3, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'CLR': 1, 'PIO': 4, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PIO:plan-2': 3, 'PX4:plan-2': 4, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.34, per 1000 atoms: 0.23 Number of scatterers: 14680 At special positions: 0 Unit cell: (101.2, 101.2, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2630 8.00 N 2285 7.00 C 9665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.47 Conformation dependent library (CDL) restraints added in 570.8 milliseconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 40.4% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.563A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.638A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 248 through 272 removed outlier: 3.790A pdb=" N ALA A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 310 removed outlier: 3.936A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 removed outlier: 4.005A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.537A pdb=" N ILE A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.563A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.638A pdb=" N LEU B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 248 through 272 removed outlier: 3.790A pdb=" N ALA B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 310 removed outlier: 3.935A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 420 removed outlier: 4.006A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 3.537A pdb=" N ILE B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.562A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.638A pdb=" N LEU C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 248 through 272 removed outlier: 3.791A pdb=" N ALA C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 310 removed outlier: 3.936A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 removed outlier: 4.005A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.538A pdb=" N ILE C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 71 through 74 removed outlier: 3.563A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.638A pdb=" N LEU D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.791A pdb=" N ALA D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 310 removed outlier: 3.936A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 420 removed outlier: 4.006A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix removed outlier: 3.537A pdb=" N ILE D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 Processing helix chain 'E' and resid 71 through 74 removed outlier: 3.562A pdb=" N ALA E 74 " --> pdb=" O PRO E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.637A pdb=" N LEU E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 239 through 244 Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.790A pdb=" N ALA E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 310 removed outlier: 3.936A pdb=" N LEU E 298 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 299 " --> pdb=" O PHE E 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 420 removed outlier: 4.005A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix removed outlier: 3.537A pdb=" N ILE E 417 " --> pdb=" O PHE E 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 418 " --> pdb=" O TYR E 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.425A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.165A 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 108 removed outlier: 6.455A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE A 108 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG A 131 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.666A 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: 7.391A pdb=" N CYS A 209 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG A 196 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A 211 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP A 194 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 213 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 192 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS A 215 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.425A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.164A 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 108 removed outlier: 6.455A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 108 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG B 131 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.666A 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: 7.390A pdb=" N CYS B 209 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG B 196 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B 211 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP B 194 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG B 213 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU B 192 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS B 215 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.426A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.165A 