Starting phenix.real_space_refine on Sun Jun 15 15:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bih_44590/06_2025/9bih_44590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bih_44590/06_2025/9bih_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_44590/06_2025/9bih_44590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bih_44590/06_2025/9bih_44590.map" model { file = "/net/cci-nas-00/data/ceres_data/9bih_44590/06_2025/9bih_44590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bih_44590/06_2025/9bih_44590.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.79, per 1000 atoms: 0.61 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: 3.90 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 6.98 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: 6.50 Time building geometry restraints manager: 4.70 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=" CG1 ILE B 86 " pdb=" CD1 ILE B 86 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CB ASN A 30 " pdb=" CG ASN A 30 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" P U G 1 " pdb=" OP2 U G 1 " ideal model delta sigma weight residual 1.485 1.456 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" CA VAL D 67 " pdb=" CB VAL D 67 " ideal model delta sigma weight residual 1.546 1.534 0.012 8.80e-03 1.29e+04 1.94e+00 ... (remaining 18042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 23587 1.19 - 2.37: 967 2.37 - 3.56: 135 3.56 - 4.75: 34 4.75 - 5.93: 9 Bond angle restraints: 24732 Sorted by residual: angle pdb=" CA VAL B 23 " pdb=" C VAL B 23 " pdb=" N PRO B 24 " ideal model delta sigma weight residual 116.57 119.46 -2.89 9.80e-01 1.04e+00 8.73e+00 angle pdb=" C4' U G 14 " pdb=" C3' U G 14 " pdb=" C2' U G 14 " ideal model delta sigma weight residual 102.60 105.30 -2.70 1.00e+00 1.00e+00 7.30e+00 angle pdb=" N SER C 313 " pdb=" CA SER C 313 " pdb=" C SER C 313 " ideal model delta sigma weight residual 114.04 110.80 3.24 1.24e+00 6.50e-01 6.82e+00 angle pdb=" N SER F 313 " pdb=" CA SER F 313 " pdb=" C SER F 313 " ideal model delta sigma weight residual 114.56 111.44 3.12 1.27e+00 6.20e-01 6.02e+00 angle pdb=" C3' U G 14 " pdb=" C2' U G 14 " pdb=" C1' U G 14 " ideal model delta sigma weight residual 101.30 103.69 -2.39 1.00e+00 1.00e+00 5.69e+00 ... (remaining 24727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 9952 15.53 - 31.07: 673 31.07 - 46.60: 126 46.60 - 62.13: 59 62.13 - 77.66: 24 Dihedral angle restraints: 10834 sinusoidal: 4800 harmonic: 6034 Sorted by residual: dihedral pdb=" O4' U G 14 " pdb=" C2' U G 14 " pdb=" C1' U G 14 " pdb=" C3' U G 14 " ideal model delta sinusoidal sigma weight residual 25.00 -17.40 42.40 1 8.00e+00 1.56e-02 3.92e+01 dihedral pdb=" C4' U G 14 " pdb=" C3' U G 14 " pdb=" C2' U G 14 " pdb=" C1' U G 14 " ideal model delta sinusoidal sigma weight residual 36.00 1.55 34.45 1 8.00e+00 1.56e-02 2.63e+01 dihedral pdb=" C4' U G 14 " pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" C2' U G 14 " ideal model delta sinusoidal sigma weight residual 3.00 -31.38 34.38 1 8.00e+00 1.56e-02 2.62e+01 ... (remaining 10831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1575 0.031 - 0.062: 756 0.062 - 0.093: 362 0.093 - 0.124: 165 0.124 - 0.155: 23 Chirality restraints: 2881 Sorted by residual: chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CB ILE C 97 " pdb=" CA ILE C 97 " pdb=" CG1 ILE C 97 " pdb=" CG2 ILE C 97 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 2878 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO D 51 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 65 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO F 66 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 50 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO F 51 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 51 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 51 " 0.022 5.00e-02 4.00e+02 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2079 2.74 - 3.28: 15999 3.28 - 3.82: 29215 3.82 - 4.36: 36432 4.36 - 4.90: 61745 Nonbonded interactions: 145470 Sorted by model distance: nonbonded pdb=" O GLY D 77 " pdb=" OG1 THR D 121 " model vdw 2.204 3.040 