Starting phenix.real_space_refine on Thu Aug 6 16:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxl_71973/08_2026/9pxl_71973.map" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 32 5.16 5 C 10004 2.51 5 N 2640 2.21 5 O 3084 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "C" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "D" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "E" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.97, per 1000 atoms: 0.25 Number of scatterers: 15768 At special positions: 0 Unit cell: (136.526, 136.526, 116.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 8 15.00 O 3084 8.00 N 2640 7.00 C 10004 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 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 894.3 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 32 sheets defined 50.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.669A pdb=" N LEU A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 151 through 154 Processing helix chain 'A' and resid 163 through 184 Proline residue: A 178 - end of helix removed outlier: 3.683A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.615A pdb=" N ARG A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.604A pdb=" N GLY A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 330 removed outlier: 3.728A pdb=" N TYR A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.671A pdb=" N LEU B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 128 through 150 Processing helix chain 'B' and resid 151 through 154 Processing helix chain 'B' and resid 163 through 184 Proline residue: B 178 - end of helix removed outlier: 3.683A pdb=" N TYR B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.615A pdb=" N ARG B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.605A pdb=" N GLY B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 330 removed outlier: 3.728A pdb=" N TYR B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.670A pdb=" N LEU C 16 " --> pdb=" O TYR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 128 through 150 Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 163 through 184 Proline residue: C 178 - end of helix removed outlier: 3.683A pdb=" N TYR C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 207 through 221 removed outlier: 3.615A pdb=" N ARG C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.604A pdb=" N GLY C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 330 removed outlier: 3.728A pdb=" N TYR C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.668A pdb=" N LEU D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 128 through 150 Processing helix chain 'D' and resid 151 through 154 Processing helix chain 'D' and resid 163 through 184 Proline residue: D 178 - end of helix removed outlier: 3.683A pdb=" N TYR D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 207 through 221 removed outlier: 3.615A pdb=" N ARG D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 267 removed outlier: 3.605A pdb=" N GLY D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 330 removed outlier: 3.729A pdb=" N TYR D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 384 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'E' and resid 27 through 61 removed outlier: 3.598A pdb=" N SER E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Proline residue: E 40 - end of helix Processing helix chain 'E' and resid 62 through 101 Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 116 through 139 Processing helix chain 'F' and resid 27 through 61 removed outlier: 3.678A pdb=" N SER F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Proline residue: F 40 - end of helix Processing helix chain 'F' and resid 62 through 100 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 116 through 139 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 38 through 61 Processing helix chain 'G' and resid 62 through 101 Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 139 Processing helix chain 'H' and resid 27 through 38 Processing helix chain 'H' and resid 38 through 61 Processing helix chain 'H' and resid 62 through 101 Proline residue: H 79 - end of helix Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 116 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 8.466A pdb=" N ASP A 74 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 32 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS A 76 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 34 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS A 3 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 33 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 5 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 35 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 7 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 103 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.700A pdb=" N LEU A 193 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU A 226 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 195 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 251 " --> pdb=" O THR A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.772A pdb=" N ASN A 233 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.227A