Starting phenix.real_space_refine on Tue Jan 21 22:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bih_44590/01_2025/9bih_44590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bih_44590/01_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_44590/01_2025/9bih_44590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bih_44590/01_2025/9bih_44590.map" model { file = "/net/cci-nas-00/data/ceres_data/9bih_44590/01_2025/9bih_44590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bih_44590/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.81, per 1000 atoms: 0.62 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: 4.59 Conformation dependent library (CDL) restraints added in 2.3 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: 6.76 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: 6.93 Time building geometry restraints manager: 5.33 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.500 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.310 ------------------------------------------------------------------------------- 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= 0.514 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 *********************** 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 : 2.067 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: 0.2987 time to fit residues: 238.8467 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 : 2.000 ------------------------------------------------------------------------------- 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 = 53205.857| |-----------------------------------------------------------------------------| 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= 0.269 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 *********************** 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 : 1.910 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: 0.8773 (m) cc_final: 0.8259 (p) REVERT: B 267 GLU cc_start: 0.7140 (mp0) cc_final: 0.6811 (mp0) REVERT: B 272 MET cc_start: 0.7904 (ppp) cc_final: 0.7612 (ppp) REVERT: C 48 THR cc_start: 0.8814 (m) cc_final: 0.8590 (p) REVERT: C 272 MET cc_start: 0.7887 (ppp) cc_final: 0.7602 (ppp) REVERT: D 34 THR cc_start: 0.7570 (t) cc_final: 0.7333 (m) REVERT: D 78 VAL cc_start: 0.9187 (t) cc_final: 0.8970 (p) REVERT: D 225 ARG cc_start: 0.9004 (ttm170) cc_final: 0.8764 (ttm170) REVERT: E 47 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8542 (mmmt) REVERT: E 78 VAL cc_start: 0.8796 (t) cc_final: 0.8578 (p) REVERT: E 216 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8848 (mp0) REVERT: E 217 LEU cc_start: 0.8683 (mt) cc_final: 0.7489 (mt) REVERT: E 342 PHE cc_start: 0.7854 (t80) cc_final: 0.7059 (t80) REVERT: F 78 VAL cc_start: 0.8486 (t) cc_final: 0.8122 (t) REVERT: F 86 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8267 (mp) REVERT: F 156 VAL cc_start: 0.9273 (t) cc_final: 0.9041 (p) REVERT: F 217 LEU cc_start: 0.8390 (mt) cc_final: 0.8061 (mt) outliers start: 50 outliers final: 26 residues processed: 322 average time/residue: 0.2924 time to fit residues: 143.2147 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 : 2.316 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 170 optimal weight: 3.9990 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS E 75 ASN E 338 HIS F 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.057819 restraints weight = 53527.235| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.51 r_work: 0.2787 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18047 Z= 0.150 Angle : 0.536 8.396 24732 Z= 0.278 Chirality : 0.043 0.180 2881 Planarity : 0.004 0.043 2979 Dihedral : 10.552 74.029 3006 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.01 % Allowed : 15.03 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.18), residues: 2071 helix: 0.51 (0.22), residues: 529 sheet: 0.00 (0.29), residues: 312 loop : -0.55 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 333 HIS 0.013 0.001 HIS E 338 PHE 0.019 0.001 PHE F 330 TYR 0.011 0.001 TYR C 226 ARG 0.007 0.001 ARG C 225 *********************** 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 272 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 1.824 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: A 1 MET cc_start: 0.6758 (mmm) cc_final: 0.6234 (mmm) REVERT: A 280 PHE cc_start: 0.8303 (t80) cc_final: 0.8077 (t80) REVERT: B 198 SER cc_start: 0.8513 (m) cc_final: 0.8158 (p) REVERT: B 267 GLU cc_start: 0.7048 (mp0) cc_final: 0.6839 (mp0) REVERT: B 272 MET cc_start: 0.7817 (ppp) cc_final: 0.7451 (ppp) REVERT: B 338 HIS cc_start: 0.8513 (m90) cc_final: 0.8132 (m90) REVERT: C 30 ASN cc_start: 0.8398 (p0) cc_final: 0.8152 (p0) REVERT: C 42 GLU cc_start: 0.8340 (pp20) cc_final: 0.7876 (tm-30) REVERT: C 48 THR cc_start: 0.8771 (m) cc_final: 0.8567 (p) REVERT: C 131 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6056 (mt0) REVERT: C 210 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7138 (mmp) REVERT: C 219 MET cc_start: 0.8672 (ttt) cc_final: 0.8471 (ttt) REVERT: C 272 MET cc_start: 0.8049 (ppp) cc_final: 0.7788 (ppp) REVERT: C 280 PHE cc_start: 0.8573 (t80) cc_final: 0.8369 (t80) REVERT: C 331 MET cc_start: 0.8085 (tpp) cc_final: 0.7877 (tmm) REVERT: D 1 MET cc_start: 0.8138 (pmm) cc_final: 0.7935 (pmm) REVERT: D 62 ARG cc_start: 0.8825 (ptt-90) cc_final: 0.8545 (ptt-90) REVERT: D 78 VAL cc_start: 0.9345 (t) cc_final: 0.9077 (p) REVERT: E 285 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8357 (tp40) REVERT: E 342 PHE cc_start: 0.8077 (t80) cc_final: 0.7722 (t80) REVERT: F 156 VAL cc_start: 0.9265 (t) cc_final: 0.9006 (p) REVERT: F 330 PHE cc_start: 0.9139 (m-10) cc_final: 0.8904 (m-10) outliers start: 37 outliers final: 24 residues processed: 261 average time/residue: 0.2767 time to fit residues: 112.0469 Evaluate side-chains 223 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 VAL Chi-restraints excluded: chain B residue 167 THR 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 32 VAL Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 44 PHE 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 F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 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: 1.9990 chunk 195 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 155 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 ASN D 96 HIS E 15 HIS F 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056657 restraints weight = 53350.253| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.53 r_work: 0.2777 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18047 Z= 0.209 Angle : 0.558 10.399 24732 Z= 0.297 Chirality : 0.043 0.147 2881 Planarity : 0.004 0.044 2979 Dihedral : 10.532 73.987 3006 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 2.82 % Allowed : 15.41 % Favored : 81.77 % 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: -0.22 (0.18), residues: 2071 helix: 0.58 (0.23), residues: 529 sheet: 0.17 (0.29), residues: 318 loop : -0.52 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 87 HIS 0.017 0.001 HIS E 15 PHE 0.053 0.002 PHE E 16 TYR 0.041 0.002 TYR B 238 ARG 0.007 0.001 ARG C 139 *********************** 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 226 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 267 GLU cc_start: 0.7291 (mp0) cc_final: 0.6954 (mp0) REVERT: B 338 HIS cc_start: 0.8645 (m90) cc_final: 0.8250 (m90) REVERT: C 42 GLU cc_start: 0.8803 (pp20) cc_final: 0.8360 (tm-30) REVERT: C 48 THR cc_start: 0.9253 (m) cc_final: 0.8921 (p) REVERT: C 131 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: C 210 MET cc_start: 0.7972 (mmp) cc_final: 0.7149 (mmp) REVERT: C 331 MET cc_start: 0.8338 (tpp) cc_final: 0.8127 (tmm) REVERT: E 285 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8331 (tp40) REVERT: E 331 MET cc_start: 0.6951 (mmp) cc_final: 0.6581 (mmp) outliers start: 52 outliers final: 30 residues processed: 208 average time/residue: 0.3034 time to fit residues: 96.0975 Evaluate side-chains 175 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP 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 97 ILE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 237 VAL 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 142 VAL Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 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 246 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 97 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN C 83 ASN C 131 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.081423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053633 restraints weight = 53965.855| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.49 r_work: 0.2681 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 1.