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 213 " pdb=" OH TYR B 226 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP F 213 " pdb=" OH TYR F 226 " model vdw 2.226 3.040 nonbonded pdb=" OE2 GLU A 0 " pdb=" OG SER A 2 " model vdw 2.228 3.040 ... (remaining 145465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.180 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 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= 0.331 Angle : 0.570 5.934 24732 Z= 0.309 Chirality : 0.047 0.155 2881 Planarity : 0.004 0.046 2979 Dihedral : 12.119 77.665 6944 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP D 87 HIS 0.006 0.001 HIS C 15 PHE 0.021 0.002 PHE A 269 TYR 0.013 0.002 TYR A 343 ARG 0.003 0.001 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.18801 ( 659) hydrogen bonds : angle 8.22967 ( 1825) covalent geometry : bond 0.00786 (18047) covalent geometry : angle 0.57023 (24732) *********************** 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 : 2.123 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: C 233 PHE cc_start: 0.7224 (m-80) cc_final: 0.6317 (m-80) REVERT: D 301 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6938 (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: 0.6264 (t80) REVERT: F 300 LEU cc_start: 0.7390 (tp) cc_final: 0.6859 (tp) REVERT: F 321 VAL cc_start: 0.7706 (t) cc_final: 0.7292 (p) outliers start: 30 outliers final: 3 residues processed: 535 average time/residue: 0.3601 time to fit residues: 286.6226 Evaluate side-chains 292 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 288 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 175 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN B 310 GLN B 338 HIS C 12 ASN C 83 ASN C 131 GLN C 164 ASN D 15 HIS D 29 ASN D 96 HIS E 243 HIS F 197 GLN F 250 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057616 restraints weight = 53205.991| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.52 r_work: 0.2787 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18047 Z= 0.183 Angle : 0.711 15.819 24732 Z= 0.366 Chirality : 0.046 0.172 2881 Planarity : 0.005 0.051 2979 Dihedral : 10.882 74.305 3012 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.71 % Allowed : 12.86 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2071 helix: 0.02 (0.21), residues: 534 sheet: 0.36 (0.34), residues: 242 loop : -0.77 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 333 HIS 0.005 0.001 HIS E 243 PHE 0.039 0.003 PHE C 222 TYR 0.020 0.002 TYR A 180 ARG 0.009 0.001 ARG E 127 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 659) hydrogen bonds : angle 5.71259 ( 1825) covalent geometry : bond 0.00415 (18047) covalent geometry : angle 0.71067 (24732) *********************** 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 343 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 1.987 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: B 198 SER cc_start: 0.8774 (m) cc_final: 0.8259 (p) REVERT: B 267 GLU cc_start: 0.7136 (mp0) cc_final: 0.6809 (mp0) REVERT: B 272 MET cc_start: 0.7903 (ppp) cc_final: 0.7610 (ppp) REVERT: C 48 THR cc_start: 0.8814 (m) cc_final: 0.8587 (p) REVERT: C 272 MET cc_start: 0.7889 (ppp) cc_final: 0.7604 (ppp) REVERT: D 34 THR cc_start: 0.7569 (t) cc_final: 0.7332 (m) REVERT: D 78 VAL cc_start: 0.9185 (t) cc_final: 0.8969 (p) REVERT: D 225 ARG cc_start: 0.9003 (ttm170) cc_final: 0.8763 (ttm170) REVERT: E 47 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8543 (mmmt) REVERT: E 78 VAL cc_start: 0.8796 (t) cc_final: 0.8578 (p) REVERT: E 216 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8849 (mp0) REVERT: E 217 LEU cc_start: 0.8683 (mt) cc_final: 0.7487 (mt) REVERT: E 342 PHE cc_start: 0.7857 (t80) cc_final: 0.7065 (t80) REVERT: F 78 VAL cc_start: 0.8487 (t) cc_final: 0.8123 (t) REVERT: F 86 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8266 (mp) REVERT: F 156 VAL cc_start: 0.9272 (t) cc_final: 0.9040 (p) REVERT: F 217 LEU cc_start: 0.8371 (mt) cc_final: 0.8050 (mt) outliers start: 50 outliers final: 26 residues processed: 322 average time/residue: 0.2908 time to fit residues: 143.1135 Evaluate side-chains 240 