pdb=" N ALA A 276 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 77 removed outlier: 8.467A pdb=" N ASP B 74 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 32 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS B 76 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 34 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 3 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR B 33 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 5 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 35 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 7 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 103 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AB4, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.700A pdb=" N LEU B 193 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU B 226 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 195 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 251 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.771A pdb=" N ASN B 233 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.237A pdb=" N ALA B 276 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 74 through 77 removed outlier: 8.465A pdb=" N ASP C 74 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 32 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LYS C 76 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 34 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS C 3 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR C 33 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 5 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL C 35 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 7 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 103 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AC3, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.700A pdb=" N LEU C 193 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU C 226 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 195 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 251 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.772A pdb=" N ASN C 233 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.225A pdb=" N ALA C 276 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AC7, first strand: chain 'D' and resid 74 through 77 removed outlier: 8.468A pdb=" N ASP D 74 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 32 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS D 76 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 34 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS D 3 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR D 33 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 5 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL D 35 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE D 7 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 103 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 84 Processing sheet with id=AD1, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AD2, first strand: chain 'D' and resid 223 through 227 removed outlier: 6.701A pdb=" N LEU D 193 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 226 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 195 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 251 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.772A pdb=" N ASN D 233 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.228A pdb=" N ALA D 276 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 343 through 346 865 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5180 1.34 - 1.46: 2694 1.46 - 1.57: 8083 1.57 - 1.69: 11 1.69 - 1.80: 64 Bond restraints: 16032 Sorted by residual: bond pdb=" O3P FAD C 401 " pdb=" P FAD C 401 " ideal model delta sigma weight residual 1.660 1.580 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3P FAD B 401 " pdb=" P FAD B 401 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" O3P FAD D 401 " pdb=" P FAD D 401 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3P FAD A 401 " pdb=" P FAD A 401 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O5B FAD A 401 " pdb=" PA FAD A 401 " ideal model delta sigma weight residual 1.634 1.565 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 21571 2.29 - 4.58: 153 4.58 - 6.87: 28 6.87 - 9.16: 11 9.16 - 11.45: 1 Bond angle restraints: 21764 Sorted by residual: angle pdb=" C LEU F 24 " pdb=" N LYS F 25 " pdb=" CA LYS F 25 " ideal model delta sigma weight residual 120.09 125.13 -5.04 1.25e+00 6.40e-01 1.63e+01 angle pdb=" CA LEU E 23 " pdb=" CB LEU E 23 " pdb=" CG LEU E 23 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" C PRO F 26 " pdb=" N GLU F 27 " pdb=" CA GLU F 27 " ideal model delta sigma weight residual 120.63 125.17 -4.54 1.61e+00 3.86e-01 7.96e+00 angle pdb=" O1P FAD D 401 " pdb=" P FAD D 401 " pdb=" O2P FAD D 401 " ideal model delta sigma weight residual 122.50 114.94 7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" O1P FAD A 401 " pdb=" P FAD A 401 " pdb=" O2P FAD A 401 " ideal model delta sigma weight residual 122.50 114.94 7.56 3.00e+00 1.11e-01 6.34e+00 ... (remaining 21759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 8840 16.26 - 32.52: 758 32.52 - 48.77: 