Starting phenix.real_space_refine on Sat Sep 12 17:10:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj2_25915/09_2026/7tj2_25915.map" } resolution = 3.2 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= 0.005 sd= 0.107 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 62 5.49 5 S 57 5.16 5 C 10718 2.51 5 N 2788 2.21 5 O 3458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17083 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2733 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 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: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 257} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNAv2': 31} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 29} Chain: "H" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 651 Classifications: {'RNAv2': 31} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna3p': 30} Time building chain proxies: 3.76, per 1000 atoms: 0.22 Number of scatterers: 17083 At special positions: 0 Unit cell: (119.087, 121.835, 134.659, 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 57 16.00 P 62 15.00 O 3458 8.00 N 2788 7.00 C 10718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 630.8 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3746 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 42 sheets defined 25.2% alpha, 23.6% beta 30 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.92 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 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 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 77 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 227 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 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 77 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.750A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) 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 77 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 251 through 262 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 77 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 227 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.752A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 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 77 Processing helix chain 'F' and resid 130 through 138 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: 3.776A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 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: 6.658A 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: 7.238A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 155 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.186A 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 161 through 163 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.825A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 343 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.237A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 155 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.237A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 316 through 323 Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 155 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323 removed outlier: 5.239A pdb=" N LYS C 335 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.659A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 155 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 320 through 323 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.659A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 155 " --> pdb=" O TYR E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'E' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 316 through 323 Processing sheet with id=AD9, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 155 " --> pdb=" O TYR F 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AE5, first strand: chain 'F' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323 636 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5248 1.34 - 1.45: 2661 1.45 - 1.57: 9439 1.57 - 1.69: 122 1.69 - 1.81: 85 Bond restraints: 17555 Sorted by residual: bond pdb=" C ALA E 118 " pdb=" N PRO E 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" C ALA B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.10e+00 