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 328 ILE Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 173 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 86 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 86 ILE 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 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS E 75 ASN E 338 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.083975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.057202 restraints weight = 53709.124| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.52 r_work: 0.2778 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6318 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= 0.115 Angle : 0.541 8.128 24732 Z= 0.282 Chirality : 0.043 0.186 2881 Planarity : 0.004 0.043 2979 Dihedral : 10.528 74.014 3006 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.22 % Allowed : 14.76 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2071 helix: 0.58 (0.23), residues: 529 sheet: 0.02 (0.29), residues: 312 loop : -0.55 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 59 HIS 0.014 0.001 HIS E 338 PHE 0.019 0.001 PHE F 330 TYR 0.011 0.001 TYR D 238 ARG 0.007 0.001 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 659) hydrogen bonds : angle 5.10782 ( 1825) covalent geometry : bond 0.00259 (18047) covalent geometry : angle 0.54088 (24732) *********************** 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 251 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6914 (mmm) cc_final: 0.6578 (mtp) REVERT: B 267 GLU cc_start: 0.7044 (mp0) cc_final: 0.6772 (mp0) REVERT: B 272 MET cc_start: 0.8061 (ppp) cc_final: 0.7724 (ppp) REVERT: B 331 MET cc_start: 0.8097 (tmm) cc_final: 0.7876 (tmm) REVERT: B 338 HIS cc_start: 0.8592 (m90) cc_final: 0.8242 (m90) REVERT: C 42 GLU cc_start: 0.8517 (pp20) cc_final: 0.8105 (tm-30) REVERT: C 48 THR cc_start: 0.9003 (m) cc_final: 0.8743 (p) REVERT: C 131 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6337 (mt0) REVERT: C 210 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7156 (mmp) REVERT: C 219 MET cc_start: 0.8741 (ttt) cc_final: 0.8521 (ttt) REVERT: D 105 MET cc_start: 0.8743 (mmm) cc_final: 0.8515 (mmm) REVERT: E 122 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7133 (t) REVERT: E 285 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8321 (tp40) REVERT: E 342 PHE cc_start: 0.8231 (t80) cc_final: 0.7760 (t80) REVERT: F 156 VAL cc_start: 0.9321 (t) cc_final: 0.9061 (p) REVERT: F 203 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7540 (tp30) REVERT: F 228 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8640 (mm) outliers start: 41 outliers final: 26 residues processed: 235 average time/residue: 0.2746 time to fit residues: 100.5250 Evaluate side-chains 206 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A 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 29 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 228 LEU 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 73 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN C 131 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN E 15 HIS F 96 HIS F 250 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055722 restraints weight = 53738.702| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.54 r_work: 0.2761 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.9661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 18047 Z= 0.201 Angle : 0.638 13.611 24732 Z= 0.337 Chirality : 0.045 0.207 2881 Planarity : 0.004 0.042 2979 Dihedral : 10.760 73.971 3006 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 3.09 % Allowed : 14.87 % Favored : 82.