105 48.77 - 65.03: 32 65.03 - 81.29: 41 Dihedral angle restraints: 9776 sinusoidal: 3936 harmonic: 5840 Sorted by residual: dihedral pdb=" CA LYS E 25 " pdb=" C LYS E 25 " pdb=" N PRO E 26 " pdb=" CA PRO E 26 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ALA D 355 " pdb=" C ALA D 355 " pdb=" N ILE D 356 " pdb=" CA ILE D 356 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ALA C 355 " pdb=" C ALA C 355 " pdb=" N ILE C 356 " pdb=" CA ILE C 356 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 9773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1672 0.032 - 0.064: 570 0.064 - 0.097: 174 0.097 - 0.129: 142 0.129 - 0.161: 6 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA PRO E 26 " pdb=" N PRO E 26 " pdb=" C PRO E 26 " pdb=" CB PRO E 26 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" C2B FAD C 401 " pdb=" C1B FAD C 401 " pdb=" C3B FAD C 401 " pdb=" O2B FAD C 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" C2B FAD D 401 " pdb=" C1B FAD D 401 " pdb=" C3B FAD D 401 " pdb=" O2B FAD D 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2561 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 373 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C LYS B 373 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS B 373 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 374 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 373 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C LYS D 373 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS D 373 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU D 374 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 373 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C LYS C 373 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS C 373 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 374 " -0.010 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3193 2.78 - 3.31: 15204 3.31 - 3.84: 26597 3.84 - 4.37: 31300 4.37 - 4.90: 53820 Nonbonded interactions: 130114 Sorted by model distance: nonbonded pdb=" O GLU F 30 " pdb=" OG1 THR F 33 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR E 90 " pdb=" NH1 ARG F 136 " model vdw 2.257 3.120 nonbonded pdb=" O VAL G 28 " pdb=" OG SER G 31 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR G 90 " pdb=" NH1 ARG H 136 " model vdw 2.275 3.120 nonbonded pdb=" OG SER D 342 " pdb=" OD2 ASP E 68 " model vdw 2.300 3.040 ... (remaining 130109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 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 : 0.004 0.080 16032 Z= 0.183 Angle : 0.544 11.452 21764 Z= 0.269 Chirality : 0.042 0.161 2564 Planarity : 0.003 0.041 2760 Dihedral : 13.214 81.289 6032 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.33 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 1.63 (0.19), residues: 2028 helix: 1.89 (0.17), residues: 976 sheet: 0.77 (0.34), residues: 264 loop : 0.27 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.009 0.001 TYR F 53 PHE 0.010 0.001 PHE A 83 TRP 0.016 0.002 TRP C 315 HIS 0.004 0.001 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (16032) covalent geometry : angle 0.54378 / 0.27 (21764) hydrogen bonds : bond 0.11240 / 7.44 ( 865) hydrogen bonds : angle 5.35928 / 3.78 ( 2427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.773 Fit side-chains REVERT: E 51 LYS cc_start: 0.7518 (tmtt) cc_final: 0.7056 (tmtt) REVERT: G 51 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7040 (tmtt) REVERT: H 51 LYS cc_start: 0.7494 (tmtt) cc_final: 0.7036 (tmtt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.8253 time to fit residues: 162.5371 Evaluate side-chains 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN A 383 HIS B 312 GLN B 383 HIS C 383 HIS D 383 HIS E 38 GLN H 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.045549 restraints weight = 33851.570| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.21 r_work: 0.2453 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16032 Z= 0.122 Angle : 0.492 9.464 21764 Z= 0.251 Chirality : 0.042 0.151 2564 Planarity : 0.004 0.039 2760 Dihedral : 4.582 30.015 2352 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.92 % Favored : 97.93 % Rotamer: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % 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: 2.14 (0.19), residues: 2028 helix: 2.52 (0.17), residues: 988 sheet: 0.89 (0.34), residues: 264 loop : 0.22 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.004 0.001 TYR D 380 PHE 0.009 0.001 PHE B 83 TRP 0.015 0.002 TRP B 315 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16032) covalent geometry : angle 0.49210 / 0.25 (21764) hydrogen bonds : bond 0.04262 / 2.95 ( 865) hydrogen bonds : angle 4.03868 / 2.84 ( 2427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.620 Fit side-chains REVERT: E 51 LYS cc_start: 0.7621 (tmtt) cc_final: 0.7113 (tmtt) REVERT: G 51 LYS cc_start: 0.7629 (tmtt) cc_final: 0.7118 (tmtt) REVERT: H 37 ASP cc_start: 0.8720 (m-30) cc_final: 0.8461 (m-30) REVERT: H 51 LYS cc_start: 0.7618 (tmtt) cc_final: 0.7112 (tmtt) outliers start: 3 outliers final: 1 residues processed: 165 average time/residue: 0.7635 time to fit residues: 136.8956 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 