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 108 removed outlier: 6.455A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE C 108 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG C 131 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.666A 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: 7.391A pdb=" N CYS C 209 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG C 196 " --> pdb=" O CYS C 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU C 211 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP C 194 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG C 213 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU C 192 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS C 215 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.425A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.165A 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 108 removed outlier: 6.456A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D 108 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG D 131 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.665A 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: 7.390A pdb=" N CYS D 209 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG D 196 " --> pdb=" O CYS D 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU D 211 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP D 194 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG D 213 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU D 192 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS D 215 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.425A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.164A 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 108 removed outlier: 6.455A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE E 108 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG E 131 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.666A 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: 7.390A pdb=" N CYS E 209 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG E 196 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU E 211 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP E 194 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG E 213 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU E 192 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS E 215 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 200 through 201 765 hydrogen bonds defined for protein. 2205 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: 2.45 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2257 1.32 - 1.44: 4108 1.44 - 1.56: 8410 1.56 - 1.69: 55 1.69 - 1.81: 165 Bond restraints: 14995 Sorted by residual: bond pdb=" C9 PX4 E 505 " pdb=" O5 PX4 E 505 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C9 PX4 B 501 " pdb=" O5 PX4 B 501 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C9 PX4 A 504 " pdb=" O5 PX4 A 504 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C9 PX4 C 501 " pdb=" O5 PX4 C 501 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C9 PX4 D 501 " pdb=" O5 PX4 D 501 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 14990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 19358 1.72 - 3.44: 705 3.44 - 5.15: 122 5.15 - 6.87: 25 6.87 - 8.59: 10 Bond angle restraints: 20220 Sorted by residual: angle pdb=" O VAL B 304 " pdb=" C VAL B 304 " pdb=" N ASN B 305 " ideal model delta sigma weight residual 121.87 116.54 5.33 9.70e-01 1.06e+00 3.02e+01 angle pdb=" O VAL A 304 " pdb=" C VAL A 304 " pdb=" N ASN A 305 " ideal model delta sigma weight residual 121.87 116.58 5.29 9.70e-01 1.06e+00 2.98e+01 angle pdb=" O VAL D 304 " pdb=" C VAL D 304 " pdb=" N ASN D 305 " ideal model delta sigma weight residual 121.87 116.60 5.27 9.70e-01 1.06e+00 2.95e+01 angle pdb=" O VAL E 304 " pdb=" C VAL E 304 " pdb=" N ASN E 305 " ideal model delta sigma weight residual 121.87 116.62 5.25 9.70e-01 1.06e+00 2.93e+01 angle pdb=" O VAL C 304 " pdb=" C VAL C 304 " pdb=" N ASN C 305 " ideal model delta sigma weight residual 121.87 116.62 5.25 9.70e-01 1.06e+00 2.92e+01 ... (remaining 20215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 8081 15.26 - 30.51: 944 30.51 - 45.77: 225 45.77 - 61.03: 65 61.03 - 76.28: 10 Dihedral angle restraints: 9325 sinusoidal: 4250 harmonic: 5075 Sorted by residual: dihedral pdb=" C THR C 112 " pdb=" N THR C 112 " pdb=" CA THR C 112 " pdb=" CB THR C 112 " ideal model delta harmonic sigma weight residual -122.00 -138.01 16.01 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" C THR B 112 " pdb=" N THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta harmonic sigma weight residual -122.00 -138.00 16.00 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" C THR E 112 " pdb=" N THR E 112 " pdb=" CA THR E 112 " pdb=" CB THR E 112 " ideal model delta harmonic sigma weight residual -122.00 -137.99 15.99 0 2.50e+00 1.60e-01 4.09e+01 ... (remaining 9322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2062 0.090 - 0.181: 183 0.181 - 0.271: 5 0.271 - 0.361: 0 0.361 - 