Starting phenix.real_space_refine on Sat Jul 4 01:41:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bih_44590/07_2026/9bih_44590.map" } resolution = 3.24 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= -0.002 sd= 0.066 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 55 5.49 5 S 66 5.16 5 C 11071 2.51 5 N 2852 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s 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: 17576 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2744 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 14, 'TRANS': 334} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 591 Classifications: {'RNA': 28} Modifications used: {'p5*END': 1, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 571 Classifications: {'RNA': 27} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna3p': 26} Time building chain proxies: 4.46, per 1000 atoms: 0.25 Number of scatterers: 17576 At special positions: 0 Unit cell: (112.604, 122.958, 132.019, 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 66 16.00 P 55 15.00 O 3532 8.00 N 2852 7.00 C 11071 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: 1.38 Conformation dependent library (CDL) restraints added in 737.2 milliseconds 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 26.5% alpha, 24.9% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.510A pdb=" N LEU A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.700A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.519A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.521A pdb=" N LEU B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.688A pdb=" N LEU C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.500A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.545A pdb=" N LEU D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.562A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.517A pdb=" N LEU E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 309 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 removed outlier: 3.576A pdb=" N LEU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 removed outlier: 3.743A pdb=" N LEU F 134 " --> pdb=" O GLY F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.539A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.532A pdb=" N LEU F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.627A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.026A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.026A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 8.073A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 276 through 282 removed outlier: 3.503A pdb=" N TYR A 279 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.190A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.649A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.219A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.219A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 8.074A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 265 through 267 removed outlier: 4.766A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 317 through 323 Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.633A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.255A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 155 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.255A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC4, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.997A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.845A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 317 through 323 Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.562A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.161A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.161A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 8.043A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.629A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.556A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.416A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.416A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 8.094A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 265 through 267 removed outlier: 4.770A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 322 removed outlier: 5.477A pdb=" N LYS E 335 