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2071 helix: 0.41 (0.23), residues: 534 sheet: 0.23 (0.31), residues: 264 loop : -0.65 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 87 HIS 0.019 0.001 HIS E 15 PHE 0.055 0.002 PHE E 16 TYR 0.024 0.002 TYR D 226 ARG 0.011 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 659) hydrogen bonds : angle 5.11090 ( 1825) covalent geometry : bond 0.00461 (18047) covalent geometry : angle 0.63838 (24732) *********************** 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 196 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 98 SER cc_start: 0.9547 (OUTLIER) cc_final: 0.9256 (m) REVERT: A 166 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9075 (p) REVERT: A 210 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: A 329 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.9116 (p) REVERT: B 203 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7825 (tm-30) REVERT: B 267 GLU cc_start: 0.7731 (mp0) cc_final: 0.7384 (mp0) REVERT: B 331 MET cc_start: 0.8209 (tmm) cc_final: 0.7786 (tmm) REVERT: B 338 HIS cc_start: 0.8615 (m90) cc_final: 0.8211 (m90) REVERT: C 42 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: C 48 THR cc_start: 0.9569 (m) cc_final: 0.9318 (p) REVERT: C 210 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: C 265 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8050 (pt0) REVERT: C 331 MET cc_start: 0.8310 (tmm) cc_final: 0.7822 (ppp) REVERT: D 45 GLU cc_start: 0.8968 (tt0) cc_final: 0.8583 (tm-30) REVERT: D 47 LYS cc_start: 0.9578 (mmmt) cc_final: 0.8859 (mmtm) REVERT: D 92 ASP cc_start: 0.9219 (t0) cc_final: 0.9017 (t0) REVERT: D 106 THR cc_start: 0.9653 (OUTLIER) cc_final: 0.9412 (p) REVERT: D 253 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8655 (mp) REVERT: D 338 HIS cc_start: 0.8322 (t-90) cc_final: 0.8025 (t70) REVERT: E 122 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8950 (t) REVERT: E 225 ARG cc_start: 0.8959 (ptm160) cc_final: 0.8713 (ptm160) REVERT: E 285 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8663 (tp40) REVERT: F 37 ASP cc_start: 0.8418 (t0) cc_final: 0.8114 (t0) REVERT: F 225 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8414 (ttp80) outliers start: 57 outliers final: 23 residues processed: 181 average time/residue: 0.2943 time to fit residues: 82.0513 Evaluate side-chains 134 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 210 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 106 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 176 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054651 restraints weight = 52668.045| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.52 r_work: 0.2689 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 1.0049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18047 Z= 0.109 Angle : 0.517 9.884 24732 Z= 0.267 Chirality : 0.042 0.180 2881 Planarity : 0.004 0.042 2979 Dihedral : 10.590 73.873 3006 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 16.06 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2071 helix: 0.74 (0.23), residues: 529 sheet: 0.02 (0.28), residues: 348 loop : -0.51 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 87 HIS 0.006 0.001 HIS E 15 PHE 0.022 0.001 PHE E 330 TYR 0.013 0.001 TYR C 343 ARG 0.005 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 659) hydrogen bonds : angle 4.81762 ( 1825) covalent geometry : bond 0.00246 (18047) covalent geometry : angle 0.51727 (24732) *********************** 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 153 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: A 291 CYS cc_start: 0.8984 (m) cc_final: 0.8708 (m) REVERT: A 331 MET cc_start: 0.8824 (tpp) cc_final: 0.8510 (tpt) REVERT: B 1 MET cc_start: 0.8614 (mmm) cc_final: 0.8084 (mtp) REVERT: B 129 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8783 (p0) REVERT: B 203 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7758 (tm-30) REVERT: B 267 GLU cc_start: 0.7672 (mp0) cc_final: 0.7406 (mp0) REVERT: B 331 MET cc_start: 0.8391 (tmm) cc_final: 0.7852 (tmm) REVERT: B 338 HIS cc_start: 0.8642 (m90) cc_final: 0.8228 (m90) REVERT: C 42 GLU cc_start: 0.8855 (pp20) cc_final: 0.8397 (tm-30) REVERT: C 48 THR cc_start: 0.9428 (m) cc_final: 0.9142 (p) REVERT: C 205 LYS cc_start: 0.8940 (tptp) cc_final: 0.8720 (mmtm) REVERT: C 210 MET cc_start: 0.8329 (mmp) cc_final: 0.7662 (mmm) REVERT: C 219 MET cc_start: 0.8945 (ttt) cc_final: 0.8702 (ttt) REVERT: C 265 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8048 (pt0) REVERT: C 331 MET cc_start: 0.8178 (tmm) cc_final: 0.7558 (ppp) REVERT: D 92 ASP cc_start: 0.9292 (t0) cc_final: 