0.451: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA THR B 112 " pdb=" N THR B 112 " pdb=" C THR B 112 " pdb=" CB THR B 112 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA THR E 112 " pdb=" N THR E 112 " pdb=" C THR E 112 " pdb=" CB THR E 112 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA THR C 112 " pdb=" N THR C 112 " pdb=" C THR C 112 " pdb=" CB THR C 112 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2252 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 174 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C 175 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 175 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 175 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 174 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 175 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 174 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO D 175 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 175 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 175 " 0.055 5.00e-02 4.00e+02 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 35 2.43 - 3.05: 8390 3.05 - 3.67: 19786 3.67 - 4.28: 31767 4.28 - 4.90: 54096 Nonbonded interactions: 114074 Sorted by model distance: nonbonded pdb=" CG1 VAL E 111 " pdb=" O HOH D 604 " model vdw 1.819 3.460 nonbonded pdb=" CG1 VAL D 111 " pdb=" O HOH C 604 " model vdw 1.819 3.460 nonbonded pdb=" CG1 VAL C 111 " pdb=" O HOH B 604 " model vdw 1.819 3.460 nonbonded pdb=" CG1 VAL A 111 " pdb=" O HOH E 604 " model vdw 1.820 3.460 nonbonded pdb=" CG1 VAL B 111 " pdb=" O HOH A 604 " model vdw 1.820 3.460 ... (remaining 114069 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 423 or (resid 506 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C9 or name O5 or name O6 )) or (resid 508 and (n \ ame C1A or name C2A or name C3A or name C4A or name C5A or name C6A or name C7A \ or name O1A or name O2C)))) selection = (chain 'B' and (resid 8 through 423 or (resid 506 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C9 or name O5 or name O6 )) or (resid 508 and (n \ ame C1A or name C2A or name C3A or name C4A or name C5A or name C6A or name C7A \ or name O1A or name O2C)))) selection = (chain 'C' and (resid 8 through 423 or (resid 506 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C9 or name O5 or name O6 )) or (resid 508 and (n \ ame C1A or name C2A or name C3A or name C4A or name C5A or name C6A or name C7A \ or name O1A or name O2C)))) selection = (chain 'D' and (resid 8 through 423 or (resid 506 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C9 or name O5 or name O6 )) or (resid 508 and (n \ ame C1A or name C2A or name C3A or name C4A or name C5A or name C6A or name C7A \ or name O1A or name O2C)))) selection = (chain 'E' and (resid 8 through 423 or resid 506 or resid 508)) } 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.420 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.141 15005 Z= 0.417 Angle : 0.760 8.588 20250 Z= 0.459 Chirality : 0.053 0.451 2255 Planarity : 0.006 0.104 2475 Dihedral : 13.857 76.283 6025 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.32 % Allowed : 9.35 % Favored : 90.32 % Cbeta Deviations : 0.30 % 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: 0.97 (0.21), residues: 1690 helix: 1.48 (0.21), residues: 555 sheet: 0.99 (0.28), residues: 445 loop : -0.21 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 309 TYR 0.015 0.001 TYR E 301 PHE 0.029 0.002 PHE E 121 TRP 0.008 0.001 TRP C 286 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.42 (14995) covalent geometry : angle 0.75883 / 0.46 (20220) hydrogen bonds : bond 0.18970 / 12.68 ( 670) hydrogen bonds : angle 5.96356 / 4.04 ( 2205) link_BETA1-4 : bond 0.00427 / 0.22 ( 5) link_BETA1-4 : angle 1.56018 / 0.92 ( 15) link_NAG-ASN : bond 0.00045 / 0.02 ( 5) link_NAG-ASN : angle 1.05688 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.581 Fit side-chains REVERT: E 177 GLN cc_start: 0.8623 (mt0) cc_final: 0.8371 (mt0) outliers start: 5 outliers final: 1 residues processed: 133 average time/residue: 0.6456 time to fit residues: 94.2604 Evaluate side-chains 123 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN B 245 ASN C 245 ASN D 245 ASN E 186 GLN E 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.084790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.063407 restraints weight = 26293.712| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.62 r_work: 0.2674 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15005 Z= 0.153 Angle : 0.509 5.242 20250 Z= 0.275 Chirality : 0.042 0.167 2255 Planarity : 0.004 0.062 2475 Dihedral : 7.410 99.786 2672 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.06 % Allowed : 9.48 % Favored : 88.45 % 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: 1.35 (0.21), residues: 1690 helix: 2.23 (0.21), residues: 545 sheet: 0.94 (0.27), residues: 450 loop : -0.17 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 20 TYR 0.014 0.001 TYR C 301 PHE 0.011 0.001 PHE E 99 TRP 0.007 0.001 TRP C 286 HIS 0.002 0.001 