bond pdb=" C ALA D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.339 1.375 -0.035 3.40e-02 8.65e+02 1.08e+00 bond pdb=" C ALA A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 bond pdb=" C ALA C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 ... (remaining 17550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 23569 1.12 - 2.24: 295 2.24 - 3.35: 229 3.35 - 4.47: 13 4.47 - 5.59: 2 Bond angle restraints: 24108 Sorted by residual: angle pdb=" C THR F 49 " pdb=" N LEU F 50 " pdb=" CA LEU F 50 " ideal model delta sigma weight residual 121.48 124.92 -3.44 2.04e+00 2.40e-01 2.84e+00 angle pdb=" C GLN F 310 " pdb=" N ASP F 311 " pdb=" CA ASP F 311 " ideal model delta sigma weight residual 121.54 124.60 -3.06 1.91e+00 2.74e-01 2.56e+00 angle pdb=" C3' U G 24 " pdb=" C2' U G 24 " pdb=" O2' U G 24 " ideal model delta sigma weight residual 109.80 114.47 -4.67 3.00e+00 1.11e-01 2.43e+00 angle pdb=" C GLN C 310 " pdb=" N ASP C 311 " pdb=" CA ASP C 311 " ideal model delta sigma weight residual 121.54 124.39 -2.85 1.91e+00 2.74e-01 2.22e+00 angle pdb=" C GLN E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 124.20 -2.66 1.91e+00 2.74e-01 1.94e+00 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 9987 17.63 - 35.26: 266 35.26 - 52.88: 84 52.88 - 70.51: 29 70.51 - 88.14: 1 Dihedral angle restraints: 10367 sinusoidal: 4560 harmonic: 5807 Sorted by residual: dihedral pdb=" C4' U G 24 " pdb=" C3' U G 24 " pdb=" C2' U G 24 " pdb=" C1' U G 24 " ideal model delta sinusoidal sigma weight residual 36.35 -33.67 70.01 1 3.10e+00 1.04e-01 6.58e+02 dihedral pdb=" O4' U G 24 " pdb=" C4' U G 24 " pdb=" C3' U G 24 " pdb=" C2' U G 24 " ideal model delta sinusoidal sigma weight residual -35.15 21.38 -56.53 1 4.00e+00 6.25e-02 2.69e+02 dihedral pdb=" O4' U G 24 " pdb=" C2' U G 24 " pdb=" C1' U G 24 " pdb=" C3' U G 24 " ideal model delta sinusoidal sigma weight residual -94.41 -35.32 -59.08 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2464 0.067 - 0.133: 296 0.133 - 0.200: 0 0.200 - 0.267: 62 0.267 - 0.333: 2 Chirality restraints: 2824 Sorted by residual: chirality pdb=" P G H 17 " pdb=" OP1 G H 17 " pdb=" OP2 G H 17 " pdb=" O5' G H 17 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C2' U G 24 " pdb=" C3' U G 24 " pdb=" O2' U G 24 " pdb=" C1' U G 24 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" P A H 29 " pdb=" OP1 A H 29 " pdb=" OP2 A H 29 " pdb=" O5' A H 29 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2821 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 334 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C CYS B 334 " 0.020 2.00e-02 2.50e+03 pdb=" O CYS B 334 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 335 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO D 51 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO B 51 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.015 5.00e-02 4.00e+02 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1067 2.74 - 3.28: 15965 3.28 - 3.82: 28253 3.82 - 4.36: 34467 4.36 - 4.90: 58658 Nonbonded interactions: 138410 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY F 77 " pdb=" OG1 THR F 121 " model vdw 2.196 3.040 ... (remaining 138405 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' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C \ or name O or name CB )) or resid 2 through 345)) 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.002 0.036 17555 Z= 0.079 Angle : 0.430 5.591 24108 Z= 0.203 Chirality : 0.054 0.333 2824 Planarity : 0.003 0.027 2873 Dihedral : 9.803 88.139 6621 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.64 % Allowed : 2.37 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1990 helix: 1.26 (0.24), residues: 492 sheet: 0.55 (0.33), residues: 316 loop : -0.48 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 199 TYR 0.006 0.001 TYR A 226 PHE 0.006 0.001 PHE A 342 TRP 0.004 0.001 TRP C 87 HIS 0.001 0.000 HIS F 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 (17555) covalent geometry : angle 0.42966 / 0.20 (24108) hydrogen bonds : bond 0.19934 / 12.93 ( 655) hydrogen bonds : angle 8.24035 / 5.89 ( 1829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 389 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8597 (mttt) cc_final: 0.8350 (mmtm) REVERT: A 267 GLU