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18047 Z= 0.342 Angle : 0.619 9.408 24732 Z= 0.328 Chirality : 0.046 0.179 2881 Planarity : 0.004 0.056 2979 Dihedral : 10.875 73.987 3006 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.26 % Allowed : 14.65 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.35 (0.18), residues: 2071 helix: 0.45 (0.23), residues: 535 sheet: 0.09 (0.29), residues: 312 loop : -0.58 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 87 HIS 0.008 0.001 HIS A 96 PHE 0.046 0.002 PHE E 16 TYR 0.015 0.002 TYR A 33 ARG 0.008 0.001 ARG E 62 *********************** 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 189 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8473 (ttp) REVERT: A 331 MET cc_start: 0.9008 (tpp) cc_final: 0.8760 (tpt) REVERT: B 1 MET cc_start: 0.8663 (mmm) cc_final: 0.8344 (mtp) REVERT: B 203 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8164 (tm-30) REVERT: B 291 CYS cc_start: 0.8637 (m) cc_final: 0.8381 (m) REVERT: B 331 MET cc_start: 0.8346 (tmm) cc_final: 0.7741 (tmm) REVERT: B 338 HIS cc_start: 0.8579 (m90) cc_final: 0.8191 (m90) REVERT: C 42 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: C 210 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: C 265 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8364 (pt0) REVERT: C 331 MET cc_start: 0.8633 (tpp) cc_final: 0.8214 (tpp) REVERT: D 225 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8685 (ptm-80) REVERT: D 338 HIS cc_start: 0.8010 (t70) cc_final: 0.7461 (t70) REVERT: E 19 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8637 (mt0) REVERT: E 203 GLU cc_start: 0.9089 (mp0) cc_final: 0.8836 (pm20) REVERT: E 210 MET cc_start: 0.7716 (ttm) cc_final: 0.7500 (ttm) REVERT: F 37 ASP cc_start: 0.8433 (t0) cc_final: 0.8089 (t0) REVERT: F 139 ARG cc_start: 0.8137 (ttt90) cc_final: 0.7826 (tpp80) REVERT: F 226 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7582 (m-80) outliers start: 60 outliers final: 31 residues processed: 171 average time/residue: 0.3192 time to fit residues: 82.6782 Evaluate side-chains 128 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN 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 246 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN 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 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 TYR Chi-restraints excluded: chain F residue 243 HIS 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: 2.9990 chunk 117 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 35 optimal weight: 0.0770 chunk 25 optimal weight: 4.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 F 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.082104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054359 restraints weight = 53598.213| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.46 r_work: 0.2699 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 1.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18047 Z= 0.176 Angle : 0.524 8.806 24732 Z= 0.272 Chirality : 0.043 0.169 2881 Planarity : 0.004 0.040 2979 Dihedral : 10.690 73.916 3006 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 16.33 % 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: -0.20 (0.19), residues: 2071 helix: 0.67 (0.23), residues: 533 sheet: 0.01 (0.28), residues: 348 loop : -0.50 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 333 HIS 0.003 0.001 HIS F 15 PHE 0.013 0.001 PHE E 214 TYR 0.011 0.001 TYR C 226 ARG 0.006 0.001 ARG F 225 *********************** 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 143 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (ttp) REVERT: A 331 MET cc_start: 0.9032 (tpp) cc_final: 0.8814 (tpt) REVERT: B 1 MET cc_start: 0.8728 (mmm) cc_final: 0.8417 (mtp) REVERT: B 203 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8007 (tm-30) REVERT: B 291 CYS cc_start: 0.8499 (m) cc_final: 0.8157 (m) REVERT: B 331 MET cc_start: 0.8319 (tmm) cc_final: 0.7731 (tmm) REVERT: B 338 HIS cc_start: 0.8504 (m90) cc_final: 0.8154 (m90) REVERT: C 42 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: C 210 MET cc_start: 0.8619 (mmp) cc_final: 0.8111 (mmm) REVERT: C 265 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8355 (pt0) REVERT: C 331 MET cc_start: 0.8672 (tpp) cc_final: 0.8226 (tpp) REVERT: D 225 ARG cc_start: 0.8965 (ptm-80) cc_final: 0.8636 (ptm-80) REVERT: D 253 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 338 HIS cc_start: 0.7965 (t70) cc_final: 0.7480 (t70) REVERT: E 203 GLU cc_start: 0.9095 (mp0) cc_final: 