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (14995) covalent geometry : angle 0.50880 / 0.27 (20220) hydrogen bonds : bond 0.06141 / 4.01 ( 670) hydrogen bonds : angle 4.50976 / 3.07 ( 2205) link_BETA1-4 : bond 0.00157 / 0.08 ( 5) link_BETA1-4 : angle 0.81047 / 0.49 ( 15) link_NAG-ASN : bond 0.00039 / 0.02 ( 5) link_NAG-ASN : angle 0.84949 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.592 Fit side-chains REVERT: C 163 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8955 (mmm) REVERT: C 177 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: E 177 GLN cc_start: 0.8895 (mt0) cc_final: 0.8624 (mt0) REVERT: E 186 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9069 (tp40) outliers start: 32 outliers final: 7 residues processed: 141 average time/residue: 0.5711 time to fit residues: 88.8167 Evaluate side-chains 131 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064232 restraints weight = 26681.129| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.70 r_work: 0.2690 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15005 Z= 0.108 Angle : 0.470 5.202 20250 Z= 0.251 Chirality : 0.040 0.167 2255 Planarity : 0.003 0.048 2475 Dihedral : 6.474 58.530 2670 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.74 % Allowed : 11.29 % Favored : 86.97 % 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 (0.21), residues: 1690 helix: 2.59 (0.22), residues: 545 sheet: 1.17 (0.27), residues: 425 loop : -0.34 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.014 0.001 TYR C 301 PHE 0.017 0.001 PHE E 187 TRP 0.007 0.001 TRP C 286 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14995) covalent geometry : angle 0.46951 / 0.25 (20220) hydrogen bonds : bond 0.05250 / 3.43 ( 670) hydrogen bonds : angle 4.23643 / 2.89 ( 2205) link_BETA1-4 : bond 0.00315 / 0.16 ( 5) link_BETA1-4 : angle 0.83058 / 0.50 ( 15) link_NAG-ASN : bond 0.00140 / 0.07 ( 5) link_NAG-ASN : angle 0.76169 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.420 Fit side-chains REVERT: B 177 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8497 (mm110) REVERT: C 177 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: E 177 GLN cc_start: 0.8798 (mt0) cc_final: 0.8530 (mt0) outliers start: 27 outliers final: 7 residues processed: 133 average time/residue: 0.5964 time to fit residues: 87.1226 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 226 GLN E 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.063878 restraints weight = 26545.584| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.68 r_work: 0.2686 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15005 Z= 0.118 Angle : 0.472 5.230 20250 Z= 0.252 Chirality : 0.041 0.170 2255 Planarity : 0.003 0.042 2475 Dihedral : 6.068 57.491 2670 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.55 % Allowed : 12.06 % Favored : 86.39 % 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: 1.55 (0.21), residues: 1690 helix: 2.67 (0.22), residues: 545 sheet: 1.14 (0.27), residues: 430 loop : -0.34 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 213 TYR 0.015 0.001 TYR B 301 PHE 0.011 0.001 PHE B 121 TRP 0.006 0.001 TRP A 286 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14995) covalent geometry : angle 0.47087 / 0.25 (20220) hydrogen bonds : bond 0.05202 / 3.40 ( 670) hydrogen bonds : angle 4.18659 / 2.86 ( 2205) link_BETA1-4 : bond 0.00285 / 0.14 ( 5) link_BETA1-4 : angle 0.79955 / 0.48 ( 15) link_NAG-ASN : bond 0.00073 / 0.04 ( 5) link_NAG-ASN : angle 0.89306 / 0.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.562 Fit side-chains REVERT: C 177 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: C 227 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8369 (mtt) REVERT: D 177 GLN cc_start: 0.8954 (mt0) cc_final: 0.8715 (mm110) REVERT: D 412 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8436 (mt) REVERT: E 177 GLN cc_start: 0.8776 (mt0) cc_final: 0.8480 (mt0) outliers start: 24 outliers final: 11 residues processed: 134 average time/residue: 0.5958 time to fit residues: 87.4783 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 118 optimal weight: 0.0060 chunk 131 optimal weight: 3.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062191 restraints weight = 26634.110| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.68 r_work: 0.2649 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15005 Z= 0.172 Angle : 0.515 5.352 20250 Z= 0.276 Chirality : 0.043 0.176 2255 Planarity : 0.003 0.038 2475 Dihedral : 6.114 56.522 2670 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 11.94 % Favored : 86.32 % 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: 1690 helix: 2.57 (0.22), residues: 545 sheet: 1.12 (0.28), residues: 405 loop : -0.42 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 20 TYR 0.015 0.001 TYR E 301 PHE 0.013 0.001 PHE C 48 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (14995) covalent geometry : angle 0.51376 / 0.28 (20220) hydrogen bonds : bond 0.05886 / 3.83 ( 670) hydrogen bonds : angle 4.36035 / 2.97 ( 2205) link_BETA1-4 : bond 0.00217 / 0.11 ( 5) link_BETA1-4 : angle 0.83174 / 0.52 ( 15) link_NAG-ASN : bond 0.00100 / 0.05 ( 5) link_NAG-ASN : angle 1.14184 / 0.