cc_start: 0.7933 (tt0) cc_final: 0.7638 (tm-30) REVERT: B 47 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8212 (mmtp) REVERT: B 105 MET cc_start: 0.8115 (mmm) cc_final: 0.7368 (mpp) REVERT: B 107 ASP cc_start: 0.7999 (m-30) cc_final: 0.7724 (m-30) REVERT: B 343 TYR cc_start: 0.8254 (p90) cc_final: 0.7959 (p90) REVERT: C 40 ASP cc_start: 0.8115 (m-30) cc_final: 0.7515 (m-30) REVERT: C 150 LYS cc_start: 0.8070 (mttt) cc_final: 0.7651 (mmtm) REVERT: C 153 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7777 (mm-40) REVERT: C 166 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (m) REVERT: D 19 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6789 (mm-40) REVERT: D 105 MET cc_start: 0.7242 (mmm) cc_final: 0.6931 (mpp) REVERT: D 107 ASP cc_start: 0.7880 (m-30) cc_final: 0.6838 (p0) REVERT: E 245 GLN cc_start: 0.5823 (mt0) cc_final: 0.5061 (pp30) REVERT: E 252 LEU cc_start: 0.7821 (tp) cc_final: 0.7544 (tp) REVERT: F 107 ASP cc_start: 0.8291 (m-30) cc_final: 0.8025 (m-30) REVERT: F 168 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (pp) REVERT: F 305 GLU cc_start: 0.7592 (tt0) cc_final: 0.7360 (mt-10) REVERT: F 308 LYS cc_start: 0.7097 (mttt) cc_final: 0.6499 (ptmm) outliers start: 29 outliers final: 10 residues processed: 409 average time/residue: 0.1366 time to fit residues: 84.2456 Evaluate side-chains 232 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 310 GLN B 29 ASN B 30 ASN B 83 ASN B 140 ASN B 176 GLN D 30 ASN D 83 ASN E 29 ASN E 30 ASN F 29 ASN F 30 ASN F 75 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.203522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130718 restraints weight = 19175.636| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.12 r_work: 0.3256 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17555 Z= 0.210 Angle : 0.606 12.523 24108 Z= 0.302 Chirality : 0.050 0.375 2824 Planarity : 0.004 0.061 2873 Dihedral : 8.786 86.820 2868 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.00 % Allowed : 8.76 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1990 helix: 0.77 (0.24), residues: 509 sheet: 0.50 (0.30), residues: 348 loop : -0.49 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 258 TYR 0.013 0.001 TYR F 226 PHE 0.017 0.002 PHE E 269 TRP 0.015 0.002 TRP F 333 HIS 0.004 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (17555) covalent geometry : angle 0.60638 / 0.30 (24108) hydrogen bonds : bond 0.04375 / 2.91 ( 655) hydrogen bonds : angle 5.66295 / 4.06 ( 1829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.640 Fit side-chains REVERT: A 47 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8282 (mmtm) REVERT: A 110 LYS cc_start: 0.9106 (mttt) cc_final: 0.8527 (mmtm) REVERT: A 265 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 297 ASP cc_start: 0.8791 (t0) cc_final: 0.8570 (t0) REVERT: B 105 MET cc_start: 0.8506 (mmm) cc_final: 0.7372 (mpp) REVERT: B 209 GLN cc_start: 0.7843 (tp40) cc_final: 0.7436 (pp30) REVERT: B 213 ASP cc_start: 0.7954 (m-30) cc_final: 0.7575 (m-30) REVERT: B 331 MET cc_start: 0.6925 (mmm) cc_final: 0.6365 (mmm) REVERT: B 343 TYR cc_start: 0.8171 (p90) cc_final: 0.7658 (p90) REVERT: C 150 LYS cc_start: 0.8374 (mttt) cc_final: 0.7871 (mmtm) REVERT: C 166 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7882 (m) REVERT: D 105 MET cc_start: 0.7416 (mmm) cc_final: 0.6923 (mpt) REVERT: D 194 TYR cc_start: 0.7188 (m-80) cc_final: 0.6744 (m-80) REVERT: D 297 ASP cc_start: 0.6624 (t0) cc_final: 0.6421 (t70) REVERT: E 245 GLN cc_start: 0.5737 (mt0) cc_final: 0.4909 (pp30) REVERT: F 194 TYR cc_start: 0.8348 (m-80) cc_final: 0.8096 (m-80) REVERT: F 195 PHE cc_start: 0.8048 (m-80) cc_final: 0.7839 (m-10) REVERT: F 273 ASP cc_start: 0.7840 (t70) cc_final: 0.7590 (t70) REVERT: F 300 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7394 (mp) REVERT: F 305 GLU cc_start: 0.7849 (tt0) cc_final: 0.7372 (mt-10) REVERT: F 308 LYS cc_start: 0.7112 (mttt) cc_final: 0.6729 (ptmm) REVERT: F 330 PHE cc_start: 0.7211 (m-80) cc_final: 0.6992 (m-80) outliers start: 53 outliers final: 31 residues processed: 255 average time/residue: 0.1354 time to fit residues: 52.7242 Evaluate side-chains 218 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 178 optimal weight: 30.0000 chunk 138 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 