Starting phenix.real_space_refine on Thu Sep 18 14:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bih_44590/09_2025/9bih_44590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bih_44590/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bih_44590/09_2025/9bih_44590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bih_44590/09_2025/9bih_44590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bih_44590/09_2025/9bih_44590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bih_44590/09_2025/9bih_44590.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 66 5.16 5 C 11071 2.51 5 N 2852 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2744 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 14, 'TRANS': 334} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 591 Classifications: {'RNA': 28} Modifications used: {'p5*END': 1, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 571 Classifications: {'RNA': 27} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna3p': 26} Time building chain proxies: 4.54, per 1000 atoms: 0.26 Number of scatterers: 17576 At special positions: 0 Unit cell: (112.604, 122.958, 132.019, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 55 15.00 O 3532 8.00 N 2852 7.00 C 11071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 678.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 26.5% alpha, 24.9% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.510A pdb=" N LEU A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.700A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.519A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.521A pdb=" N LEU B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.688A pdb=" N LEU C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.500A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.545A pdb=" N LEU D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.562A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.517A pdb=" N LEU E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 309 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 removed outlier: 3.576A pdb=" N LEU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 removed outlier: 3.743A pdb=" N LEU F 134 " --> pdb=" O GLY F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.539A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.532A pdb=" N LEU F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.627A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.026A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.026A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 8.073A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 276 through 282 removed outlier: 3.503A pdb=" N TYR A 279 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.190A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.649A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.219A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.219A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 8.074A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 265 through 267 removed outlier: 4.766A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 317 through 323 Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.633A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.255A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 155 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.255A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC4, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.997A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.845A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 317 through 323 Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.562A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.161A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.161A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 8.043A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.629A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.556A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.416A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.416A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 8.094A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 265 through 267 removed outlier: 4.770A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 322 removed outlier: 5.477A pdb=" N LYS E 335 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.733A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.240A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.240A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 8.061A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 163 removed outlier: 3.508A pdb=" N LEU F 168 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.543A pdb=" N GLU F 265 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 3.562A pdb=" N SER F 329 " --> pdb=" O LYS F 345 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.72 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 18047 Z= 0.331 Angle : 0.570 5.934 