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.588 Fit side-chains REVERT: B 163 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9086 (mmm) REVERT: C 114 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8160 (t70) REVERT: C 163 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9091 (mmm) REVERT: C 177 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8654 (mt0) REVERT: C 227 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8456 (mtt) REVERT: E 177 GLN cc_start: 0.8851 (mt0) cc_final: 0.8552 (mt0) outliers start: 27 outliers final: 12 residues processed: 137 average time/residue: 0.5699 time to fit residues: 86.1643 Evaluate side-chains 140 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN E 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063460 restraints weight = 26485.275| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.62 r_work: 0.2678 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15005 Z= 0.126 Angle : 0.484 5.514 20250 Z= 0.258 Chirality : 0.041 0.174 2255 Planarity : 0.003 0.035 2475 Dihedral : 5.850 57.118 2670 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.68 % Allowed : 12.26 % Favored : 86.06 % 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: 1.46 (0.20), residues: 1690 helix: 2.68 (0.22), residues: 545 sheet: 1.38 (0.28), residues: 380 loop : -0.56 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.015 0.001 TYR C 301 PHE 0.012 0.001 PHE C 121 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14995) covalent geometry : angle 0.48346 / 0.26 (20220) hydrogen bonds : bond 0.05301 / 3.45 ( 670) hydrogen bonds : angle 4.24991 / 2.90 ( 2205) link_BETA1-4 : bond 0.00316 / 0.16 ( 5) link_BETA1-4 : angle 0.83292 / 0.51 ( 15) link_NAG-ASN : bond 0.00060 / 0.03 ( 5) link_NAG-ASN : angle 1.05732 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.481 Fit side-chains REVERT: B 163 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9034 (mmm) REVERT: C 163 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.9055 (mmm) REVERT: C 177 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8641 (mt0) REVERT: C 227 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: D 177 GLN cc_start: 0.8958 (mt0) cc_final: 0.8737 (mm110) REVERT: E 177 GLN cc_start: 0.8803 (mt0) cc_final: 0.8487 (mt0) outliers start: 26 outliers final: 11 residues processed: 136 average time/residue: 0.5838 time to fit residues: 87.3840 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 GLN E 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063514 restraints weight = 26460.884| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.68 r_work: 0.2678 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15005 Z= 0.118 Angle : 0.485 7.095 20250 Z= 0.258 Chirality : 0.041 0.171 2255 Planarity : 0.003 0.033 2475 Dihedral : 5.703 59.270 2670 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.16 % Allowed : 13.03 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1690 helix: 2.72 (0.22), residues: 545 sheet: 1.41 (0.28), residues: 380 loop : -0.54 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 20 TYR 0.015 0.001 TYR C 301 PHE 0.011 0.001 PHE A 295 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14995) covalent geometry : angle 0.48380 / 0.26 (20220) hydrogen bonds : bond 0.05097 / 3.32 ( 670) hydrogen bonds : angle 4.19503 / 2.87 ( 2205) link_BETA1-4 : bond 0.00342 / 0.17 ( 5) link_BETA1-4 : angle 0.88919 / 0.54 ( 15) link_NAG-ASN : bond 0.00073 / 0.04 ( 5) link_NAG-ASN : angle 1.02213 / 0.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.592 Fit side-chains REVERT: C 163 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9062 (mmm) REVERT: C 177 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8649 (mt0) REVERT: C 227 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: D 177 GLN cc_start: 0.8967 (mt0) cc_final: 0.8760 (mm110) REVERT: E 177 GLN cc_start: 0.8804 (mt0) cc_final: 0.8500 (mt0) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.6047 time to fit residues: 87.1374 Evaluate side-chains 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.063448 restraints weight = 26762.849| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.69 r_work: 0.2677 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15005 Z= 0.116 Angle : 0.496 9.296 20250 Z= 0.261 Chirality : 0.041 0.168 2255 Planarity : 0.003 0.034 2475 Dihedral : 5.611 59.908 2670 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.23 % Allowed : 13.29 % Favored : 85.48 % 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: 1690 helix: 2.74 (0.22), residues: 545 sheet: 1.43 (0.28), residues: 380 loop : -0.53 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 20 TYR 0.015 0.001 TYR C 301 PHE 0.015 0.001 PHE E 121 TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14995) covalent geometry : angle 0.49455 / 0.26 (20220) hydrogen bonds : bond 0.05003 / 3.25 ( 670) hydrogen bonds : angle 4.18087 / 2.86 ( 2205) link_BETA1-4 : bond 0.00293 / 0.15 ( 5) link_BETA1-4 : angle 0.88706 / 0.54 ( 15) link_NAG-ASN : bond 0.00088 / 0.04 ( 5) link_NAG-ASN : angle 0.98837 / 0.