189 GLN C 75 ASN C 176 GLN E 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133438 restraints weight = 19199.664| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.94 r_work: 0.3342 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17555 Z= 0.092 Angle : 0.494 8.542 24108 Z= 0.247 Chirality : 0.047 0.246 2824 Planarity : 0.003 0.039 2873 Dihedral : 8.236 67.000 2860 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.81 % Allowed : 10.97 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1990 helix: 1.02 (0.24), residues: 509 sheet: 0.63 (0.29), residues: 348 loop : -0.53 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.014 0.001 TYR E 180 PHE 0.015 0.001 PHE F 303 TRP 0.010 0.001 TRP F 333 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (17555) covalent geometry : angle 0.49381 / 0.25 (24108) hydrogen bonds : bond 0.03269 / 2.16 ( 655) hydrogen bonds : angle 4.97034 / 3.58 ( 1829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.614 Fit side-chains REVERT: A 47 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8288 (mmtp) REVERT: A 110 LYS cc_start: 0.9101 (mttt) cc_final: 0.8564 (mmtm) REVERT: A 139 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7570 (mtp180) REVERT: B 47 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8583 (mmtp) REVERT: B 105 MET cc_start: 0.8437 (mmm) cc_final: 0.7391 (mpp) REVERT: B 209 GLN cc_start: 0.7848 (tp40) cc_final: 0.7409 (pp30) REVERT: B 213 ASP cc_start: 0.8019 (m-30) cc_final: 0.7621 (m-30) REVERT: B 331 MET cc_start: 0.6898 (mmm) cc_final: 0.6515 (mmm) REVERT: B 343 TYR cc_start: 0.8227 (p90) cc_final: 0.7843 (p90) REVERT: C 150 LYS cc_start: 0.8353 (mttt) cc_final: 0.7952 (mmtm) REVERT: C 166 VAL cc_start: 0.8196 (p) cc_final: 0.7871 (m) REVERT: D 105 MET cc_start: 0.7327 (mmm) cc_final: 0.7033 (mpp) REVERT: D 194 TYR cc_start: 0.7190 (m-80) cc_final: 0.6764 (m-80) REVERT: E 245 GLN cc_start: 0.5805 (mt0) cc_final: 0.5040 (pp30) REVERT: E 251 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5253 (mt) REVERT: F 194 TYR cc_start: 0.8364 (m-80) cc_final: 0.8119 (m-80) REVERT: F 299 LEU cc_start: 0.7277 (tt) cc_final: 0.7070 (tt) REVERT: F 300 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7630 (mt) REVERT: F 305 GLU cc_start: 0.8103 (tt0) cc_final: 0.7531 (mt-10) REVERT: F 306 ILE cc_start: 0.7647 (mt) cc_final: 0.7384 (pt) REVERT: F 308 LYS cc_start: 0.7185 (mttt) cc_final: 0.6693 (ptmm) REVERT: F 330 PHE cc_start: 0.7213 (m-80) cc_final: 0.6968 (m-80) outliers start: 32 outliers final: 17 residues processed: 241 average time/residue: 0.1396 time to fit residues: 50.9189 Evaluate side-chains 207 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 173 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 102 optimal weight: 0.0050 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.205319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153895 restraints weight = 19221.580| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 4.21 r_work: 0.3170 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17555 Z= 0.127 Angle : 0.509 7.750 24108 Z= 0.254 Chirality : 0.047 0.207 2824 Planarity : 0.003 0.040 2873 Dihedral : 8.196 67.357 2858 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.05 % Allowed : 11.36 % Favored : 85.59 % 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 are not related in a simple way. whole: 0.06 (0.19), residues: 1990 helix: 1.19 (0.24), residues: 499 sheet: 0.54 (0.28), residues: 348 loop : -0.63 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.013 0.001 TYR E 180 PHE 0.012 0.001 PHE E 280 TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (17555) covalent geometry : angle 0.50932 / 0.25 (24108) hydrogen bonds : bond 0.03284 / 2.18 ( 655) hydrogen bonds : angle 4.81889 / 3.46 ( 1829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.623 Fit side-chains REVERT: A 110 LYS cc_start: 0.9149 (mttt) cc_final: 0.8571 (mmtm) REVERT: A 139 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7574 (mtp180) REVERT: A 265 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: B 105 MET cc_start: 0.8482 (mmm) cc_final: 0.7340 (mpp) REVERT: B 173 VAL cc_start: 0.8533 (m) cc_final: 0.8306 (p) REVERT: B 209 GLN cc_start: 0.7885 (tp40) cc_final: 0.6896 (tm-30) REVERT: B 213 ASP cc_start: 0.7927 (m-30) cc_final: 0.7007 (m-30) REVERT: B 331 MET cc_start: 0.6816 (mmm) cc_final: 0.6351 (mmm) REVERT: B 343 TYR cc_start: 0.8142 (p90) cc_final: 0.7804 (p90) REVERT: C 150 LYS cc_start: 0.8404 (mttt) cc_final: 0.7948 (mmtm) REVERT: C 166 VAL cc_start: 0.8220 (p) cc_final: 0.7908 (m) REVERT: D 105 MET cc_start: 0.7347 (mmm) cc_final: 0.7052 (mpp) REVERT: D 194 TYR cc_start: 0.7189 (m-80) cc_final: 0.6688 (m-80) REVERT: D 272 MET cc_start: 0.7199 (ttp) cc_final: 0.6823 (ttt) REVERT: E 153 GLN cc_start: 0.7740 (mp10) cc_final: 0.7485 (mp10) REVERT: E 245 GLN cc_start: 0.5815 (mt0) cc_final: 0.4966 (pp30) REVERT: F 194 TYR cc_start: 0.8227 (m-80) cc_final: 0.7895 (m-80) REVERT: F 300 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7412 (mt) REVERT: F 305 GLU cc_start: 0.8135 (tt0) cc_final: 0.7862 (tm-30) REVERT: F 308 LYS cc_start: 0.7201 (mttt) cc_final: 0.6722 (ptmm) REVERT: F 330 PHE cc_start: 0.7264 (m-80) cc_final: 0.6957 (m-80) outliers start: 54 outliers final: 34 residues processed: 240 average time/residue: 0.1357 time to fit residues: 49.9189 Evaluate side-chains 220 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 146 optimal weight: 0.0870 chunk 176 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 171 optimal weight: 0.0670 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.205487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154073 restraints weight = 19041.944| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.06 r_work: 0.3183 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17555 Z= 0.118 Angle : 0.504 8.865 24108 Z= 0.249 Chirality : 0.047 0.199 2824 Planarity : 0.003 0.043 2873 Dihedral : 8.110 62.133 2857 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.11 % Allowed : 11.59 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1990 helix: 1.19 (0.24), residues: 499 sheet: 0.53 (0.28), residues: 348 loop : -0.65 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.014 0.001 TYR E 180 PHE 0.014 0.001 PHE F 259 TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17555) covalent geometry : angle 0.50378 / 0.25 (24108) hydrogen bonds : bond 0.03114 / 2.04 ( 655) hydrogen bonds : angle 4.70423 / 3.38 ( 1829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.617 Fit side-chains REVERT: A 110 LYS cc_start: 0.9112 (mttt) cc_final: 0.8573 (mmtm) REVERT: A 139 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7512 (mtp180) REVERT: A 265 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: B 47 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8585 (mmtp) REVERT: B 105 MET cc_start: 0.8486 (mmm) cc_final: 0.7483 (mpp) REVERT: B 173 VAL cc_start: 0.8577 (m) cc_final: 0.8355 (p) REVERT: B 209 GLN cc_start: 0.7907 (tp40) cc_final: 0.6922 (tm-30) REVERT: B 213 ASP cc_start: 0.7959 (m-30) cc_final: 0.7025 (m-30) REVERT: B 331 MET cc_start: 0.6786 (mmm) cc_final: 0.6350 (mmm) REVERT: B 343 TYR cc_start: 0.8194 (p90) cc_final: 0.7861 (p90) REVERT: C 150 LYS cc_start: 0.8395 (mttt) cc_final: 0.7942 (mmtm) REVERT: C 166 VAL cc_start: 0.8210 (p) cc_final: 0.7904 (m) REVERT: D 105 MET cc_start: 0.7322 (mmm) cc_final: 0.7098 (mpp) REVERT: D 131 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6584 (mm-40) REVERT: D 135 PHE cc_start: 0.7409 (t80) cc_final: 0.7188 (t80) REVERT: D 153 GLN cc_start: 0.5562 (tt0) cc_final: 0.5229 (pt0) REVERT: D 194 TYR cc_start: 0.7042 (m-80) cc_final: 0.6543 (m-80) REVERT: D 272 MET cc_start: 0.7173 (ttp) cc_final: 0.6786 (ttt) REVERT: E 153 GLN cc_start: 0.7684 (mp10) cc_final: 0.7435 (mp10) REVERT: E 194 TYR cc_start: 0.7536 (m-80) cc_final: 0.7254 (m-80) REVERT: E 245 GLN cc_start: 0.5841 (mt0) cc_final: 0.4982 (pp30) REVERT: F 194 TYR cc_start: 0.8315 (m-80) cc_final: 0.8046 (m-80) REVERT: F 255 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6782 (mm) REVERT: F 300 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7406 (mt) REVERT: F 308 LYS cc_start: 0.7167 (mttt) cc_final: 0.6657 (ptmm) REVERT: F 330 PHE cc_start: 0.7146 (m-80) cc_final: 0.6789 (m-80) outliers start: 55 outliers final: 37 residues processed: 233 average time/residue: 0.1367 time to fit residues: 48.7131 Evaluate side-chains 221 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 96 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 278 ASN