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.733A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.240A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.240A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 8.061A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.508A pdb=" N LEU F 168 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.543A pdb=" N GLU F 265 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 3.562A pdb=" N SER F 329 " --> pdb=" O LYS F 345 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5108 1.33 - 1.45: 3086 1.45 - 1.57: 9643 1.57 - 1.69: 108 1.69 - 1.81: 102 Bond restraints: 18047 Sorted by residual: bond pdb=" CG1 ILE C 86 " pdb=" CD1 ILE C 86 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.83e+00 bond pdb=" N9 A G 15 " pdb=" C4 A G 15 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.55e+00 bond pdb=" CG1 ILE B 86 " pdb=" CD1 ILE B 86 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CB ASN A 30 " pdb=" CG ASN A 30 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" P U G 1 " pdb=" OP2 U G 1 " ideal model delta sigma weight residual 1.485 1.456 0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 18042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 23587 1.19 - 2.37: 967 2.37 - 3.56: 135 3.56 - 4.75: 34 4.75 - 5.93: 9 Bond angle restraints: 24732 Sorted by residual: angle pdb=" N1 U G 14 " pdb=" C2 U G 14 " pdb=" O2 U G 14 " ideal model delta sigma weight residual 122.80 125.63 -2.83 7.00e-01 2.04e+00 1.63e+01 angle pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sigma weight residual 117.70 122.52 -4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" O2 U G 14 " pdb=" C2 U G 14 " pdb=" N3 U G 14 " ideal model delta sigma weight residual 122.20 119.80 2.40 7.00e-01 2.04e+00 1.18e+01 angle pdb=" CA VAL B 23 " pdb=" C VAL B 23 " pdb=" N PRO B 24 " ideal model delta sigma weight residual 116.57 119.46 -2.89 9.80e-01 1.04e+00 8.73e+00 angle pdb=" C4' U G 14 " pdb=" C3' U G 14 " pdb=" C2' U G 14 " ideal model delta sigma weight residual 102.60 105.30 -2.70 1.00e+00 1.00e+00 7.30e+00 ... (remaining 24727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 9952 15.53 - 31.07: 673 31.07 - 46.60: 126 46.60 - 62.13: 59 62.13 - 77.66: 24 Dihedral angle restraints: 10834 sinusoidal: 4800 harmonic: 6034 Sorted by residual: dihedral pdb=" O4' U G 14 " pdb=" C2' U G 14 " pdb=" C1' U G 14 " pdb=" C3' U G 14 " ideal model delta sinusoidal sigma weight residual 25.00 -17.40 42.40 1 8.00e+00 1.56e-02 3.92e+01 dihedral pdb=" C4' U G 14 " pdb=" C3' U G 14 " pdb=" C2' U G 14 " pdb=" C1' U G 14 " ideal model delta sinusoidal sigma weight residual 36.00 1.55 34.45 1 8.00e+00 1.56e-02 2.63e+01 dihedral pdb=" C4' U G 14 " pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" C2' U G 14 " ideal model delta sinusoidal sigma weight residual 3.00 -31.38 34.38 1 8.00e+00 1.56e-02 2.62e+01 ... (remaining 10831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1575 0.031 - 0.062: 756 0.062 - 0.093: 362 0.093 - 0.124: 165 0.124 - 0.155: 23 Chirality restraints: 2881 Sorted by residual: chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CB ILE C 97 " pdb=" CA ILE C 97 " pdb=" CG1 ILE C 97 " pdb=" CG2 ILE C 97 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 2878 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO D 51 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 65 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO F 66 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 50 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO F 51 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 51 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 51 " 0.022 5.00e-02 4.00e+02 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2079 2.74 - 3.28: 15999 3.28 - 3.82: 29215 3.82 - 4.36: 36432 4.36 - 4.90: 61745 Nonbonded interactions: 145470 Sorted by model distance: nonbonded pdb=" O GLY D 77 " pdb=" OG1 THR D 121 " model vdw 2.204 3.040 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 213 " pdb=" OH TYR B 226 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP F 213 " pdb=" OH TYR F 226 " model vdw 2.226 3.040 nonbonded pdb=" OE2 GLU A 0 " pdb=" OG SER A 2 " model vdw 2.228 3.040 ... (remaining 145465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.770 