Starting phenix.real_space_refine on Thu Aug 6 21:46:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bih_44590/08_2026/9bih_44590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bih_44590/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bih_44590/08_2026/9bih_44590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bih_44590/08_2026/9bih_44590.map" model { file = "/net/cci-nas-00/data/ceres_data/9bih_44590/08_2026/9bih_44590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bih_44590/08_2026/9bih_44590.cif" } 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-2.2rc3-6140/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: 4.19, per 1000 atoms: 0.24 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: 1.69 Conformation dependent library (CDL) restraints added in 681.4 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: 2.17 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: 2.22 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=" O4' U G 14 " pdb=" C1' U G 14 " ideal model delta sigma weight residual 1.412 1.391 0.021 1.30e-02 5.92e+03 2.49e+00 bond pdb=" C3' U G 14 " pdb=" C2' U G 14 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.10e-02 8.26e+03 2.30e+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 ... (remaining 18042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 23422 1.19 - 2.37: 1068 2.37 - 3.56: 199 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=" O5' A H 23 " pdb=" C5' A H 23 " pdb=" C4' A H 23 " ideal model delta sigma weight residual 109.40 112.14 -2.74 8.00e-01 1.56e+00 1.17e+01 angle pdb=" O5' U G 27 " pdb=" C5' U G 27 " pdb=" C4' U G 27 " ideal model delta sigma weight residual 109.40 112.13 -2.73 8.00e-01 1.56e+00 1.16e+01 ... (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: 1515 0.031 - 0.062: 759 0.062 - 0.093: 364 0.093 - 0.124: 176 0.124 - 0.155: 67 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=" C2' U H 24 " pdb=" C3' U H 24 " pdb=" O2' U H 24 " pdb=" C1' U H 24 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.72e-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: 0.760 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.770 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- 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= 0.338 Angle : 0.601 5.934 24732 Z= 0.364 Chirality : 0.050 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 0.00787 / 0.34 (18047) covalent geometry : angle 0.60076 / 0.36 (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 : 0.706 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: 0.1345 time to fit residues: 109.7101 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 : 0.661 ------------------------------------------------------------------------------- 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 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3567 r_free = 0.3567 target = 0.083732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056742 restraints weight = 51727.547| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.44 r_work: 0.2739 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18047 Z= 0.171 Angle : 0.672 13.696 24732 Z= 0.353 Chirality : 0.046 0.193 2881 Planarity : 0.005 0.053 2979 Dihedral : 10.850 74.305 3012 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.31 % Allowed : 12.64 % Favored : 84.05 % 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: 0.18 (0.22), residues: 539 sheet: 0.17 (0.31), residues: 317 loop : -0.58 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 91 TYR 0.020 0.002 TYR F 343 PHE 0.023 0.002 PHE B 16 TRP 0.012 0.001 TRP A 87 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (18047) covalent geometry : angle 0.67213 / 0.35 (24732) hydrogen bonds : bond 0.04653 / 3.14 ( 659) hydrogen bonds : angle 6.07574 / 4.31 ( 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 390 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.666 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: 0.7847 (tt0) cc_final: 0.7605 (tm-30) REVERT: A 190 LEU cc_start: 0.8250 (mp) cc_final: 0.8036 (mp) REVERT: C 245 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: D 169 ILE cc_start: 0.8392 (mt) cc_final: 0.7920 (mp) REVERT: E 84 THR cc_start: 0.5994 (t) cc_final: 0.5682 (p) REVERT: E 183 VAL cc_start: 0.7797 (t) cc_final: 0.7563 (t) REVERT: E 217 LEU cc_start: 0.8245 (mt) cc_final: 0.7759 (mt) REVERT: E 260 LYS cc_start: 0.9414 (mttt) cc_final: 0.9189 (pttt) REVERT: E 285 GLN cc_start: 0.8871 (tp40) cc_final: 0.7940 (tp40) REVERT: E 342 PHE cc_start: 0.7719 (t80) cc_final: 0.7289 (t80) REVERT: F 156 VAL cc_start: 0.8906 (t) cc_final: 0.8690 (p) outliers start: 61 outliers final: 36 residues processed: 362 average time/residue: 0.1153 time to fit residues: 66.4278 