0.8813 (pm20) REVERT: F 37 ASP cc_start: 0.8392 (t0) cc_final: 0.7998 (t0) REVERT: F 45 GLU cc_start: 0.8702 (tp30) cc_final: 0.8453 (tp30) REVERT: F 222 PHE cc_start: 0.6855 (t80) cc_final: 0.4831 (t80) REVERT: F 225 ARG cc_start: 0.8980 (ptm-80) cc_final: 0.8443 (tmm-80) outliers start: 32 outliers final: 19 residues processed: 136 average time/residue: 0.2924 time to fit residues: 62.2087 Evaluate side-chains 119 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN 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 42 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 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 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 186 VAL 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: 5.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 206 optimal weight: 20.0000 chunk 87 optimal weight: 0.0470 chunk 134 optimal weight: 2.9990 chunk 43 optimal weight: 0.0000 chunk 178 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3486 ------------------------------------------------------------------------------- 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 = 0.080497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.052428 restraints weight = 52707.391| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.48 r_work: 0.2617 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 1.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18047 Z= 0.187 Angle : 0.527 12.575 24732 Z= 0.271 Chirality : 0.043 0.190 2881 Planarity : 0.004 0.041 2979 Dihedral : 10.559 73.868 3006 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.68 % Allowed : 16.39 % 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: -0.09 (0.19), residues: 2071 helix: 0.82 (0.24), residues: 533 sheet: 0.08 (0.28), residues: 348 loop : -0.46 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 333 HIS 0.002 0.001 HIS C 250 PHE 0.012 0.001 PHE E 214 TYR 0.009 0.001 TYR E 279 ARG 0.007 0.001 ARG F 225 *********************** 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 139 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8530 (ttp) REVERT: A 331 MET cc_start: 0.9034 (tpp) cc_final: 0.8821 (tpt) REVERT: B 1 MET cc_start: 0.8802 (mmm) cc_final: 0.8447 (mtp) REVERT: B 203 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8123 (tm-30) REVERT: B 291 CYS cc_start: 0.8753 (m) cc_final: 0.8297 (m) REVERT: B 331 MET cc_start: 0.8383 (tmm) cc_final: 0.7683 (tmm) REVERT: B 338 HIS cc_start: 0.8675 (m90) cc_final: 0.8290 (m90) REVERT: C 42 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: C 210 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: C 265 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8383 (pt0) REVERT: C 331 MET cc_start: 0.8616 (tpp) cc_final: 0.8333 (tpp) REVERT: D 225 ARG cc_start: 0.9064 (ptm-80) cc_final: 0.8723 (ptm-80) REVERT: E 203 GLU cc_start: 0.9136 (mp0) cc_final: 0.8746 (pm20) REVERT: F 37 ASP cc_start: 0.8587 (t0) cc_final: 0.8170 (t0) REVERT: F 139 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7449 (ttm-80) REVERT: F 222 PHE cc_start: 0.6907 (t80) cc_final: 0.5508 (t80) REVERT: F 225 ARG cc_start: 0.9085 (ptm-80) cc_final: 0.8620 (ttp80) outliers start: 31 outliers final: 19 residues processed: 130 average time/residue: 0.3033 time to fit residues: 61.9771 Evaluate side-chains 119 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 312 LEU 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 210 MET Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 276 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 82 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 185 optimal weight: 0.0020 overall best weight: 1.6592 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.079464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051267 restraints weight = 52679.874| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.46 r_work: 0.2585 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 1.