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: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.580 Find NCS groups from input model: 0.400 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 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 0.066 18047 Z= 0.336 Angle : 0.570 5.934 24732 Z= 0.336 Chirality : 0.047 0.155 2881 Planarity : 0.004 0.046 2979 Dihedral : 12.119 77.665 6944 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.63 % Allowed : 5.15 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2071 helix: 0.17 (0.22), residues: 532 sheet: 0.30 (0.33), residues: 304 loop : -0.77 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 91 TYR 0.013 0.002 TYR A 343 PHE 0.021 0.002 PHE A 269 TRP 0.010 0.002 TRP D 87 HIS 0.006 0.001 HIS C 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.34 (18047) covalent geometry : angle 0.57025 / 0.34 (24732) hydrogen bonds : bond 0.18801 / 12.15 ( 659) hydrogen bonds : angle 8.22967 / 5.80 ( 1825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 514 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 233 PHE cc_start: 0.7224 (m-80) cc_final: 0.6318 (m-80) REVERT: D 301 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: E 84 THR cc_start: 0.5579 (t) cc_final: 0.5345 (p) REVERT: E 183 VAL cc_start: 0.7237 (t) cc_final: 0.6965 (t) REVERT: E 330 PHE cc_start: 0.7150 (m-80) cc_final: 0.6612 (m-80) REVERT: E 342 PHE cc_start: 0.6468 (t80) cc_final: 0.6265 (t80) REVERT: F 300 LEU cc_start: 0.7390 (tp) cc_final: 0.6812 (tp) REVERT: F 321 VAL cc_start: 0.7706 (t) cc_final: 0.7291 (p) outliers start: 30 outliers final: 3 residues processed: 535 average time/residue: 0.1394 time to fit residues: 113.7274 Evaluate side-chains 294 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 290 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 336 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 197 GLN B 310 GLN C 164 ASN C 245 GLN D 15 HIS E 243 HIS E 310 GLN ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.083831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056889 restraints weight = 51770.193| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.45 r_work: 0.2742 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18047 Z= 0.179 Angle : 0.691 14.194 24732 Z= 0.361 Chirality : 0.046 0.205 2881 Planarity : 0.005 0.056 2979 Dihedral : 10.885 74.230 3012 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.42 % Allowed : 12.48 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2071 helix: 0.11 (0.22), residues: 539 sheet: 0.14 (0.31), residues: 317 loop : -0.57 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 91 TYR 0.024 0.002 TYR F 343 PHE 0.024 0.002 PHE F 135 TRP 0.013 0.001 TRP A 87 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (18047) covalent geometry : angle 0.69110 / 0.36 (24732) hydrogen bonds : bond 0.04425 / 3.00 ( 659) hydrogen bonds : angle 6.02777 / 4.28 ( 1825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7873 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 190 LEU cc_start: 0.8269 (mp) cc_final: 0.8059 (mp) REVERT: C 214 PHE cc_start: 0.7799 (t80) cc_final: 0.7551 (t80) REVERT: C 245 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: D 169 ILE cc_start: 0.8402 (mt) cc_final: 0.7951 (mp) REVERT: E 1 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7486 (pmm) REVERT: E 84 THR cc_start: 0.6022 (t) cc_final: 0.5709 (p) REVERT: E 183 VAL cc_start: 0.7804 (t) cc_final: 0.7574 (t) REVERT: E 217 LEU cc_start: 0.8258 (mt) cc_final: 0.7740 (mt) REVERT: E 342 PHE cc_start: 0.7717 (t80) cc_final: 0.7345 (t80) REVERT: F 78 VAL cc_start: 0.8470 (t) cc_final: 0.7424 (p) REVERT: F 156 VAL cc_start: 0.8928 (t) cc_final: 0.8716 (p) outliers start: 63 outliers final: 35 residues processed: 365 average time/residue: 0.1219 time to fit residues: 70.5636 Evaluate side-chains 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN B 338 HIS C 12 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.084249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057457 restraints weight = 52545.349| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.39 r_work: 0.2773 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 18047 Z= 0.208 Angle : 0.662 16.531 24732 Z= 0.350 Chirality : 0.045 0.184 2881 Planarity : 0.005 0.047 2979 Dihedral : 10.761 74.134 3006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.55 % Allowed : 14.22 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2071 helix: 0.28 (0.23), residues: 534 sheet: -0.06 (0.30), residues: 312 loop : -0.68 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 225 TYR 0.034 0.002 TYR D 238 PHE 0.030 0.002 PHE E 135 TRP 0.015 0.001 TRP C 59 HIS 0.007 0.001 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (18047) covalent geometry : angle 0.66199 / 0.35 (24732) hydrogen bonds : bond 0.04414 / 2.90 ( 659) hydrogen bonds : angle 5.58451 / 3.98 ( 1825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.6468 (tm-30) cc_final: 0.6185 (tm-30) REVERT: C 105 MET cc_start: 0.7761 (mmm) cc_final: 0.7473 (mmm) REVERT: C 210 MET cc_start: 0.7746 (mpp) cc_final: 0.7328 (mmp) REVERT: C 245 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: C 331 MET cc_start: 0.7216 (tmm) cc_final: 0.6759 (ppp) REVERT: E 285 GLN cc_start: 0.8955 (tp40) cc_final: 0.8493 (tp40) REVERT: E 342 PHE cc_start: 0.7679 (t80) cc_final: 0.7351 (t80) REVERT: F 156 VAL cc_start: 0.9064 (t) cc_final: 0.8827 (p) REVERT: F 203 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7476 (tp30) REVERT: F 228 LEU cc_start: 0.8728 (mt) cc_final: 0.8515 (mp) outliers start: 47 outliers final: 30 residues processed: 302 average time/residue: 0.1229 time to fit residues: 58.8269 Evaluate side-chains 264 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN B 83 ASN C 245 GLN D 15 HIS ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS F 96 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057156 restraints weight = 52728.580| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.34 r_work: 0.2782 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 18047 Z= 0.215 Angle : 0.643 11.361 24732 Z= 0.341 Chirality : 0.046 0.183 2881 Planarity : 0.004 0.047 2979 Dihedral : 10.727 74.076 3006 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.15 % Allowed : 15.52 % Favored : 81.33 % Cbeta Deviations : 0.05 % 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: -0.64 (0.18), residues: 2071 helix: 0.29 (0.23), residues: 534 sheet: -0.14 (0.28), residues: 312 loop : -0.81 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 225 TYR 0.040 0.003 TYR E 238 PHE 0.023 0.002 PHE B 214 TRP 0.012 0.001 TRP A 59 HIS 0.008 0.001 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (18047) covalent geometry : angle 0.64289 / 0.34 (24732) hydrogen bonds : bond 0.04203 / 2.88 ( 659) hydrogen bonds : angle 5.43437 / 3.90 ( 1825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.8424 (t80) cc_final: 0.8129 (t80) REVERT: B 198 SER cc_start: 0.8718 (m) cc_final: 0.8432 (p) REVERT: B 338 HIS cc_start: 0.8336 (m90) cc_final: 0.7977 (m90) REVERT: C 272 MET cc_start: 0.8244 (ppp) cc_final: 0.7990 (ppp) REVERT: D 338 HIS cc_start: 0.7757 (t70) cc_final: 0.7110 (t70) REVERT: E 106 THR cc_start: 0.8231 (p) cc_final: 0.8024 (p) REVERT: E 122 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7358 (t) REVERT: E 285 GLN cc_start: 0.8905 (tp40) cc_final: 0.8469 (tp40) REVERT: E 342 PHE cc_start: 0.7987 (t80) cc_final: 0.7563 (t80) REVERT: F 156 VAL cc_start: 0.9220 (t) cc_final: 0.8988 (p) outliers start: 58 outliers final: 40 residues processed: 265 average time/residue: 0.1301 time to fit residues: 54.1019 Evaluate side-chains 230 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 HIS E 75 ASN E 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056841 restraints weight = 52952.021| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.38 r_work: 0.2779 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18047 Z= 0.170 Angle : 0.622 10.616 24732 Z= 0.323 Chirality : 0.045 0.206 2881 Planarity : 0.004 0.054 2979 Dihedral : 10.692 73.945 3006 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.82 % Allowed : 16.33 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2071 helix: 0.35 (0.23), residues: 534 sheet: 0.02 (0.29), residues: 282 loop : -0.74 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 62 TYR 0.033 0.002 TYR C 343 PHE 0.038 0.002 PHE C 330 TRP 0.042 0.002 TRP D 59 HIS 0.072 0.003 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (18047) covalent geometry : angle 0.62221 / 0.32 (24732) hydrogen bonds : bond 0.03702 / 2.52 ( 659) hydrogen