24732 Z= 0.309 Chirality : 0.047 0.155 2881 Planarity : 0.004 0.046 2979 Dihedral : 12.119 77.665 6944 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.63 % Allowed : 5.15 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2071 helix: 0.17 (0.22), residues: 532 sheet: 0.30 (0.33), residues: 304 loop : -0.77 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 91 TYR 0.013 0.002 TYR A 343 PHE 0.021 0.002 PHE A 269 TRP 0.010 0.002 TRP D 87 HIS 0.006 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00786 (18047) covalent geometry : angle 0.57023 (24732) hydrogen bonds : bond 0.18801 ( 659) hydrogen bonds : angle 8.22967 ( 1825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 514 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 233 PHE cc_start: 0.7224 (m-80) cc_final: 0.6318 (m-80) REVERT: D 301 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: E 84 THR cc_start: 0.5579 (t) cc_final: 0.5345 (p) REVERT: E 183 VAL cc_start: 0.7237 (t) cc_final: 0.6965 (t) REVERT: E 330 PHE cc_start: 0.7150 (m-80) cc_final: 0.6612 (m-80) REVERT: E 342 PHE cc_start: 0.6468 (t80) cc_final: 0.6265 (t80) REVERT: F 300 LEU cc_start: 0.7390 (tp) cc_final: 0.6812 (tp) REVERT: F 321 VAL cc_start: 0.7706 (t) cc_final: 0.7291 (p) outliers start: 30 outliers final: 3 residues processed: 535 average time/residue: 0.1273 time to fit residues: 103.2205 Evaluate side-chains 294 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 290 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 336 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN B 310 GLN C 12 ASN C 164 ASN D 15 HIS D 29 ASN E 243 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.083691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.056843 restraints weight = 52223.271| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.47 r_work: 0.2754 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18047 Z= 0.151 Angle : 0.643 15.866 24732 Z= 0.330 Chirality : 0.045 0.181 2881 Planarity : 0.005 0.055 2979 Dihedral : 10.743 74.251 3012 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.50 % Allowed : 12.91 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2071 helix: 0.30 (0.22), residues: 539 sheet: 0.38 (0.33), residues: 257 loop : -0.60 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.016 0.002 TYR A 180 PHE 0.022 0.002 PHE A 16 TRP 0.015 0.001 TRP A 59 HIS 0.006 0.001 HIS E 243 Details of bonding type rmsd covalent geometry : bond 0.00344 (18047) covalent geometry : angle 0.64271 (24732) hydrogen bonds : bond 0.03785 ( 659) hydrogen bonds : angle 5.68362 ( 1825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.5352 (m-10) cc_final: 0.4830 (m-10) REVERT: A 267 GLU cc_start: 0.6228 (tm-30) cc_final: 0.5895 (tm-30) REVERT: B 267 GLU cc_start: 0.6917 (mp0) cc_final: 0.6675 (mp0) REVERT: B 272 MET cc_start: 0.6693 (ppp) cc_final: 0.6456 (ppp) REVERT: C 267 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5793 (tm-30) REVERT: C 280 PHE cc_start: 0.8465 (t80) cc_final: 0.7728 (t80) REVERT: C 331 MET cc_start: 0.8012 (tpp) cc_final: 0.7801 (tmm) REVERT: D 169 ILE cc_start: 0.8488 (mt) cc_final: 0.7999 (mp) REVERT: D 328 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7100 (mm) REVERT: E 84 THR cc_start: 0.6892 (t) cc_final: 0.6683 (p) REVERT: E 217 LEU cc_start: 0.8426 (mt) cc_final: 0.8056 (mt) REVERT: E 285 GLN cc_start: 0.8984 (tp40) cc_final: 0.7930 (tp40) REVERT: E 342 PHE cc_start: 0.7786 (t80) cc_final: 0.7195 (t80) REVERT: F 26 SER cc_start: 0.6234 (OUTLIER) cc_final: 0.5954 (m) REVERT: F 37 ASP cc_start: 0.7277 (t0) cc_final: 0.7075 (t0) REVERT: F 75 ASN cc_start: 0.6732 (m-40) cc_final: 0.6510 (m-40) REVERT: F 78 VAL cc_start: 0.8351 (t) cc_final: 0.8000 (t) REVERT: F 84 THR cc_start: 0.7266 (t) cc_final: 0.7015 (t) REVERT: F 156 VAL cc_start: 0.9103 (t) cc_final: 0.8878 (p) outliers start: 46 outliers final: 22 residues processed: 333 average time/residue: 0.1142 time to fit residues: 59.8037 Evaluate side-chains 274 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 167 THR 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 156 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 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 26 SER Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 0.9990 chunk 179 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 ASN E 15 HIS F 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.085153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058862 restraints weight = 53651.737| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.41 r_work: 0.2858 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18047 Z= 0.132 Angle : 0.556 9.435 24732 Z= 0.292 Chirality : 0.043 0.176 2881 Planarity : 0.004 0.044 2979 Dihedral : 10.514 73.978 3006 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.50 % Allowed : 14.16 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2071 helix: 0.60 (0.23), residues: 533 sheet: 0.04 (0.29), residues: 312 loop : -0.51 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.023 