46 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN D 312 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.044535 restraints weight = 34287.090| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 2.23 r_work: 0.2424 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16032 Z= 0.138 Angle : 0.479 7.829 21764 Z= 0.247 Chirality : 0.043 0.144 2564 Planarity : 0.004 0.040 2760 Dihedral : 4.300 23.649 2352 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.27 % Rotamer: Outliers : 0.48 % Allowed : 6.13 % Favored : 93.39 % 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: 2.23 (0.19), residues: 2028 helix: 2.66 (0.17), residues: 988 sheet: 0.80 (0.34), residues: 268 loop : 0.20 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 305 TYR 0.008 0.001 TYR A 380 PHE 0.009 0.001 PHE B 326 TRP 0.015 0.002 TRP C 315 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16032) covalent geometry : angle 0.47932 / 0.25 (21764) hydrogen bonds : bond 0.04334 / 2.99 ( 865) hydrogen bonds : angle 3.89630 / 2.75 ( 2427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.643 Fit side-chains REVERT: E 51 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7108 (tmtt) REVERT: G 51 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7116 (tmtt) REVERT: H 37 ASP cc_start: 0.8731 (m-30) cc_final: 0.8498 (m-30) REVERT: H 51 LYS cc_start: 0.7609 (tmtt) cc_final: 0.7076 (tmtt) REVERT: H 136 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7924 (ttt180) outliers start: 8 outliers final: 0 residues processed: 160 average time/residue: 0.7926 time to fit residues: 137.5378 Evaluate side-chains 159 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN G 47 ASN H 38 GLN H 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.043626 restraints weight = 34363.127| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.25 r_work: 0.2399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16032 Z= 0.165 Angle : 0.494 7.382 21764 Z= 0.256 Chirality : 0.043 0.137 2564 Planarity : 0.004 0.042 2760 Dihedral : 4.356 23.387 2352 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.01 % Allowed : 6.31 % Favored : 92.68 % 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: 2.21 (0.19), residues: 2028 helix: 2.68 (0.17), residues: 988 sheet: 0.81 (0.34), residues: 268 loop : 0.13 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 305 TYR 0.008 0.001 TYR A 380 PHE 0.009 0.001 PHE B 326 TRP 0.015 0.002 TRP C 315 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16032) covalent geometry : angle 0.49414 / 0.26 (21764) hydrogen bonds : bond 0.04581 / 3.16 ( 865) hydrogen bonds : angle 3.89604 / 2.75 ( 2427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.800 Fit side-chains REVERT: E 51 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7112 (tmtt) REVERT: F 37 ASP cc_start: 0.8982 (m-30) cc_final: 0.8630 (m-30) REVERT: G 37 ASP cc_start: 0.8880 (m-30) cc_final: 0.8576 (m-30) REVERT: G 51 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7067 (tmtt) REVERT: H 37 ASP cc_start: 0.8747 (m-30) cc_final: 0.8506 (m-30) REVERT: H 51 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7052 (tmtt) REVERT: H 136 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7901 (ttt180) outliers start: 17 outliers final: 7 residues processed: 165 average time/residue: 0.7879 time to fit residues: 141.2718 Evaluate side-chains 168 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN F 38 GLN G 47 ASN H 38 GLN H 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.042849 restraints weight = 34586.344| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 2.26 r_work: 0.2377 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16032 Z= 0.201 Angle : 0.521 7.045 21764 Z= 0.269 Chirality : 0.045 0.139 2564 Planarity : 0.004 0.043 2760 Dihedral : 4.461 23.260 2352 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.07 % Allowed : 7.14 % Favored : 91.79 % 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: 2.09 (0.19), residues: 2028 helix: 2.71 (0.17), residues: 980 sheet: 0.35 (0.29), residues: 332 loop : 0.05 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 305 TYR 0.008 0.001 TYR D 380 PHE 0.010 0.001 PHE B 326 TRP 0.015 0.002 TRP C 315 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (16032) covalent geometry : angle 0.52102 / 0.27 (21764) hydrogen bonds : bond 0.04938 / 3.40 ( 865) hydrogen bonds : angle 3.97315 / 2.81 ( 2427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.625 Fit side-chains REVERT: E 51 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7037 (tmtt) REVERT: F 37 ASP cc_start: 0.8988 (m-30) cc_final: 0.8635 (m-30) REVERT: G 37 ASP cc_start: 0.8852 (m-30) cc_final: 0.8530 (m-30) REVERT: G 51 LYS cc_start: 0.7648 (tmtt) cc_final: 0.7046 (tmtt) REVERT: H 37 ASP cc_start: 0.8774 (m-30) cc_final: 0.8543 (m-30) REVERT: H 51 LYS cc_start: 0.7633 (tmtt) cc_final: 0.7038 (tmtt) REVERT: H 136 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7920 (ttt180) outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.7830 time to fit residues: 142.1064 Evaluate side-chains 170 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.044777 restraints weight = 34373.588| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 