bonds : angle 5.25462 / 3.78 ( 1825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7381 (mmm) cc_final: 0.7153 (mtp) REVERT: B 338 HIS cc_start: 0.8416 (m90) cc_final: 0.8081 (m90) REVERT: C 42 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 48 THR cc_start: 0.9028 (m) cc_final: 0.8710 (p) REVERT: C 210 MET cc_start: 0.7982 (mpp) cc_final: 0.7503 (mmp) REVERT: C 331 MET cc_start: 0.8490 (tmm) cc_final: 0.7823 (ppp) REVERT: D 105 MET cc_start: 0.8662 (mmm) cc_final: 0.8394 (tpt) REVERT: E 122 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7871 (t) REVERT: E 225 ARG cc_start: 0.8778 (ptm160) cc_final: 0.8575 (ptm160) REVERT: E 285 GLN cc_start: 0.9057 (tp40) cc_final: 0.8747 (tp40) REVERT: E 342 PHE cc_start: 0.7983 (t80) cc_final: 0.7398 (t80) REVERT: F 228 LEU cc_start: 0.8773 (mt) cc_final: 0.8566 (mp) outliers start: 52 outliers final: 37 residues processed: 217 average time/residue: 0.1320 time to fit residues: 44.7958 Evaluate side-chains 198 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.084066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057310 restraints weight = 52810.004| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.36 r_work: 0.2794 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18047 Z= 0.110 Angle : 0.555 10.342 24732 Z= 0.286 Chirality : 0.043 0.182 2881 Planarity : 0.004 0.048 2979 Dihedral : 10.630 73.986 3006 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.95 % Allowed : 17.91 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2071 helix: 0.44 (0.23), residues: 534 sheet: 0.11 (0.29), residues: 283 loop : -0.68 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 225 TYR 0.015 0.001 TYR C 226 PHE 0.017 0.001 PHE D 241 TRP 0.015 0.001 TRP D 59 HIS 0.018 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (18047) covalent geometry : angle 0.55483 / 0.29 (24732) hydrogen bonds : bond 0.03253 / 2.15 ( 659) hydrogen bonds : angle 5.09234 / 3.67 ( 1825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 HIS cc_start: 0.8431 (m90) cc_final: 0.8109 (m90) REVERT: C 42 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 48 THR cc_start: 0.9092 (m) cc_final: 0.8788 (p) REVERT: C 331 MET cc_start: 0.8485 (tmm) cc_final: 0.7934 (ppp) REVERT: D 105 MET cc_start: 0.8579 (mmm) cc_final: 0.8328 (tpt) REVERT: D 338 HIS cc_start: 0.7758 (t70) cc_final: 0.7088 (t70) REVERT: E 122 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7870 (t) REVERT: E 285 GLN cc_start: 0.9050 (tp40) cc_final: 0.8697 (tp40) REVERT: E 330 PHE cc_start: 0.8561 (m-80) cc_final: 0.8136 (m-80) REVERT: E 342 PHE cc_start: 0.8209 (t80) cc_final: 0.7574 (t80) outliers start: 36 outliers final: 27 residues processed: 187 average time/residue: 0.1294 time to fit residues: 38.1426 Evaluate side-chains 185 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 193 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 164 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057543 restraints weight = 53254.559| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.41 r_work: 0.2799 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18047 Z= 0.103 Angle : 0.540 11.469 24732 Z= 0.279 Chirality : 0.043 0.175 2881 Planarity : 0.004 0.049 2979 Dihedral : 10.556 73.985 3006 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.95 % Allowed : 18.12 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2071 helix: 0.46 (0.23), residues: 534 sheet: 0.20 (0.29), residues: 288 loop : -0.60 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 127 TYR 0.013 0.001 TYR C 226 PHE 0.015 0.001 PHE F 233 TRP 0.009 0.001 TRP D 87 HIS 0.007 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (18047) covalent geometry : angle 0.54018 / 0.28 (24732) hydrogen bonds : bond 0.03104 / 2.10 ( 659) hydrogen bonds : angle 4.95887 / 3.56 ( 1825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 HIS cc_start: 0.8486 (m90) cc_final: 0.8145 (m90) REVERT: C 42 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 48 THR cc_start: 0.9209 (m) cc_final: 0.8905 (p) REVERT: C 215 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8962 (pp) REVERT: C 331 MET cc_start: 0.8512 (tmm) cc_final: 0.7940 (ppp) REVERT: D 105 MET cc_start: 0.8593 (mmm) cc_final: 0.8370 (tpt) REVERT: D 338 HIS cc_start: 0.7745 (t70) cc_final: 0.7151 (t70) REVERT: E 