0.8943 (t0) REVERT: D 225 ARG cc_start: 0.9168 (ptm160) cc_final: 0.8925 (ptm160) REVERT: D 338 HIS cc_start: 0.8330 (t-90) cc_final: 0.8099 (t70) REVERT: E 19 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8392 (mm-40) REVERT: E 122 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8593 (t) REVERT: F 37 ASP cc_start: 0.8439 (t0) cc_final: 0.8063 (t0) REVERT: F 45 GLU cc_start: 0.8656 (tp30) cc_final: 0.8336 (tp30) REVERT: F 222 PHE cc_start: 0.7017 (t80) cc_final: 0.6050 (t80) REVERT: F 225 ARG cc_start: 0.8991 (ptm-80) cc_final: 0.8430 (ttp80) outliers start: 31 outliers final: 20 residues processed: 144 average time/residue: 0.3579 time to fit residues: 81.8288 Evaluate side-chains 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP 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 243 HIS Chi-restraints excluded: chain C residue 292 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 132 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 106 optimal weight: 6.9990 chunk 117 optimal weight: 0.0270 chunk 151 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.083277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055663 restraints weight = 52749.850| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.54 r_work: 0.2711 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.0269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18047 Z= 0.087 Angle : 0.493 9.548 24732 Z= 0.253 Chirality : 0.042 0.144 2881 Planarity : 0.003 0.047 2979 Dihedral : 10.437 73.995 3006 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.68 % Allowed : 15.63 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2071 helix: 0.80 (0.23), residues: 529 sheet: -0.04 (0.27), residues: 343 loop : -0.42 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 87 HIS 0.002 0.000 HIS E 15 PHE 0.014 0.001 PHE E 303 TYR 0.009 0.001 TYR E 33 ARG 0.003 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.02605 ( 659) hydrogen bonds : angle 4.62144 ( 1825) covalent geometry : bond 0.00189 (18047) covalent geometry : angle 0.49299 (24732) *********************** 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 149 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 SER cc_start: 0.9518 (OUTLIER) cc_final: 0.9300 (m) REVERT: A 210 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8394 (ttp) REVERT: A 219 MET cc_start: 0.8339 (ttt) cc_final: 0.7981 (tmm) REVERT: A 291 CYS cc_start: 0.8926 (m) cc_final: 0.8536 (m) REVERT: A 331 MET cc_start: 0.8901 (tpp) cc_final: 0.8598 (tpt) REVERT: B 129 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8802 (p0) REVERT: B 203 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7658 (tm-30) REVERT: B 267 GLU cc_start: 0.7706 (mp0) cc_final: 0.7378 (mp0) REVERT: B 331 MET cc_start: 0.8351 (tmm) cc_final: 0.7913 (tmm) REVERT: B 338 HIS cc_start: 0.8635 (m90) cc_final: 0.8233 (m90) REVERT: C 42 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: C 48 THR cc_start: 0.9365 (m) cc_final: 0.9149 (p) REVERT: C 203 GLU cc_start: 0.8701 (tp30) cc_final: 0.8491 (tp30) REVERT: C 210 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: C 219 MET cc_start: 0.8957 (ttt) cc_final: 0.8673 (ttt) REVERT: C 265 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8187 (pt0) REVERT: C 331 MET cc_start: 0.8187 (tmm) cc_final: 0.7553 (ppp) REVERT: D 92 ASP cc_start: 0.9296 (t0) cc_final: 0.8933 (t0) REVERT: D 338 HIS cc_start: 0.8332 (t-90) cc_final: 0.7970 (t70) REVERT: E 122 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8611 (t) REVERT: F 37 ASP cc_start: 0.8447 (t0) cc_final: 0.8019 (t0) REVERT: F 222 PHE cc_start: 0.6906 (t80) cc_final: 0.5932 (t80) REVERT: F 225 ARG cc_start: 0.8975 (ptm-80) cc_final: 0.8428 (ttp80) outliers start: 31 outliers final: 15 residues processed: 137 average time/residue: 0.2866 time to fit residues: 61.7003 Evaluate side-chains 121 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 140 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.082286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054240 restraints weight = 52924.671| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.50 r_work: 0.2681 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 1.