2.25 r_work: 0.2431 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16032 Z= 0.104 Angle : 0.468 7.300 21764 Z= 0.241 Chirality : 0.042 0.163 2564 Planarity : 0.004 0.048 2760 Dihedral : 4.263 22.109 2352 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.23 % Favored : 98.67 % Rotamer: Outliers : 0.36 % Allowed : 8.51 % Favored : 91.13 % 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: 2.24 (0.19), residues: 2028 helix: 2.70 (0.17), residues: 988 sheet: 0.85 (0.34), residues: 268 loop : 0.14 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 305 TYR 0.007 0.001 TYR A 380 PHE 0.009 0.001 PHE D 83 TRP 0.017 0.002 TRP A 315 HIS 0.002 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (16032) covalent geometry : angle 0.46828 / 0.24 (21764) hydrogen bonds : bond 0.03751 / 2.60 ( 865) hydrogen bonds : angle 3.74865 / 2.65 ( 2427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 0.676 Fit side-chains REVERT: E 51 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7104 (tmtt) REVERT: F 37 ASP cc_start: 0.9008 (m-30) cc_final: 0.8677 (m-30) REVERT: G 37 ASP cc_start: 0.8853 (m-30) cc_final: 0.8545 (m-30) REVERT: G 51 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7062 (tmtt) REVERT: H 37 ASP cc_start: 0.8785 (m-30) cc_final: 0.8548 (m-30) REVERT: H 51 LYS cc_start: 0.7619 (tmtt) cc_final: 0.7052 (tmtt) REVERT: H 136 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7909 (ttt180) outliers start: 6 outliers final: 0 residues processed: 172 average time/residue: 0.7528 time to fit residues: 141.0658 Evaluate side-chains 164 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 155 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN E 47 ASN F 38 GLN F 47 ASN G 38 GLN H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.044126 restraints weight = 34080.966| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.19 r_work: 0.2427 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16032 Z= 0.151 Angle : 0.497 6.999 21764 Z= 0.256 Chirality : 0.043 0.169 2564 Planarity : 0.004 0.053 2760 Dihedral : 4.302 22.233 2352 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 0.71 % Allowed : 8.39 % Favored : 90.89 % 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: 2.22 (0.19), residues: 2028 helix: 2.68 (0.17), residues: 988 sheet: 0.90 (0.34), residues: 268 loop : 0.12 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 305 TYR 0.008 0.001 TYR B 380 PHE 0.009 0.001 PHE B 326 TRP 0.015 0.002 TRP A 315 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16032) covalent geometry : angle 0.49713 / 0.26 (21764) hydrogen bonds : bond 0.04326 / 2.99 ( 865) hydrogen bonds : angle 3.82362 / 2.70 ( 2427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.644 Fit side-chains REVERT: E 37 ASP cc_start: 0.9095 (m-30) cc_final: 0.8715 (m-30) REVERT: E 51 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7149 (tmtt) REVERT: F 37 ASP cc_start: 0.9025 (m-30) cc_final: 0.8697 (m-30) REVERT: G 37 ASP cc_start: 0.8862 (m-30) cc_final: 0.8556 (m-30) REVERT: G 51 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7081 (tmtt) REVERT: H 37 ASP cc_start: 0.8797 (m-30) cc_final: 0.8578 (m-30) REVERT: H 51 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7077 (tmtt) REVERT: H 136 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7891 (ttt180) outliers start: 12 outliers final: 3 residues processed: 167 average time/residue: 0.7676 time to fit residues: 139.3515 Evaluate side-chains 168 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN F 47 ASN H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.044358 restraints weight = 34446.759| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 2.20 r_work: 0.2434 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9249 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16032 Z= 0.140 Angle : 0.498 8.933 21764 Z= 0.257 Chirality : 0.043 0.195 2564 Planarity : 0.004 0.057 2760 Dihedral : 4.298 21.755 2352 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.47 % Rotamer: Outliers : 0.83 % Allowed : 8.45 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 2028 helix: 2.68 (0.17), residues: 988 sheet: 0.95 (0.34), residues: 268 loop : 0.13 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 305 TYR 0.008 0.001 TYR B 380 PHE 0.009 0.001 PHE C 326 TRP 0.016 0.002 TRP B 315 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16032) covalent geometry : angle 0.49811 / 0.26 (21764) hydrogen bonds : bond 0.04172 / 2.88 ( 865) hydrogen bonds : angle 3.80399 / 2.69 ( 2427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.650 Fit side-chains REVERT: E 37 ASP cc_start: 0.9110 (m-30) cc_final: 0.8718 (m-30) REVERT: E 51 LYS cc_start: 0.7674 (tmtt) cc_final: 0.7089 (tmtt) REVERT: F 37 ASP cc_start: 0.9036 (m-30) cc_final: 0.8710 (m-30) REVERT: G 37 ASP cc_start: 0.8866 (m-30) cc_final: 0.8556 (m-30) REVERT: G 51 LYS cc_start: 0.7673 (tmtt) cc_final: 0.7074 (tmtt) REVERT: H 37 ASP cc_start: 0.8803 (m-30) cc_final: 0.8577 (m-30) REVERT: H 51 LYS cc_start: 0.7673 (tmtt) cc_final: 0.7078 (tmtt) REVERT: H 136 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7917 (ttt180) outliers start: 14 outliers final: 6 residues processed: 