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18047 Z= 0.207 Angle : 0.522 12.782 24732 Z= 0.268 Chirality : 0.043 0.169 2881 Planarity : 0.004 0.043 2979 Dihedral : 10.595 73.893 3006 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 15.90 % Favored : 82.15 % 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: -0.07 (0.19), residues: 2071 helix: 0.78 (0.24), residues: 533 sheet: 0.12 (0.28), residues: 349 loop : -0.42 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 333 HIS 0.004 0.001 HIS E 96 PHE 0.025 0.001 PHE C 303 TYR 0.010 0.001 TYR C 226 ARG 0.005 0.001 ARG F 225 *********************** 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 139 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (ttp) REVERT: A 265 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8755 (tm-30) REVERT: A 331 MET cc_start: 0.9025 (tpp) cc_final: 0.8809 (tpt) REVERT: B 1 MET cc_start: 0.8879 (mmm) cc_final: 0.8586 (mtp) REVERT: B 203 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8126 (tm-30) REVERT: B 291 CYS cc_start: 0.8964 (m) cc_final: 0.8514 (m) REVERT: B 331 MET cc_start: 0.8247 (tmm) cc_final: 0.7529 (tmm) REVERT: B 338 HIS cc_start: 0.8789 (m90) cc_final: 0.8417 (m90) REVERT: C 42 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: C 48 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9227 (p) REVERT: C 210 MET cc_start: 0.8868 (mmp) cc_final: 0.8597 (mmm) REVERT: C 265 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8534 (pt0) REVERT: C 331 MET cc_start: 0.8553 (tpp) cc_final: 0.8296 (tpp) REVERT: D 225 ARG cc_start: 0.9095 (ptm-80) cc_final: 0.8761 (ptm-80) REVERT: E 110 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9072 (mmmm) REVERT: E 203 GLU cc_start: 0.9181 (mp0) cc_final: 0.8723 (pm20) REVERT: E 260 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9049 (pptt) REVERT: E 331 MET cc_start: 0.8542 (mmp) cc_final: 0.8272 (mmp) REVERT: F 37 ASP cc_start: 0.8659 (t0) cc_final: 0.8233 (t0) REVERT: F 139 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7769 (ttm-80) REVERT: F 222 PHE cc_start: 0.6977 (t80) cc_final: 0.5674 (t80) REVERT: F 225 ARG cc_start: 0.9129 (ptm-80) cc_final: 0.8541 (ttp80) REVERT: F 331 MET cc_start: 0.8088 (mmp) cc_final: 0.7290 (tpt) outliers start: 36 outliers final: 24 residues processed: 133 average time/residue: 0.3021 time to fit residues: 62.4774 Evaluate side-chains 127 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 LEU 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 48 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 26 SER 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 237 VAL Chi-restraints excluded: chain E residue 260 LYS 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 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0104 ------------------------------------------------------------------------------- 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 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.080083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052013 restraints weight = 52796.255| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.47 r_work: 0.2607 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 1.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18047 Z= 0.157 Angle : 0.507 11.758 24732 Z= 0.260 Chirality : 0.042 0.170 2881 Planarity : 0.004 0.050 2979 Dihedral : 10.509 73.857 3006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.41 % Allowed : 16.39 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.19), residues: 2071 helix: 0.81 (0.24), residues: 529 sheet: 0.14 (0.28), residues: 349 loop : -0.40 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 333 HIS 0.002 0.000 HIS E 338 PHE 0.021 0.001 PHE C 303 TYR 0.009 0.001 TYR C 226 ARG 0.006 0.001 ARG F 225 *********************** 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 131 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8614 (ttp) REVERT: A 265 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8662 (tm-30) REVERT: A 331 MET cc_start: 0.8988 (tpp) cc_final: 0.8782 (tpt) REVERT: B 1 MET cc_start: 0.8824 (mmm) cc_final: 0.8489 (mtp) REVERT: B 203 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8041 (tm-30) REVERT: B 291 CYS cc_start: 0.8885 (m) cc_final: 0.8444 (m) REVERT: B 331 MET cc_start: 0.8270 (tmm) cc_final: 0.7522 (tmm) REVERT: B 338 HIS cc_start: 0.8781 (m90) cc_final: 0.8471 (m90) REVERT: C 42 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: C 210 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8731 (mmm) REVERT: C 265 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8483 (pt0) REVERT: C 331 MET cc_start: 0.8536 (tpp) cc_final: 0.8109 (tpp) REVERT: D 225 ARG cc_start: 0.9108 (ptm-80) cc_final: 0.8770 (ptm-80) REVERT: E 110 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9133 (mmmm) REVERT: E 203 GLU cc_start: 0.9131 (mp0) cc_final: 0.8683 (pm20) REVERT: F 37 ASP cc_start: 