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18047 Z= 0.123 Angle : 0.513 10.653 24732 Z= 0.264 Chirality : 0.042 0.158 2881 Planarity : 0.004 0.050 2979 Dihedral : 10.476 73.930 3006 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 15.46 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2071 helix: 0.96 (0.24), residues: 529 sheet: 0.10 (0.27), residues: 349 loop : -0.37 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 333 HIS 0.003 0.001 HIS D 96 PHE 0.012 0.001 PHE E 330 TYR 0.010 0.001 TYR D 226 ARG 0.003 0.000 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 659) hydrogen bonds : angle 4.68064 ( 1825) covalent geometry : bond 0.00284 (18047) covalent geometry : angle 0.51341 (24732) *********************** 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 135 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 3.082 Fit side-chains revert: symmetry clash REVERT: A 98 SER cc_start: 0.9571 (OUTLIER) cc_final: 0.9223 (m) REVERT: A 203 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7875 (tm-30) REVERT: A 210 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: A 331 MET cc_start: 0.9185 (tpp) cc_final: 0.8928 (tpt) REVERT: B 203 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7967 (tm-30) REVERT: B 291 CYS cc_start: 0.8567 (m) cc_final: 0.8201 (m) REVERT: B 331 MET cc_start: 0.8305 (tmm) cc_final: 0.7905 (tmm) REVERT: B 338 HIS cc_start: 0.8493 (m90) cc_final: 0.8122 (m90) REVERT: C 42 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8574 (tm-30) REVERT: C 203 GLU cc_start: 0.8605 (tp30) cc_final: 0.8363 (tp30) REVERT: C 210 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: C 219 MET cc_start: 0.9105 (ttt) cc_final: 0.8772 (ttt) REVERT: C 265 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8424 (pt0) REVERT: C 331 MET cc_start: 0.8233 (tmm) cc_final: 0.7524 (ppp) REVERT: D 92 ASP cc_start: 0.9162 (t0) cc_final: 0.8753 (t0) REVERT: D 225 ARG cc_start: 0.8764 (ptm-80) cc_final: 0.8530 (ptm-80) REVERT: D 253 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8532 (mp) REVERT: D 338 HIS cc_start: 0.8152 (t-90) cc_final: 0.7927 (t70) REVERT: E 203 GLU cc_start: 0.8995 (mp0) cc_final: 0.8776 (pm20) REVERT: F 37 ASP cc_start: 0.8429 (t0) cc_final: 0.8147 (t0) REVERT: F 222 PHE cc_start: 0.6963 (t80) cc_final: 0.6037 (t80) REVERT: F 225 ARG cc_start: 0.9032 (ptm-80) cc_final: 0.8489 (ttp80) outliers start: 32 outliers final: 19 residues processed: 125 average time/residue: 0.3240 time to fit residues: 63.4644 Evaluate side-chains 122 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE 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 253 ILE Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3508 r_free = 0.3508 target = 0.080123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.052059 restraints weight = 52870.659| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.38 r_work: 0.2625 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 1.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18047 Z= 0.164 Angle : 0.536 10.201 24732 Z= 0.277 Chirality : 0.043 0.145 2881 Planarity : 0.004 0.058 2979 Dihedral : 10.654 73.990 3006 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.90 % Allowed : 15.68 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 2071 helix: 0.93 (0.24), residues: 528 sheet: 0.30 (0.30), residues: 299 loop : -0.43 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 333 HIS 0.005 0.001 HIS C 15 PHE 0.014 0.001 PHE F 135 TYR 0.016 0.001 TYR A 33 ARG 0.007 0.001 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 659) hydrogen bonds : angle 4.76839 ( 1825) covalent geometry : bond 0.00375 (18047) covalent geometry : angle 0.53611 (24732) *********************** 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 136 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8612 (ttp) REVERT: A 265 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8567 (tm-30) REVERT: A 331 MET cc_start: 0.9117 (tpp) cc_final: 0.8895 (tpt) REVERT: B 1 MET cc_start: 0.8456 (mtp) cc_final: 0.8080 (ppp) REVERT: B 203 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8123 (tm-30) REVERT: B 291 CYS cc_start: 0.8894 (m) cc_final: 0.8585 (m) REVERT: B 331 MET cc_start: 0.8324 (tmm) cc_final: 0.7874 (tmm) REVERT: B 338 HIS cc_start: 0.8629 (m90) cc_final: 0.8284 (m90) REVERT: C 42 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: C 203 GLU cc_start: 0.8778 (tp30) cc_final: 0.8502 (tp30) REVERT: C 205 LYS cc_start: 0.9325 (mmmt) cc_final: 0.8745 (pttp) REVERT: C 210 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: C 219 MET cc_start: 0.9144 (ttt) cc_final: 0.8715 (ttt) REVERT: C 265 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8544 (pt0) REVERT: C 331 MET cc_start: 0.8373 (tmm) cc_final: 0.7507 (ppp) REVERT: D 92 ASP cc_start: 0.9287 (t0) cc_final: 0.8838 (t0) REVERT: D 338 HIS cc_start: 0.8059 (t-90) cc_final: 0.7804 (t70) REVERT: E 220 ASP cc_start: 0.9547 (m-30) cc_final: 0.9285 (p0) REVERT: E 265 GLU cc_start: 0.8912 (tp30) cc_final: 0.8425 (tp30) REVERT: F 37 ASP cc_start: 0.8410 (t0) cc_final: 0.8033 (t0) REVERT: F 139 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7654 (mtp85) REVERT: F 222 PHE cc_start: 0.7099 (t80) cc_final: 0.6125 (t80) REVERT: F 225 ARG cc_start: 0.9004 (ptm-80) cc_final: 0.8427 (ttp80) REVERT: F 331 MET cc_start: 0.7980 (mmp) cc_final: 0.7170 (tpt) outliers start: 35 outliers final: 24 residues processed: 128 average time/residue: 0.3273 time to fit residues: 66.8098 Evaluate side-chains 118 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A 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 42 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE 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 142 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3508 r_free = 0.3508 target = 0.080416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.052359 restraints weight = 52788.371| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.47 r_work: 0.2614 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 1.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18047 Z= 0.087 Angle : 0.494 10.161 24732 Z= 0.253 Chirality : 0.042 0.156 2881 Planarity : 0.003 0.052 2979 Dihedral : 10.461 73.866 3006 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.30 % Allowed : 16.39 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 2071 helix: 0.87 (0.24), residues: 532 sheet: 0.15 (0.27), residues: 349 loop : -0.33 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 333 HIS 0.002 0.001 HIS C 15 PHE 0.011 0.001 PHE F 124 TYR 0.007 0.001 TYR C 226 ARG 0.006 0.000 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 659) hydrogen bonds : angle 4.58585 ( 1825) covalent geometry : bond 0.00194 (18047) covalent geometry : angle 0.49384 (24732) *********************** 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 122 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (ttp) REVERT: A 265 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8456 (tm-30) REVERT: A 331 MET cc_start: 0.8943 (tpp) cc_final: 0.8702 (tpt) REVERT: B 203 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8113 (tm-30) REVERT: B 291 CYS cc_start: 0.8845 (m) cc_final: 0.8399 (m) REVERT: B 331 MET cc_start: 0.8331 (tmm) cc_final: 0.7829 (tmm) REVERT: B 338 HIS cc_start: 0.8822 (m90) cc_final: 0.8502 (m90) REVERT: C 42 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: C 203 GLU cc_start: 0.8914 (tp30) cc_final: 0.8628 (tp30) REVERT: C 205 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8590 (pttp) REVERT: C 210 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: C 219 MET cc_start: 0.9024 (ttt) cc_final: 0.8633 (ttt) REVERT: C 265 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8531 (pt0) REVERT: C 331 MET cc_start: 0.8297 (tmm) cc_final: 0.7441 (ppp) REVERT: D 92 ASP cc_start: 0.9353 (t0) cc_final: 0.8887 (t0) REVERT: D 338 HIS cc_start: 0.8412 (t-90) cc_final: 0.8174 (t70) REVERT: E 220 ASP cc_start: 0.9570 (m-30) cc_final: 0.9306 (p0) REVERT: E 265 GLU cc_start: 0.8978 (tp30) cc_final: 0.8493 (tp30) REVERT: F 37 ASP cc_start: 0.8594 (t0) cc_final: 0.8174 (t0) REVERT: F 222 PHE cc_start: 0.7105 (t80) cc_final: 0.6287 (t80) REVERT: F 225 ARG cc_start: 0.8969 (ptm-80) cc_final: 0.8435 (ttp80) REVERT: F 331 MET cc_start: 0.8099 (mmp) cc_final: 0.7245 (tpt) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.2958 time to fit residues: 54.2788 Evaluate side-chains 113 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 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 142 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052518 restraints weight = 52959.285| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.38 r_work: 0.2640 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 1.