168 average time/residue: 0.7460 time to fit residues: 136.4406 Evaluate side-chains 169 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 106 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN F 38 GLN G 38 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.043947 restraints weight = 34340.227| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 2.21 r_work: 0.2422 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16032 Z= 0.157 Angle : 0.514 7.793 21764 Z= 0.265 Chirality : 0.043 0.217 2564 Planarity : 0.005 0.062 2760 Dihedral : 4.329 21.980 2352 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.01 % Allowed : 8.39 % Favored : 90.60 % 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: 2.15 (0.19), residues: 2028 helix: 2.65 (0.17), residues: 988 sheet: 0.99 (0.36), residues: 244 loop : 0.02 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 305 TYR 0.008 0.001 TYR A 380 PHE 0.009 0.001 PHE D 326 TRP 0.015 0.002 TRP B 315 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (16032) covalent geometry : angle 0.51385 / 0.27 (21764) hydrogen bonds : bond 0.04402 / 3.04 ( 865) hydrogen bonds : angle 3.85134 / 2.72 ( 2427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.691 Fit side-chains REVERT: E 37 ASP cc_start: 0.9104 (m-30) cc_final: 0.8733 (m-30) REVERT: E 51 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7131 (tmtt) REVERT: F 37 ASP cc_start: 0.9048 (m-30) cc_final: 0.8713 (m-30) REVERT: G 37 ASP cc_start: 0.8867 (m-30) cc_final: 0.8557 (m-30) REVERT: G 51 LYS cc_start: 0.7677 (tmtt) cc_final: 0.7073 (tmtt) REVERT: H 37 ASP cc_start: 0.8777 (m-30) cc_final: 0.8553 (m-30) REVERT: H 51 LYS cc_start: 0.7679 (tmtt) cc_final: 0.7074 (tmtt) REVERT: H 136 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7891 (ttt180) outliers start: 17 outliers final: 8 residues processed: 164 average time/residue: 0.7680 time to fit residues: 136.8632 Evaluate side-chains 172 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 198 optimal weight: 0.8980 chunk 142 optimal weight: 0.0670 chunk 136 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN F 38 GLN G 38 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.045462 restraints weight = 34090.584| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.19 r_work: 0.2465 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9233 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16032 Z= 0.109 Angle : 0.493 8.014 21764 Z= 0.254 Chirality : 0.042 0.221 2564 Planarity : 0.004 0.061 2760 Dihedral : 4.181 21.559 2352 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % Rotamer: Outliers : 0.60 % Allowed : 8.69 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 2028 helix: 2.69 (0.17), residues: 988 sheet: 1.02 (0.34), residues: 268 loop : 0.17 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 305 TYR 0.008 0.001 TYR G 53 PHE 0.008 0.001 PHE B 83 TRP 0.017 0.002 TRP A 315 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16032) covalent geometry : angle 0.49295 / 0.25 (21764) hydrogen bonds : bond 0.03623 / 2.50 ( 865) hydrogen bonds : angle 3.69350 / 2.61 ( 2427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.599 Fit side-chains REVERT: E 37 ASP cc_start: 0.9114 (m-30) cc_final: 0.8726 (m-30) REVERT: E 51 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7090 (tmtt) REVERT: F 37 ASP cc_start: 0.9068 (m-30) cc_final: 0.8730 (m-30) REVERT: F 112 ARG cc_start: 0.8900 (ttp-110) cc_final: 0.8661 (ttp80) REVERT: G 37 ASP cc_start: 0.8848 (m-30) cc_final: 0.8558 (m-30) REVERT: G 51 LYS cc_start: 0.7665 (tmtt) cc_final: 0.7062 (tmtt) REVERT: H 37 ASP cc_start: 0.8775 (m-30) cc_final: 0.8559 (m-30) REVERT: H 51 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7069 (tmtt) REVERT: H 136 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7970 (ttt180) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.7347 time to fit residues: 133.5373 Evaluate side-chains 170 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 54 optimal weight: 0.0030 chunk 174 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN F 38 GLN H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.043348 restraints weight = 34220.131| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 2.20 r_work: 0.2406 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2293 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16032 Z= 0.199 Angle : 0.544 7.170 21764 Z= 0.280 Chirality : 0.045 0.211 2564 Planarity : 0.005 0.066 2760 Dihedral : 4.392 22.266 2352 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 0.60 % Allowed : 8.87 % Favored : 90.54 % 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: 2.13 (0.19), residues: 2028 helix: 2.64 (0.17), residues: 988 sheet: 0.98 (0.36), residues: 244 loop : -0.01 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 305 TYR 0.009 0.001 TYR B 380 PHE 0.010 0.001 PHE B 326 TRP 0.014 0.002 TRP D 315 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (16032) covalent geometry : angle 0.54405 / 0.28 (21764) hydrogen bonds : bond 0.04820 / 3.32 ( 865) hydrogen bonds : angle 3.91492 / 2.77 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7456.58 seconds wall clock time: 127 minutes 28.82 seconds (7648.82 seconds total)