0.001 TYR D 238 PHE 0.018 0.001 PHE F 330 TRP 0.009 0.001 TRP E 333 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00301 (18047) covalent geometry : angle 0.55592 (24732) hydrogen bonds : bond 0.03411 ( 659) hydrogen bonds : angle 5.04911 ( 1825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6591 (mmm) cc_final: 0.6170 (mmm) REVERT: A 105 MET cc_start: 0.7109 (tpp) cc_final: 0.6900 (tpp) REVERT: A 280 PHE cc_start: 0.8191 (t80) cc_final: 0.7849 (t80) REVERT: B 198 SER cc_start: 0.8435 (m) cc_final: 0.8071 (p) REVERT: B 272 MET cc_start: 0.7565 (ppp) cc_final: 0.7215 (ppp) REVERT: B 292 VAL cc_start: 0.7962 (p) cc_final: 0.7748 (m) REVERT: B 338 HIS cc_start: 0.8591 (m-70) cc_final: 0.8104 (m90) REVERT: C 30 ASN cc_start: 0.8351 (p0) cc_final: 0.8108 (p0) REVERT: C 210 MET cc_start: 0.8002 (mpp) cc_final: 0.6981 (mtm) REVERT: E 216 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: E 255 LEU cc_start: 0.9218 (mt) cc_final: 0.9015 (mt) REVERT: E 285 GLN cc_start: 0.8850 (tp40) cc_final: 0.8412 (tp40) REVERT: E 342 PHE cc_start: 0.7569 (t80) cc_final: 0.7279 (t80) REVERT: F 37 ASP cc_start: 0.7262 (t0) cc_final: 0.7002 (t0) REVERT: F 156 VAL cc_start: 0.9170 (t) cc_final: 0.8906 (p) REVERT: F 249 LEU cc_start: 0.6450 (tp) cc_final: 0.6190 (mt) outliers start: 46 outliers final: 27 residues processed: 285 average time/residue: 0.1173 time to fit residues: 51.5680 Evaluate side-chains 232 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 50 LEU 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 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 15 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 0.0000 chunk 180 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 83 ASN E 75 ASN F 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.058413 restraints weight = 52809.150| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.38 r_work: 0.2818 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18047 Z= 0.108 Angle : 0.524 9.152 24732 Z= 0.273 Chirality : 0.042 0.162 2881 Planarity : 0.004 0.045 2979 Dihedral : 10.464 74.047 3006 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.39 % Allowed : 15.57 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.18), residues: 2071 helix: 0.81 (0.23), residues: 529 sheet: 0.09 (0.29), residues: 313 loop : -0.52 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.017 0.001 TYR C 343 PHE 0.024 0.001 PHE E 16 TRP 0.008 0.001 TRP E 333 HIS 0.015 0.001 HIS E 15 Details of bonding type rmsd covalent geometry : bond 0.00244 (18047) covalent geometry : angle 0.52396 (24732) hydrogen bonds : bond 0.02929 ( 659) hydrogen bonds : angle 4.85205 ( 1825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.8446 (t80) cc_final: 0.8125 (t80) REVERT: B 272 MET cc_start: 0.7987 (ppp) cc_final: 0.7763 (ppp) REVERT: B 338 HIS cc_start: 0.8661 (m-70) cc_final: 0.8141 (m90) REVERT: C 30 ASN cc_start: 0.8313 (p0) cc_final: 0.8074 (p0) REVERT: C 42 GLU cc_start: 0.8548 (pp20) cc_final: 0.8189 (tm-30) REVERT: C 331 MET cc_start: 0.7576 (tmm) cc_final: 0.7025 (ppp) REVERT: E 47 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8749 (mmmt) REVERT: E 225 ARG cc_start: 0.8774 (ptm160) cc_final: 0.8543 (ptm160) REVERT: E 285 GLN cc_start: 0.8940 (tp40) cc_final: 0.8477 (tp40) REVERT: E 292 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8131 (m) REVERT: E 330 PHE cc_start: 0.8452 (m-80) cc_final: 0.8083 (m-80) REVERT: F 156 VAL cc_start: 0.9203 (t) cc_final: 0.8948 (p) REVERT: F 225 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8550 (tmm-80) outliers start: 44 outliers final: 24 residues processed: 224 average time/residue: 0.1260 time to fit residues: 44.0008 Evaluate side-chains 200 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 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 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 292 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 225 ARG Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 80 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 338 HIS ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS E 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.083526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056052 restraints weight = 53755.519| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.53 r_work: 0.2778 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 1.0115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18047 Z= 0.186 Angle : 0.638 16.461 24732 Z= 0.330 Chirality : 0.045 0.175 2881 Planarity : 0.004 0.041 2979 Dihedral : 10.724 73.903 3006 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.20 % Allowed : 15.41 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.18), residues: 2071 helix: 0.63 (0.23), residues: 529 sheet: 0.37 (0.30), residues: 257 loop : -0.71 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 62 TYR 0.018 0.002 TYR A 33 PHE 0.020 0.002 PHE E 214 TRP 0.015 0.002 TRP E 333 HIS 0.008 0.002 HIS E 15 Details of