Evaluate side-chains 309 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 210 MET 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 D residue 272 MET Chi-restraints excluded: chain D residue 291 CYS 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: 0.6980 chunk 179 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN B 5 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS C 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.083875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057258 restraints weight = 52507.549| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.35 r_work: 0.2782 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 18047 Z= 0.216 Angle : 0.697 18.627 24732 Z= 0.365 Chirality : 0.047 0.259 2881 Planarity : 0.005 0.066 2979 Dihedral : 10.742 74.186 3006 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.55 % Allowed : 14.49 % Favored : 82.96 % 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: -0.60 (0.18), residues: 2071 helix: 0.18 (0.22), residues: 534 sheet: -0.13 (0.29), residues: 312 loop : -0.70 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 225 TYR 0.029 0.002 TYR C 343 PHE 0.040 0.002 PHE E 135 TRP 0.018 0.002 TRP C 59 HIS 0.008 0.002 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (18047) covalent geometry : angle 0.69710 / 0.36 (24732) hydrogen bonds : bond 0.04575 / 3.04 ( 659) hydrogen bonds : angle 5.58499 / 3.99 ( 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 317 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.7918 (t80) cc_final: 0.7631 (t80) REVERT: B 214 PHE cc_start: 0.7149 (t80) cc_final: 0.6889 (t80) REVERT: C 105 MET cc_start: 0.8071 (mmm) cc_final: 0.7573 (mmm) REVERT: C 210 MET cc_start: 0.7790 (mpp) cc_final: 0.7462 (mmp) REVERT: C 245 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7723 (tp-100) REVERT: C 246 LEU cc_start: 0.6534 (tp) cc_final: 0.6175 (tp) REVERT: C 331 MET cc_start: 0.7284 (tmm) cc_final: 0.7081 (ppp) REVERT: E 221 GLU cc_start: 0.9089 (tp30) cc_final: 0.8878 (tp30) REVERT: E 285 GLN cc_start: 0.9020 (tp40) cc_final: 0.8630 (tp40) REVERT: E 342 PHE cc_start: 0.7563 (t80) cc_final: 0.7332 (t80) REVERT: F 36 VAL cc_start: 0.9043 (t) cc_final: 0.8835 (m) REVERT: F 156 VAL cc_start: 0.9095 (t) cc_final: 0.8853 (p) outliers start: 47 outliers final: 29 residues processed: 299 average time/residue: 0.1230 time to fit residues: 58.3876 Evaluate side-chains 256 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 B residue 183 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 142 VAL Chi-restraints excluded: chain D residue 156 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 132 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 41 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: 8.9990 chunk 146 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN B 83 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 243 HIS F 96 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.057162 restraints weight = 52879.907| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.34 r_work: 0.2785 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 18047 Z= 0.204 Angle : 0.631 12.080 24732 Z= 0.331 Chirality : 0.045 0.223 2881 Planarity : 0.004 0.050 2979 Dihedral : 10.707 74.134 3006 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.36 % Allowed : 15.41 % Favored : 81.23 % 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: -0.63 (0.18), residues: 2071 helix: 0.27 (0.23), residues: 534 sheet: 0.02 (0.29), residues: 317 loop : -0.83 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG D 62 TYR 0.032 0.002 TYR B 238 PHE 0.034 0.002 PHE A 303 TRP 0.016 0.001 TRP D 59 HIS 0.008 0.001 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (18047) covalent geometry : angle 0.63116 / 0.33 (24732) hydrogen bonds : bond 0.04051 / 2.75 ( 659) hydrogen bonds : angle 5.32934 / 3.80 ( 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 279 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7942 (ttp) cc_final: 0.7701 (ttt) REVERT: A 280 PHE cc_start: 0.8474 (t80) cc_final: 0.8184 (t80) REVERT: B 198 SER cc_start: 0.8698 (m) cc_final: 0.8391 (p) REVERT: B 338 HIS cc_start: 0.8351 (m90) cc_final: 0.7993 (m90) REVERT: C 331 MET cc_start: 0.7725 (tmm) cc_final: 0.7464 (tmm) REVERT: D 34 THR cc_start: 0.8202 (t) cc_final: 0.7956 (m) REVERT: D 105 MET cc_start: 0.8638 (mmm) cc_final: 0.8289 (mmm) REVERT: E 47 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8912 (mmmt) REVERT: E 106 THR cc_start: 0.8308 (p) cc_final: 0.8094 (p) REVERT: E 122 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7276 (t) REVERT: E 163 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7116 (tp) REVERT: E 221 GLU cc_start: 0.9042 (tp30) cc_final: 0.8792 (tp30) REVERT: E 225 ARG cc_start: 0.8547 (ptm160) cc_final: 0.8110 (ptm160) REVERT: E 285 GLN cc_start: 0.8973 (tp40) cc_final: 0.8569 (tp40) REVERT: E 330 PHE cc_start: 0.8451 (m-80) cc_final: 0.7751 (m-80) REVERT: E 342 PHE cc_start: 0.7991 (t80) cc_final: 0.7663 (t80) REVERT: F 156 VAL cc_start: 0.9241 (t) cc_final: 0.9009 (p) outliers start: 62 outliers final: 37 residues processed: 257 average time/residue: 0.1285 time to fit residues: 51.4297 Evaluate side-chains 224 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 32 VAL Chi-restraints excluded: chain B residue 50 LEU 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 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 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 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 163 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 243 HIS 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 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 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 195 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.083459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056870 restraints weight = 53072.556| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.33 r_work: 0.2779 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.7168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18047 Z= 0.175 Angle : 0.603 11.368 24732 Z= 0.316 Chirality : 0.044 0.256 2881 Planarity : 0.004 0.061 2979 Dihedral : 10.668 74.035 3006 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.60 % Allowed : 16.82 % Favored : 80.58 % 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: -0.63 (0.18), residues: 2071 helix: 0.31 (0.23), residues: 534 sheet: -0.10 (0.29), residues: 287 loop : -0.81 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 139 TYR 0.030 0.002 TYR D 238 PHE 0.040 0.002 PHE E 241 TRP 0.011 0.001 TRP D 59 HIS 0.083 0.003 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (18047) covalent geometry : angle 0.60320 / 0.32 (24732) hydrogen bonds : bond 0.03672 / 2.46 ( 659) hydrogen bonds : angle 5.14146 / 3.69 ( 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 219 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7422 (mmm) cc_final: 0.7197 (mtp) REVERT: B 219 MET cc_start: 0.8438 (mmm) cc_final: 0.8188 (mmm) REVERT: B 338 HIS cc_start: 0.8407 (m90) cc_final: 0.8073 (m90) REVERT: C 48 THR cc_start: 0.9043 (m) cc_final: 0.8767 (p) REVERT: C 210 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7320 (mmp) REVERT: C 215 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8936 (pp) REVERT: D 105 MET cc_start: 0.8738 (mmm) cc_final: 0.8483 (tpt) REVERT: D 338 HIS cc_start: 0.7787 (t70) cc_final: 0.7118 (t70) REVERT: E 285 GLN cc_start: 0.9096 (tp40) cc_final: 0.8726 (tp40) REVERT: E 330 PHE cc_start: 0.8679 (m-80) cc_final: 0.7898 (m-80) REVERT: E 342 PHE cc_start: 0.8063 (t80) cc_final: 0.7609 (t80) REVERT: F 47 LYS cc_start: 0.9377 (mmmt) cc_final: 0.9149 (mmtm) REVERT: F 92 ASP cc_start: 0.8716 (t70) cc_final: 0.8177 (t0) outliers start: 48 outliers final: 29 residues processed: 200 average time/residue: 0.1144 time to fit residues: 36.2575 Evaluate side-chains 179 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 32 VAL 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 210 MET 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 132 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 307 ILE 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 301 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 27 optimal weight: 0.0670 chunk 130 optimal weight: 0.3980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057498 restraints weight = 52728.430| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.34 r_work: 0.2792 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.7379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18047 Z= 0.101 Angle : 0.557 14.450 24732 Z= 0.284 Chirality : 0.043 0.166 2881 Planarity : 0.004 0.047 2979 Dihedral : 10.605 74.098 3006 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 17.74 % Favored : 80.20 % 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: -0.49 (0.18), residues: 2071 helix: 0.47 (0.23), residues: 529 sheet: 0.08 (0.29), residues: 288 loop : -0.76 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 225 TYR 0.016 0.001 TYR C 226 PHE 0.018 0.001 PHE C 330 TRP 0.011 0.001 TRP F 333 HIS 0.013 0.001 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (18047) covalent geometry : angle 0.55697 / 0.28 (24732) hydrogen bonds : bond 0.03205 / 2.15 ( 659) hydrogen bonds : angle 4.96397 / 3.55 ( 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 201 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 HIS cc_start: 0.8453 (m90) cc_final: 0.8081 (m90) REVERT: C 48 THR cc_start: 0.9162 (m) cc_final: 0.8889 (p) REVERT: C 210 MET cc_start: 0.7804 (mmp) cc_final: 0.7024 (mmm) REVERT: C 215 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8943 (pp) REVERT: C 331 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8091 (ppp) REVERT: D 105 MET cc_start: 0.8702 (mmm) cc_final: 0.8437 (tpt) REVERT: D 338 HIS cc_start: 0.7774 (t70) cc_final: 0.7391 (t70) REVERT: E 105 MET cc_start: 0.8489 (mmm) cc_final: 0.8181 (mmm) REVERT: E 225 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7630 (tmm-80) REVERT: E 285 GLN cc_start: 0.9099 (tp40) cc_final: 0.8735 (tp40) REVERT: E 330 PHE cc_start: 0.8727 (m-80) cc_final: 0.7925 (m-80) REVERT: E 342 PHE cc_start: 0.8108 (t80) cc_final: 0.7606 (t80) outliers start: 38 outliers final: 28 residues processed: 184 average time/residue: 0.1206 time to fit residues: 34.9280 Evaluate side-chains 178 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 VAL 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 331 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 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 166 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 34 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 193 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.083833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057045 restraints weight = 53450.232| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.39 r_work: 0.2781 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.8001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18047 Z= 0.117 Angle : 0.546 12.501 24732 Z= 0.283 Chirality : 0.043 0.140 2881 Planarity : 0.004 0.051 2979 Dihedral : 10.551 74.099 3006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.39 % Allowed : 17.74 % Favored : 79.87 % 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: -0.38 (0.18), residues: 2071 helix: 0.51 (0.23), residues: 533 sheet: 0.16 (0.29), residues: 323 loop : -0.69 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 225 TYR 0.015 0.001 TYR F 226 PHE 0.022 0.001 PHE E 214 TRP 0.017 0.001 TRP F 333 HIS 0.007 0.001 HIS E 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18047) covalent geometry : angle 0.54629 / 0.28 (24732) hydrogen bonds : bond 0.03199 / 2.15 ( 659) hydrogen bonds : angle 4.89994 / 3.52 ( 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 182 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8073 (ttt) cc_final: 0.7858 (tmm) REVERT: B 338 HIS cc_start: 0.8528 (m90) cc_final: 0.8175 (m90) REVERT: C 42 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 48 THR cc_start: 0.9193 (m) cc_final: 0.8894 (p) REVERT: C 210 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: C 214 PHE cc_start: 0.8404 (t80) cc_final: 0.8159 (t80) REVERT: C 215 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 331 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8127 (ppp) REVERT: D 42 GLU cc_start: 0.8687 (tt0) cc_final: 0.8392 (tm-30) REVERT: D 105 MET cc_start: 0.8809 (mmm) cc_final: 0.8559 (tpt) REVERT: D 225 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8681 (ptm-80) REVERT: D 338 HIS cc_start: 0.7787 (t70) cc_final: 0.7164 (t70) REVERT: E 203 GLU cc_start: 0.9062 (mp0) cc_final: 0.8843 (pm20) REVERT: E 285 GLN cc_start: 0.9125 (tp40) cc_final: 0.8831 (tp40) REVERT: F 92 ASP cc_start: 0.8766 (t70) cc_final: 0.8498 (t0) REVERT: F 225 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8422 (tmm-80) outliers start: 44 outliers final: 32 residues processed: 166 average time/residue: 0.1197 time to fit residues: 31.1122 Evaluate side-chains 163 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 272 MET 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 210 MET 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 331 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 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 166 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 34 THR 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: 0.4980 chunk 78 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 245 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.083228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056212 restraints weight = 53190.072| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.41 r_work: 0.2759 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.8726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18047 Z= 0.154 Angle : 0.575 13.388 24732 Z= 0.296 Chirality : 0.044 0.243 2881 Planarity : 0.004 0.049 2979 Dihedral : 10.588 74.051 3006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.22 % Allowed : 18.01 % Favored : 79.76 % 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: 0.46 (0.23), residues: 539 sheet: 0.12 (0.28), residues: 323 loop : -0.67 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 91 TYR 0.016 0.001 TYR E 279 PHE 0.039 0.002 PHE E 330 TRP 0.015 0.001 TRP F 333 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (18047) covalent geometry : angle 0.57483 / 0.30 (24732) hydrogen bonds : bond 0.03195 / 2.12 ( 659) hydrogen bonds : angle 4.91443 / 3.52 ( 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 165 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9133 (t) REVERT: B 331 MET cc_start: 0.7980 (tmm) cc_final: 0.7562 (tmm) REVERT: B 338 HIS cc_start: 0.8581 (m90) cc_final: 0.8216 (m90) REVERT: C 42 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 48 THR cc_start: 0.9352 (m) cc_final: 0.9048 (p) REVERT: C 210 MET cc_start: 0.8036 (mmp) cc_final: 0.7248 (mmm) REVERT: C 214 PHE cc_start: 0.8636 (t80) cc_final: 0.8312 (t80) REVERT: C 215 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8954 (pp) REVERT: C 265 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8108 (pt0) REVERT: C 331 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8124 (ppp) REVERT: D 42 GLU cc_start: 0.8817 (tt0) cc_final: 0.8576 (tm-30) REVERT: D 225 ARG cc_start: 0.8943 (ptm-80) cc_final: 0.8599 (ptm-80) REVERT: D 338 HIS cc_start: 0.7698 (t70) cc_final: 0.7175 (t70) REVERT: E 105 MET cc_start: 0.8864 (mmm) cc_final: 0.8585 (mmt) REVERT: E 255 LEU cc_start: 0.9218 (mt) cc_final: 0.8955 (mt) REVERT: E 285 GLN cc_start: 0.9187 (tp40) cc_final: 0.8873 (tp40) REVERT: E 331 MET cc_start: 0.8078 (mmm) cc_final: 0.7799 (mmm) REVERT: F 92 ASP cc_start: 0.8851 (t70) cc_final: 0.8564 (t0) REVERT: F 225 ARG cc_start: 0.8907 (ptm-80) cc_final: 0.8333 (tmm-80) outliers start: 41 outliers final: 32 residues processed: 153 average time/residue: 0.1246 time to fit residues: 30.1581 Evaluate side-chains 152 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 VAL 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 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 331 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 142 VAL Chi-restraints excluded: chain D residue 272 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 166 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 34 THR 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 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: 3.9990 chunk 8 optimal weight: 0.9990 chunk 121 optimal weight: 0.0370 chunk 204 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 104 optimal weight: 1.9990 chunk 170 optimal weight: 0.0060 chunk 142 optimal weight: 0.8980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057181 restraints weight = 53105.644| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.38 r_work: 0.2788 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.8827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18047 Z= 0.094 Angle : 0.552 13.699 24732 Z= 0.279 Chirality : 0.042 0.140 2881 Planarity : 0.004 0.046 2979 Dihedral : 10.544 74.093 3006 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.79 % Allowed : 18.67 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2071 helix: 0.56 (0.23), residues: 533 sheet: 0.10 (0.27), residues: 323 loop : -0.64 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 139 TYR 0.011 0.001 TYR C 226 PHE 0.019 0.001 PHE E 330 TRP 0.011 0.001 TRP F 87 HIS 0.002 0.000 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (18047) covalent geometry : angle 0.55231 / 0.28 (24732) hydrogen bonds : bond 0.02967 / 1.95 ( 659) hydrogen bonds : angle 4.79346 / 3.43 ( 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 155 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8297 (mmm) cc_final: 0.7752 (mtp) REVERT: B 32 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.9072 (t) REVERT: B 331 MET cc_start: 0.8029 (tmm) cc_final: 0.7593 (tmm) REVERT: B 338 HIS cc_start: 0.8535 (m90) cc_final: 0.8156 (m90) REVERT: C 42 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 48 THR cc_start: 0.9282 (m) cc_final: 0.9017 (p) REVERT: C 205 LYS cc_start: 0.8837 (tptp) cc_final: 0.8636 (mmtm) REVERT: C 210 MET cc_start: 0.8021 (mmp) cc_final: 0.7229 (mmm) REVERT: C 214 PHE cc_start: 0.8619 (t80) cc_final: 0.8320 (t80) REVERT: C 215 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8962 (pp) REVERT: C 265 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8094 (pt0) REVERT: C 331 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8124 (ppp) REVERT: D 225 ARG cc_start: 0.8960 (ptm-80) cc_final: 0.8638 (ptm-80) REVERT: D 338 HIS cc_start: 0.7628 (t70) cc_final: 0.7082 (t70) REVERT: E 105 MET cc_start: 0.8845 (mmm) cc_final: 0.8590 (mmt) REVERT: E 139 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7698 (tpt-90) REVERT: E 285 GLN cc_start: 0.9171 (tp40) cc_final: 0.8859 (tp40) REVERT: E 331 MET cc_start: 0.8260 (mmm) cc_final: 0.7992 (mmm) REVERT: F 225 ARG cc_start: 0.8953 (ptm-80) cc_final: 0.8368 (tmm-80) outliers start: 33 outliers final: 27 residues processed: 146 average time/residue: 0.1244 time to fit residues: 28.8378 Evaluate side-chains 146 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 VAL 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 331 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 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 166 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 34 THR 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 146 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 51 optimal weight: 0.0270 chunk 106 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.084072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057164 restraints weight = 53173.183| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.43 r_work: 0.2786 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.8988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18047 Z= 0.099 Angle : 0.554 13.614 24732 Z= 0.279 Chirality : 0.042 0.160 2881 Planarity : 0.004 0.045 2979 Dihedral : 10.501 74.112 3006 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 18.88 % Favored : 79.38 % 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: -0.32 (0.18), residues: 2071 helix: 0.51 (0.23), residues: 534 sheet: 0.05 (0.26), residues: 353 loop : -0.59 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 225 TYR 0.010 0.001 TYR C 226 PHE 0.019 0.001 PHE E 342 TRP 0.009 0.001 TRP F 87 HIS 0.002 0.000 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (18047) covalent geometry : angle 0.55402 / 0.28 (24732) hydrogen bonds : bond 0.02919 / 1.92 ( 659) hydrogen bonds : angle 4.72961 / 3.39 ( 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 149 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8295 (mmm) cc_final: 0.7801 (mtp) REVERT: B 32 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9064 (t) REVERT: B 331 MET cc_start: 0.8069 (tmm) cc_final: 0.7622 (tmm) REVERT: B 338 HIS cc_start: 0.8552 (m90) cc_final: 0.8175 (m90) REVERT: C 42 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 48 THR cc_start: 0.9277 (m) cc_final: 0.9021 (p) REVERT: C 210 MET cc_start: 0.8098 (mmp) cc_final: 0.7384 (mmm) REVERT: C 214 PHE cc_start: 0.8684 (t80) cc_final: 0.8386 (t80) REVERT: C 265 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8123 (pt0) REVERT: C 331 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8144 (ppp) REVERT: D 225 ARG cc_start: 0.8967 (ptm-80) cc_final: 0.8631 (ptm-80) REVERT: D 338 HIS cc_start: 0.7620 (t70) cc_final: 0.7091 (t70) REVERT: E 105 MET cc_start: 0.8884 (mmm) cc_final: 0.8619 (mmt) REVERT: E 139 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7750 (tpt-90) REVERT: E 285 GLN cc_start: 0.9174 (tp40) cc_final: 0.8813 (tp40) REVERT: E 331 MET cc_start: 0.8307 (mmm) cc_final: 0.7956 (mmm) REVERT: F 225 ARG cc_start: 0.8927 (ptm-80) cc_final: 0.8306 (tmm-80) outliers start: 32 outliers final: 29 residues processed: 140 average time/residue: 0.1187 time to fit residues: 26.1668 Evaluate side-chains 145 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 VAL 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 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 331 MET 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 166 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 34 THR 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: 6.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 182 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.082578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055308 restraints weight = 53381.048| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.46 r_work: 0.2724 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.9650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18047 Z= 0.127 Angle : 0.574 13.567 24732 Z= 0.290 Chirality : 0.043 0.338 2881 Planarity : 0.004 0.054 2979 Dihedral : 10.519 74.090 3006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.79 % Allowed : 18.99 % Favored : 79.22 % 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: -0.26 (0.18), residues: 2071 helix: 0.51 (0.24), residues: 538 sheet: 0.24 (0.28), residues: 323 loop : -0.57 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 91 TYR 0.009 0.001 TYR D 33 PHE 0.017 0.001 PHE C 204 TRP 0.009 0.001 TRP E 87 HIS 0.006 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18047) covalent geometry : angle 0.57358 / 0.29 (24732) hydrogen bonds : bond 0.03121 / 2.08 ( 659) hydrogen bonds : angle 4.78023 / 3.42 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.97 seconds wall clock time: 65 minutes 11.14 seconds (3911.14 seconds total)