0.8672 (t0) cc_final: 0.8225 (t0) REVERT: F 139 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7858 (ttm-80) REVERT: F 222 PHE cc_start: 0.7017 (t80) cc_final: 0.5776 (t80) REVERT: F 225 ARG cc_start: 0.9046 (ptm-80) cc_final: 0.8473 (ttp80) REVERT: F 331 MET cc_start: 0.8093 (mmp) cc_final: 0.7291 (tpt) outliers start: 26 outliers final: 19 residues processed: 126 average time/residue: 0.3156 time to fit residues: 61.7163 Evaluate side-chains 123 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 LEU 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 C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 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 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 1 optimal weight: 3.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.081824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.053826 restraints weight = 52833.568| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.40 r_work: 0.2678 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 1.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18047 Z= 0.142 Angle : 0.504 11.588 24732 Z= 0.257 Chirality : 0.042 0.177 2881 Planarity : 0.004 0.052 2979 Dihedral : 10.421 73.908 3006 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.03 (0.19), residues: 2071 helix: 0.82 (0.24), residues: 528 sheet: 0.15 (0.28), residues: 339 loop : -0.33 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 333 HIS 0.002 0.000 HIS E 338 PHE 0.022 0.001 PHE C 303 TYR 0.009 0.001 TYR C 226 ARG 0.006 0.000 ARG F 225 ********************** 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 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 2.052 Fit side-chains REVERT: A 166 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 265 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8747 (tm-30) REVERT: A 331 MET cc_start: 0.9121 (tpp) cc_final: 0.8920 (tpt) REVERT: B 1 MET cc_start: 0.8785 (mmm) cc_final: 0.8542 (mtp) REVERT: B 203 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8028 (tm-30) REVERT: B 291 CYS cc_start: 0.8748 (m) cc_final: 0.8444 (m) REVERT: B 331 MET cc_start: 0.8228 (tmm) cc_final: 0.7581 (tmm) REVERT: B 338 HIS cc_start: 0.8669 (m90) cc_final: 0.8436 (m90) REVERT: C 42 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: C 331 MET cc_start: 0.8521 (tpp) cc_final: 0.8062 (tpp) REVERT: D 338 HIS cc_start: 0.8134 (t70) cc_final: 0.7800 (t70) REVERT: E 110 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9236 (mmmm) REVERT: E 203 GLU cc_start: 0.9033 (mp0) cc_final: 0.8618 (pm20) REVERT: E 331 MET cc_start: 0.8546 (mmp) cc_final: 0.8170 (mmp) REVERT: F 37 ASP cc_start: 0.8503 (t0) cc_final: 0.8107 (t0) REVERT: F 139 ARG cc_start: 0.8308 (mtp180) cc_final: 0.8050 (ttm-80) REVERT: F 222 PHE cc_start: 0.7093 (t80) cc_final: 0.5730 (t80) REVERT: F 225 ARG cc_start: 0.9118 (ptm-80) cc_final: 0.8507 (ttp80) REVERT: F 331 MET cc_start: 0.8089 (mmp) cc_final: 0.7378 (tpt) outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 0.2879 time to fit residues: 53.9364 Evaluate side-chains 118 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 LEU 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 237 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 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 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 291 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 89 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** D 338 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 = 0.3507 r_free = 0.3507 target = 0.080211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.052019 restraints weight = 53177.601| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.39 r_work: 0.2621 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 1.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18047 Z= 0.240 Angle : 0.523 10.886 24732 Z= 0.271 Chirality : 0.043 0.178 2881 Planarity : 0.004 0.054 2979 Dihedral : 10.491 73.891 3006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -0.02 (0.19), residues: 2071 helix: 0.74 (0.24), residues: 533 sheet: 0.13 (0.28), residues: 339 loop : -0.35 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 333 HIS 0.003 0.001 HIS D 96 PHE 0.020 0.001 PHE C 303 TYR 0.011 0.001 TYR C 226 ARG 0.006 0.001 ARG D 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7895.26 seconds wall clock time: 141 minutes 38.82 seconds (8498.82 seconds total)