bonding type rmsd covalent geometry : bond 0.00427 (18047) covalent geometry : angle 0.63770 (24732) hydrogen bonds : bond 0.03798 ( 659) hydrogen bonds : angle 5.05415 ( 1825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8208 (ttp) REVERT: B 1 MET cc_start: 0.8554 (mmm) cc_final: 0.8160 (mtp) REVERT: B 129 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8719 (p0) REVERT: B 203 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7995 (tm-30) REVERT: B 210 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7806 (mtm) REVERT: B 338 HIS cc_start: 0.8576 (m90) cc_final: 0.8196 (m90) REVERT: C 42 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: C 265 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8218 (pt0) REVERT: D 338 HIS cc_start: 0.8241 (t-170) cc_final: 0.7950 (t70) REVERT: E 19 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8517 (mm-40) REVERT: E 78 VAL cc_start: 0.9251 (t) cc_final: 0.9032 (p) REVERT: E 136 ARG cc_start: 0.9437 (ttm110) cc_final: 0.9171 (ttm110) REVERT: E 225 ARG cc_start: 0.8900 (ptm160) cc_final: 0.8587 (ptm160) REVERT: E 285 GLN cc_start: 0.9179 (tp40) cc_final: 0.8946 (tp40) REVERT: F 37 ASP cc_start: 0.8389 (t0) cc_final: 0.7989 (t0) REVERT: F 202 GLN cc_start: 0.9393 (mp10) cc_final: 0.9130 (mp10) REVERT: F 225 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8596 (tmm-80) outliers start: 59 outliers final: 27 residues processed: 190 average time/residue: 0.1379 time to fit residues: 39.0273 Evaluate side-chains 140 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 27 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.082956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055279 restraints weight = 52385.922| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.52 r_work: 0.2708 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 1.0373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18047 Z= 0.104 Angle : 0.535 12.212 24732 Z= 0.272 Chirality : 0.043 0.163 2881 Planarity : 0.004 0.040 2979 Dihedral : 10.595 73.915 3006 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.57 % Allowed : 16.82 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2071 helix: 0.76 (0.24), residues: 528 sheet: 0.29 (0.28), residues: 318 loop : -0.50 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 139 TYR 0.014 0.001 TYR C 343 PHE 0.012 0.001 PHE B 214 TRP 0.014 0.001 TRP F 333 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00235 (18047) covalent geometry : angle 0.53494 (24732) hydrogen bonds : bond 0.02882 ( 659) hydrogen bonds : angle 4.71085 ( 1825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8344 (ttp) REVERT: A 331 MET cc_start: 0.8971 (tpp) cc_final: 0.8635 (tpt) REVERT: B 1 MET cc_start: 0.8624 (mmm) cc_final: 0.8213 (mtp) REVERT: B 129 ASP cc_start: 0.9044 (m-30) cc_final: 0.8810 (p0) REVERT: B 203 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7854 (tm-30) REVERT: B 210 MET cc_start: 0.8206 (mtm) cc_final: 0.7929 (ttp) REVERT: B 338 HIS cc_start: 0.8658 (m90) cc_final: 0.8246 (m90) REVERT: C 42 GLU cc_start: 0.8863 (pp20) cc_final: 0.8388 (tm-30) REVERT: C 265 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8219 (pt0) REVERT: C 331 MET cc_start: 0.8736 (tmm) cc_final: 0.8164 (ppp) REVERT: E 136 ARG cc_start: 0.9432 (ttm110) cc_final: 0.9146 (ttm110) REVERT: E 225 ARG cc_start: 0.8998 (ptm160) cc_final: 0.8721 (ptm160) REVERT: E 285 GLN cc_start: 0.9164 (tp40) cc_final: 0.8942 (tp40) REVERT: F 37 ASP cc_start: 0.8412 (t0) cc_final: 0.7972 (t0) REVERT: F 62 ARG cc_start: 0.9075 (ptt-90) cc_final: 0.8778 (ptt-90) REVERT: F 225 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8718 (tmm-80) outliers start: 29 outliers final: 16 residues processed: 145 average time/residue: 0.1441 time to fit residues: 31.7745 Evaluate side-chains 121 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain D residue 48 THR 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 272 MET 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 225 ARG Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 102 optimal weight: 0.0570 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.5902 ------------------------------------------------------------------------------- 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 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.081319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053681 restraints weight = 53349.194| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.40 r_work: 0.2677 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 1.