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.550 Fit side-chains REVERT: C 163 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9065 (mmm) REVERT: C 177 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (mt0) REVERT: C 227 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: D 177 GLN cc_start: 0.8963 (mt0) cc_final: 0.8751 (mm110) REVERT: E 177 GLN cc_start: 0.8779 (mt0) cc_final: 0.8470 (mt0) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 0.6234 time to fit residues: 86.6045 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 122 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.063977 restraints weight = 26891.051| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.63 r_work: 0.2689 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15005 Z= 0.110 Angle : 0.498 9.829 20250 Z= 0.262 Chirality : 0.041 0.166 2255 Planarity : 0.003 0.038 2475 Dihedral : 5.438 58.023 2670 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.03 % Allowed : 13.55 % Favored : 85.42 % 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: 1.60 (0.21), residues: 1690 helix: 2.77 (0.22), residues: 545 sheet: 1.15 (0.27), residues: 430 loop : -0.36 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 20 TYR 0.015 0.001 TYR B 301 PHE 0.010 0.001 PHE A 295 TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14995) covalent geometry : angle 0.49741 / 0.26 (20220) hydrogen bonds : bond 0.04833 / 3.15 ( 670) hydrogen bonds : angle 4.13970 / 2.84 ( 2205) link_BETA1-4 : bond 0.00337 / 0.17 ( 5) link_BETA1-4 : angle 0.91047 / 0.56 ( 15) link_NAG-ASN : bond 0.00110 / 0.06 ( 5) link_NAG-ASN : angle 0.92666 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.473 Fit side-chains REVERT: C 163 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9055 (mmm) REVERT: C 177 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mt0) REVERT: C 227 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8198 (mtt) REVERT: D 177 GLN cc_start: 0.8944 (mt0) cc_final: 0.8727 (mm110) REVERT: E 177 GLN cc_start: 0.8747 (mt0) cc_final: 0.8413 (mt0) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 0.6004 time to fit residues: 84.2298 Evaluate side-chains 128 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063214 restraints weight = 26691.029| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.63 r_work: 0.2674 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15005 Z= 0.127 Angle : 0.516 9.645 20250 Z= 0.271 Chirality : 0.041 0.166 2255 Planarity : 0.003 0.044 2475 Dihedral : 5.434 55.858 2670 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.84 % Allowed : 13.48 % Favored : 85.68 % 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 (0.21), residues: 1690 helix: 2.73 (0.22), residues: 545 sheet: 1.12 (0.27), residues: 430 loop : -0.37 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 20 TYR 0.015 0.001 TYR E 301 PHE 0.016 0.001 PHE C 121 TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (14995) covalent geometry : angle 0.51523 / 0.27 (20220) hydrogen bonds : bond 0.05141 / 3.35 ( 670) hydrogen bonds : angle 4.20862 / 2.87 ( 2205) link_BETA1-4 : bond 0.00280 / 0.14 ( 5) link_BETA1-4 : angle 0.93363 / 0.57 ( 15) link_NAG-ASN : bond 0.00053 / 0.03 ( 5) link_NAG-ASN : angle 0.99637 / 0.56 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.566 Fit side-chains REVERT: C 163 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9046 (mmm) REVERT: C 177 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8692 (mt0) REVERT: C 227 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: E 177 GLN cc_start: 0.8771 (mt0) cc_final: 0.8461 (mt0) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.6795 time to fit residues: 92.0726 Evaluate side-chains 128 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 116 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.063924 restraints weight = 26571.763| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.67 r_work: 0.2688 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15005 Z= 0.109 Angle : 0.499 9.410 20250 Z= 0.261 Chirality : 0.041 0.164 2255 Planarity : 0.003 0.040 2475 Dihedral : 5.207 58.809 2670 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.77 % Allowed : 13.48 % Favored : 85.74 % 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: 1.61 (0.21), residues: 1690 helix: 2.71 (0.22), residues: 550 sheet: 1.15 (0.27), residues: 430 loop : -0.31 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 20 TYR 0.015 0.001 TYR C 301 PHE 0.016 0.001 PHE D 121 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14995) covalent geometry : angle 0.49820 / 0.26 (20220) hydrogen bonds : bond 0.04748 / 3.09 ( 670) hydrogen bonds : angle 4.11577 / 2.82 ( 2205) link_BETA1-4 : bond 0.00347 / 0.18 ( 5) link_BETA1-4 : angle 0.92693 / 0.56 ( 15) link_NAG-ASN : bond 0.00141 / 0.07 ( 5) link_NAG-ASN : angle 0.87954 / 0.49 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4179.97 seconds wall clock time: 72 minutes 7.66 seconds (4327.66 seconds total)