210 MET cc_start: 0.7548 (ppp) cc_final: 0.7343 (ppp) REVERT: E 285 GLN cc_start: 0.9108 (tp40) cc_final: 0.8810 (tp40) REVERT: F 92 ASP cc_start: 0.8667 (t70) cc_final: 0.8347 (t0) outliers start: 36 outliers final: 26 residues processed: 186 average time/residue: 0.1364 time to fit residues: 39.4335 Evaluate side-chains 172 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 194 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN F 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.082173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.054743 restraints weight = 53599.840| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.44 r_work: 0.2715 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.9614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 18047 Z= 0.236 Angle : 0.724 23.345 24732 Z= 0.374 Chirality : 0.048 0.330 2881 Planarity : 0.005 0.088 2979 Dihedral : 10.773 73.939 3006 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.66 % Allowed : 18.34 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2071 helix: 0.19 (0.23), residues: 541 sheet: -0.05 (0.29), residues: 322 loop : -0.70 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 225 TYR 0.024 0.002 TYR C 226 PHE 0.033 0.002 PHE E 330 TRP 0.023 0.002 TRP F 333 HIS 0.005 0.001 HIS E 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (18047) covalent geometry : angle 0.72410 / 0.37 (24732) hydrogen bonds : bond 0.04295 / 2.91 ( 659) hydrogen bonds : angle 5.30456 / 3.83 ( 1825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9087 (p) REVERT: A 331 MET cc_start: 0.9147 (tpp) cc_final: 0.8861 (tpt) REVERT: B 1 MET cc_start: 0.8521 (mmm) cc_final: 0.8100 (mtp) REVERT: B 210 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7811 (mtm) REVERT: B 338 HIS cc_start: 0.8553 (m90) cc_final: 0.8178 (m90) REVERT: C 210 MET cc_start: 0.8167 (mpp) cc_final: 0.7826 (mmm) REVERT: C 214 PHE cc_start: 0.8835 (t80) cc_final: 0.8586 (t80) REVERT: C 265 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8223 (pt0) REVERT: C 331 MET cc_start: 0.8798 (tmm) cc_final: 0.8181 (ppp) REVERT: D 338 HIS cc_start: 0.7864 (t70) cc_final: 0.7294 (t70) REVERT: E 139 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7682 (tpt-90) REVERT: E 285 GLN cc_start: 0.9213 (tp40) cc_final: 0.8911 (tp40) REVERT: E 331 MET cc_start: 0.8361 (mmm) cc_final: 0.7985 (mmm) REVERT: F 96 HIS cc_start: 0.8786 (m170) cc_final: 0.8449 (m170) REVERT: F 225 ARG cc_start: 0.8944 (ptm-80) cc_final: 0.8507 (tmm-80) outliers start: 49 outliers final: 35 residues processed: 164 average time/residue: 0.1390 time to fit residues: 35.2839 Evaluate side-chains 147 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 204 optimal weight: 50.0000 chunk 181 optimal weight: 7.9990 chunk 147 optimal weight: 0.3980 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 170 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN C 245 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.082894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055565 restraints weight = 53283.414| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.41 r_work: 0.2744 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.9792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18047 Z= 0.124 Angle : 0.612 16.697 24732 Z= 0.307 Chirality : 0.044 0.208 2881 Planarity : 0.004 0.045 2979 Dihedral : 10.705 73.866 3006 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 19.70 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2071 helix: 0.37 (0.23), residues: 539 sheet: 0.19 (0.30), residues: 293 loop : -0.63 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 139 TYR 0.019 0.001 TYR C 226 PHE 0.014 0.001 PHE B 204 TRP 0.015 0.001 TRP F 333 HIS 0.004 0.001 HIS C 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (18047) covalent geometry : angle 0.61160 / 0.31 (24732) hydrogen bonds : bond 0.03297 / 2.20 ( 659) hydrogen bonds : angle 5.06420 / 3.62 ( 1825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.9021 (tpp) cc_final: 0.8693 (tpt) REVERT: B 1 MET cc_start: 0.8566 (mmm) cc_final: 0.8201 (mtp) REVERT: B 210 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (mtm) REVERT: B 338 HIS cc_start: 0.8555 (m90) cc_final: 0.8190 (m90) REVERT: C 42 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8553 (tm-30) REVERT: C 48 THR cc_start: 0.9445 (m) cc_final: 0.9123 (p) REVERT: C 210 MET cc_start: 0.8263 (mpp) cc_final: 0.7728 (mmm) REVERT: C 214 PHE cc_start: 0.8854 (t80) cc_final: 0.8566 (t80) REVERT: C 215 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8946 (pp) REVERT: C 245 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7236 (tp40) REVERT: C 265 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8292 (pt0) REVERT: C 331 MET cc_start: 0.8812 (tmm) cc_final: 0.8187 (ppp) REVERT: D 338 HIS cc_start: 0.7781 (t70) cc_final: 0.7225 (t70) REVERT: E 210 MET cc_start: 0.7927 (ppp) cc_final: 0.7713 (ppp) REVERT: E 285 GLN cc_start: 0.9201 (tp40) cc_final: 0.8896 (tp40) REVERT: E 331 MET cc_start: 0.8365 (mmm) cc_final: 0.8006 (mmm) REVERT: F 225 ARG cc_start: 0.8984 (ptm-80) cc_final: 0.8561 (tmm-80) outliers start: 29 outliers final: 21 residues processed: 136 average time/residue: 0.1332 time to fit residues: 28.5225 Evaluate side-chains 134 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 0.0050 chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055398 restraints weight = 53230.389| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.42 r_work: 0.2735 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.9967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18047 Z= 0.134 Angle : 0.602 14.104 24732 Z= 0.303 Chirality : 0.043 0.167 2881 Planarity : 0.004 0.045 2979 Dihedral : 10.675 73.895 3006 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 20.13 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2071 helix: 0.43 (0.23), residues: 539 sheet: 0.27 (0.30), residues: 293 loop : -0.57 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.015 0.001 TYR C 226 PHE 0.022 0.001 PHE E 342 TRP 0.015 0.001 TRP F 333 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18047) covalent geometry : angle 0.60168 / 0.30 (24732) hydrogen bonds : bond 0.03228 / 2.16 ( 659) hydrogen bonds : angle 5.02508 / 3.60 ( 1825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 CYS cc_start: 0.9240 (m) cc_final: 0.8943 (m) REVERT: A 331 MET cc_start: 0.9010 (tpp) cc_final: 0.8705 (tpt) REVERT: B 1 MET cc_start: 0.8611 (mmm) cc_final: 0.8261 (mtp) REVERT: B 338 HIS cc_start: 0.8527 (m90) cc_final: 0.8164 (m90) REVERT: C 42 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 48 THR cc_start: 0.9438 (m) cc_final: 0.9147 (p) REVERT: C 105 MET cc_start: 0.8476 (mmm) cc_final: 0.8213 (mmt) REVERT: C 210 MET cc_start: 0.8398 (mpp) cc_final: 0.7768 (mmm) REVERT: C 214 PHE cc_start: 0.8875 (t80) cc_final: 0.8625 (t80) REVERT: C 265 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8258 (pt0) REVERT: C 331 MET cc_start: 0.8803 (tmm) cc_final: 0.8188 (ppp) REVERT: D 338 HIS cc_start: 0.7795 (t70) cc_final: 0.7252 (t70) REVERT: E 210 MET cc_start: 0.7867 (ppp) cc_final: 0.7664 (ppp) REVERT: E 285 GLN cc_start: 0.9216 (tp40) cc_final: 0.8986 (tp40) REVERT: E 330 PHE cc_start: 0.8957 (m-80) cc_final: 0.8485 (m-80) REVERT: E 331 MET cc_start: 0.8417 (mmm) cc_final: 0.8144 (mmm) REVERT: F 225 ARG cc_start: 0.8968 (ptm-80) cc_final: 0.8519 (tmm-80) outliers start: 26 outliers final: 24 residues processed: 131 average time/residue: 0.1307 time to fit residues: 26.5781 Evaluate side-chains 130 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054768 restraints weight = 53454.383| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.40 r_work: 0.2719 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 1.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 18047 Z= 0.143 Angle : 0.598 15.393 24732 Z= 0.299 Chirality : 0.043 0.152 2881 Planarity : 0.004 0.050 2979 Dihedral : 10.641 73.890 3006 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 20.13 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 2071 helix: 0.46 (0.23), residues: 539 sheet: -0.07 (0.27), residues: 353 loop : -0.48 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 91 TYR 0.017 0.001 TYR B 226 PHE 0.019 0.001 PHE E 135 TRP 0.014 0.001 TRP F 333 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18047) covalent geometry : angle 0.59766 / 0.30 (24732) hydrogen bonds : bond 0.03145 / 2.09 ( 659) hydrogen bonds : angle 4.96470 / 3.55 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4212.77 seconds wall clock time: 73 minutes 21.18 seconds (4401.18 seconds total)