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18047 Z= 0.140 Angle : 0.530 11.079 24732 Z= 0.275 Chirality : 0.043 0.180 2881 Planarity : 0.004 0.040 2979 Dihedral : 10.556 73.889 3006 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 16.39 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.19), residues: 2071 helix: 0.85 (0.24), residues: 528 sheet: 0.11 (0.27), residues: 349 loop : -0.45 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 139 TYR 0.014 0.001 TYR A 33 PHE 0.047 0.001 PHE E 330 TRP 0.011 0.001 TRP F 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00324 (18047) covalent geometry : angle 0.52954 (24732) hydrogen bonds : bond 0.03148 ( 659) hydrogen bonds : angle 4.73894 ( 1825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (ttp) REVERT: A 331 MET cc_start: 0.9047 (tpp) cc_final: 0.8828 (tpt) REVERT: B 1 MET cc_start: 0.8661 (mmm) cc_final: 0.8370 (mtp) REVERT: B 203 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8134 (tm-30) REVERT: B 210 MET cc_start: 0.8412 (mtm) cc_final: 0.8161 (ttp) REVERT: B 291 CYS cc_start: 0.8621 (m) cc_final: 0.8282 (m) REVERT: B 338 HIS cc_start: 0.8431 (m90) cc_final: 0.8071 (m90) REVERT: C 42 GLU cc_start: 0.8875 (pp20) cc_final: 0.8478 (tm-30) REVERT: C 215 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9097 (pt) REVERT: C 265 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8448 (pt0) REVERT: C 331 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8087 (ppp) REVERT: D 253 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8577 (mp) REVERT: E 136 ARG cc_start: 0.9397 (ttm110) cc_final: 0.8967 (ttm110) REVERT: E 225 ARG cc_start: 0.8916 (ptm160) cc_final: 0.8637 (ptm160) REVERT: F 37 ASP cc_start: 0.8251 (t0) cc_final: 0.7712 (t0) REVERT: F 222 PHE cc_start: 0.7156 (t80) cc_final: 0.5510 (t80) REVERT: F 225 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8653 (tmm-80) outliers start: 34 outliers final: 17 residues processed: 129 average time/residue: 0.1411 time to fit residues: 27.9698 Evaluate side-chains 120 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 253 ILE 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 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 255 LEU 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 144 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.051868 restraints weight = 52761.922| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.31 r_work: 0.2607 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 1.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18047 Z= 0.174 Angle : 0.557 11.267 24732 Z= 0.287 Chirality : 0.044 0.168 2881 Planarity : 0.004 0.052 2979 Dihedral : 10.710 73.985 3006 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.01 % Allowed : 16.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 2071 helix: 0.73 (0.24), residues: 527 sheet: 0.32 (0.29), residues: 319 loop : -0.47 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 225 TYR 0.015 0.001 TYR A 33 PHE 0.019 0.001 PHE A 233 TRP 0.010 0.001 TRP D 59 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00404 (18047) covalent geometry : angle 0.55701 (24732) hydrogen bonds : bond 0.03370 ( 659) hydrogen bonds : angle 4.81675 ( 1825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (ttp) REVERT: B 203 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8342 (tm-30) REVERT: B 210 MET cc_start: 0.8700 (mtm) cc_final: 0.8361 (ttp) REVERT: B 291 CYS cc_start: 0.8940 (m) cc_final: 0.8579 (m) REVERT: B 338 HIS cc_start: 0.8528 (m90) cc_final: 0.8161 (m90) REVERT: C 42 GLU cc_start: 0.8980 (pp20) cc_final: 0.8459 (tm-30) REVERT: C 331 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8220 (ppp) REVERT: D 334 CYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8195 (p) REVERT: E 13 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8645 (pttt) REVERT: F 222 PHE cc_start: 0.7338 (t80) cc_final: 0.5714 (t80) REVERT: F 225 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8628 (tmm-80) REVERT: F 331 MET cc_start: 0.8111 (mmp) cc_final: 0.7245 (tpt) outliers start: 37 outliers final: 22 residues processed: 128 average time/residue: 0.1349 time to fit residues: 26.7375 Evaluate side-chains 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain E residue 13 LYS 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 272 MET Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 204 optimal weight: 30.0000 chunk 181 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 0.0270 chunk 170 optimal weight: 4.9990 chunk 142 optimal weight: 0.0050 overall best weight: 1.4256 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.080159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052314 restraints weight = 53081.220| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.34 r_work: 0.2626 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 1.