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18047 Z= 0.120 Angle : 0.497 9.454 24732 Z= 0.254 Chirality : 0.042 0.171 2881 Planarity : 0.003 0.055 2979 Dihedral : 10.425 73.877 3006 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.25 % Allowed : 16.49 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2071 helix: 0.98 (0.24), residues: 528 sheet: 0.14 (0.28), residues: 339 loop : -0.29 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 333 HIS 0.002 0.001 HIS F 15 PHE 0.027 0.001 PHE C 303 TYR 0.009 0.001 TYR B 180 ARG 0.004 0.000 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 659) hydrogen bonds : angle 4.59024 ( 1825) covalent geometry : bond 0.00277 (18047) covalent geometry : angle 0.49654 (24732) ********************** 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 120 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.972 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8595 (tm-30) REVERT: A 331 MET cc_start: 0.9080 (tpp) cc_final: 0.8804 (tpt) REVERT: B 203 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8112 (tm-30) REVERT: B 291 CYS cc_start: 0.8895 (m) cc_final: 0.8586 (m) REVERT: B 331 MET cc_start: 0.8259 (tmm) cc_final: 0.7793 (tmm) REVERT: B 338 HIS cc_start: 0.8672 (m90) cc_final: 0.8431 (m90) REVERT: C 42 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: C 203 GLU cc_start: 0.8786 (tp30) cc_final: 0.8307 (tp30) REVERT: C 205 LYS cc_start: 0.9287 (mmmt) cc_final: 0.8921 (mmtm) REVERT: C 210 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8709 (mmm) REVERT: C 219 MET cc_start: 0.9134 (ttt) cc_final: 0.8904 (ttt) REVERT: C 331 MET cc_start: 0.8388 (tmm) cc_final: 0.7519 (ppp) REVERT: D 92 ASP cc_start: 0.9285 (t0) cc_final: 0.8820 (t0) REVERT: D 338 HIS cc_start: 0.8109 (t-90) cc_final: 0.7671 (t70) REVERT: E 220 ASP cc_start: 0.9529 (m-30) cc_final: 0.9263 (p0) REVERT: E 265 GLU cc_start: 0.9004 (tp30) cc_final: 0.8051 (tm-30) REVERT: F 37 ASP cc_start: 0.8369 (t0) cc_final: 0.7975 (t0) REVERT: F 222 PHE cc_start: 0.7156 (t80) cc_final: 0.6445 (t80) REVERT: F 225 ARG cc_start: 0.8995 (ptm-80) cc_final: 0.8463 (ttp80) REVERT: F 331 MET cc_start: 0.8147 (mmp) cc_final: 0.7411 (tpt) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 0.2781 time to fit residues: 51.1262 Evaluate side-chains 114 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE 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 142 VAL Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 89 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3523 r_free = 0.3523 target = 0.080840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053073 restraints weight = 52980.613| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.36 r_work: 0.2652 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 1.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18047 Z= 0.104 Angle : 0.494 9.635 24732 Z= 0.253 Chirality : 0.042 0.163 2881 Planarity : 0.003 0.053 2979 Dihedral : 10.404 73.879 3006 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.36 % Allowed : 16.71 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 2071 helix: 0.83 (0.24), residues: 532 sheet: 0.18 (0.28), residues: 339 loop : -0.28 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 333 HIS 0.002 0.000 HIS E 338 PHE 0.028 0.001 PHE C 303 TYR 0.008 0.001 TYR F 238 ARG 0.005 0.000 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.02658 ( 659) hydrogen bonds : angle 4.56351 ( 1825) covalent geometry : bond 0.00241 (18047) covalent geometry : angle 0.49390 (24732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8782.16 seconds wall clock time: 157 minutes 25.57 seconds (9445.57 seconds total)