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18047 Z= 0.125 Angle : 0.524 11.655 24732 Z= 0.268 Chirality : 0.043 0.151 2881 Planarity : 0.004 0.057 2979 Dihedral : 10.597 73.892 3006 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.36 % Allowed : 16.93 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.19), residues: 2071 helix: 0.74 (0.24), residues: 528 sheet: 0.18 (0.28), residues: 349 loop : -0.45 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 225 TYR 0.011 0.001 TYR A 33 PHE 0.023 0.001 PHE C 303 TRP 0.008 0.001 TRP F 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00285 (18047) covalent geometry : angle 0.52444 (24732) hydrogen bonds : bond 0.03011 ( 659) hydrogen bonds : angle 4.68929 ( 1825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8590 (ttp) REVERT: A 331 MET cc_start: 0.9227 (tpt) cc_final: 0.8932 (tpt) REVERT: B 203 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8298 (tm-30) REVERT: B 210 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: B 291 CYS cc_start: 0.8883 (m) cc_final: 0.8557 (m) REVERT: B 338 HIS cc_start: 0.8595 (m90) cc_final: 0.8281 (m90) REVERT: C 42 GLU cc_start: 0.8933 (pp20) cc_final: 0.8359 (tm-30) REVERT: C 265 GLU cc_start: 0.7760 (pt0) cc_final: 0.7245 (pp20) REVERT: C 331 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8224 (ppp) REVERT: D 253 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8746 (mp) REVERT: E 13 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8764 (pttt) REVERT: F 222 PHE cc_start: 0.7363 (t80) cc_final: 0.5781 (t80) REVERT: F 225 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8712 (tmm-80) REVERT: F 331 MET cc_start: 0.8100 (mmp) cc_final: 0.7296 (tpt) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.1383 time to fit residues: 25.2997 Evaluate side-chains 118 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 13 LYS 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 272 MET 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 217 LEU Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.080982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053370 restraints weight = 52895.058| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.31 r_work: 0.2652 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 1.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18047 Z= 0.096 Angle : 0.513 10.580 24732 Z= 0.262 Chirality : 0.042 0.184 2881 Planarity : 0.004 0.058 2979 Dihedral : 10.459 73.874 3006 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 16.87 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.19), residues: 2071 helix: 0.68 (0.24), residues: 532 sheet: 0.16 (0.28), residues: 339 loop : -0.36 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 225 TYR 0.008 0.001 TYR E 33 PHE 0.017 0.001 PHE C 303 TRP 0.009 0.001 TRP B 87 HIS 0.002 0.000 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00216 (18047) covalent geometry : angle 0.51300 (24732) hydrogen bonds : bond 0.02795 ( 659) hydrogen bonds : angle 4.57328 ( 1825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.768 Fit side-chains REVERT: A 265 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8663 (mp0) REVERT: A 331 MET cc_start: 0.9172 (tpt) cc_final: 0.8902 (tpt) REVERT: B 203 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8121 (tm-30) REVERT: B 210 MET cc_start: 0.8756 (mtm) cc_final: 0.8346 (ttp) REVERT: B 291 CYS cc_start: 0.8900 (m) cc_final: 0.8535 (m) REVERT: B 338 HIS cc_start: 0.8716 (m90) cc_final: 0.8331 (m90) REVERT: C 42 GLU cc_start: 0.8921 (pp20) cc_final: 0.8389 (tm-30) REVERT: C 210 MET cc_start: 0.8938 (mmm) cc_final: 0.8701 (mmm) REVERT: C 265 GLU cc_start: 0.7748 (pt0) cc_final: 0.7332 (pp20) REVERT: C 331 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8201 (ppp) REVERT: D 225 ARG cc_start: 0.8875 (ptm-80) cc_final: 0.8610 (tmm-80) REVERT: E 13 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8750 (pttt) REVERT: F 222 PHE cc_start: 0.7373 (t80) cc_final: 0.5903 (t80) REVERT: F 225 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8812 (tmm-80) REVERT: F 331 MET cc_start: 0.8122 (mmp) cc_final: 0.7293 (tpt) outliers start: 28 outliers final: 17 residues processed: 124 average time/residue: 0.1403 time to fit residues: 26.9867 Evaluate side-chains 115 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 243 HIS Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 13 LYS 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 276 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 117 optimal weight: 0.0980 chunk 182 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.054164 restraints weight = 54123.428| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.48 r_work: 0.2734 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 1.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18047 Z= 0.096 Angle : 0.512 11.629 24732 Z= 0.262 Chirality : 0.042 0.169 2881 Planarity : 0.004 0.058 2979 Dihedral : 10.405 73.910 3006 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.25 % Allowed : 17.31 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 2071 helix: 0.68 (0.24), residues: 533 sheet: 0.19 (0.28), residues: 339 loop : -0.35 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 136 TYR 0.008 0.001 TYR A 33 PHE 0.030 0.001 PHE C 303 TRP 0.045 0.001 TRP E 333 HIS 0.002 0.000 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00219 (18047) covalent geometry : angle 0.51170 (24732) hydrogen bonds : bond 0.02761 ( 659) hydrogen bonds : angle 4.53542 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.80 seconds wall clock time: 65 minutes 52.06 seconds (3952.06 seconds total)