F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.203536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150538 restraints weight = 18977.861| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 4.16 r_work: 0.3123 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17555 Z= 0.180 Angle : 0.545 8.573 24108 Z= 0.269 Chirality : 0.048 0.197 2824 Planarity : 0.003 0.043 2873 Dihedral : 8.190 61.578 2857 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.11 % Allowed : 12.72 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1990 helix: 1.06 (0.24), residues: 499 sheet: 0.45 (0.29), residues: 348 loop : -0.71 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.013 0.001 TYR E 180 PHE 0.013 0.001 PHE A 269 TRP 0.011 0.002 TRP C 87 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (17555) covalent geometry : angle 0.54507 / 0.27 (24108) hydrogen bonds : bond 0.03445 / 2.28 ( 655) hydrogen bonds : angle 4.83537 / 3.47 ( 1829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.604 Fit side-chains REVERT: A 110 LYS cc_start: 0.9124 (mttt) cc_final: 0.8573 (mmtm) REVERT: A 139 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7571 (mtp180) REVERT: B 105 MET cc_start: 0.8610 (mmm) cc_final: 0.7507 (mpp) REVERT: B 173 VAL cc_start: 0.8636 (m) cc_final: 0.8419 (p) REVERT: B 209 GLN cc_start: 0.7950 (tp40) cc_final: 0.6982 (tm-30) REVERT: B 213 ASP cc_start: 0.7934 (m-30) cc_final: 0.6963 (m-30) REVERT: B 331 MET cc_start: 0.6895 (mmm) cc_final: 0.6573 (mmm) REVERT: B 343 TYR cc_start: 0.8217 (p90) cc_final: 0.7905 (p90) REVERT: C 150 LYS cc_start: 0.8406 (mttt) cc_final: 0.7930 (mmtm) REVERT: C 166 VAL cc_start: 0.8280 (p) cc_final: 0.7983 (m) REVERT: D 105 MET cc_start: 0.7443 (mmm) cc_final: 0.7162 (mpp) REVERT: D 131 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6560 (mm-40) REVERT: D 153 GLN cc_start: 0.5516 (tt0) cc_final: 0.5100 (pt0) REVERT: D 194 TYR cc_start: 0.7043 (m-80) cc_final: 0.6545 (m-80) REVERT: E 153 GLN cc_start: 0.7716 (mp10) cc_final: 0.7471 (mp10) REVERT: E 245 GLN cc_start: 0.5772 (mt0) cc_final: 0.4979 (pp30) REVERT: E 251 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5512 (mt) REVERT: F 219 MET cc_start: 0.6739 (mtt) cc_final: 0.6411 (pmm) REVERT: F 255 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6774 (mm) REVERT: F 300 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7415 (mt) REVERT: F 308 LYS cc_start: 0.7188 (mttt) cc_final: 0.6581 (ptmm) REVERT: F 330 PHE cc_start: 0.7183 (m-80) cc_final: 0.6854 (m-80) outliers start: 55 outliers final: 45 residues processed: 227 average time/residue: 0.1310 time to fit residues: 46.0326 Evaluate side-chains 224 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 82 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 0.0170 chunk 184 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 137 optimal weight: 0.0170 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.205568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134572 restraints weight = 19104.532| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.14 r_work: 0.3243 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17555 Z= 0.115 Angle : 0.508 9.301 24108 Z= 0.250 Chirality : 0.047 0.191 2824 Planarity : 0.003 0.045 2873 Dihedral : 8.057 61.920 2857 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.83 % Allowed : 13.40 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1990 helix: 1.16 (0.24), residues: 499 sheet: 0.51 (0.28), residues: 348 loop : -0.72 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.016 0.001 TYR E 180 PHE 0.019 0.001 PHE F 303 TRP 0.010 0.001 TRP C 87 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 (17555) covalent geometry : angle 0.50754 / 0.25 (24108) hydrogen bonds : bond 0.03033 / 1.99 ( 655) hydrogen bonds : angle 4.64287 / 3.34 ( 1829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.557 Fit side-chains REVERT: A 110 LYS cc_start: 0.9058 (mttt) cc_final: 0.8557 (mmtm) REVERT: A 139 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7408 (mtp180) REVERT: A 265 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7606 (tp30) REVERT: B 105 MET cc_start: 0.8389 (mmm) cc_final: 0.7409 (mpp) REVERT: B 203 GLU cc_start: 0.7442 (mp0) cc_final: 0.7125 (mp0) REVERT: B 209 GLN cc_start: 0.7941 (tp40) cc_final: 0.6946 (tm-30) REVERT: B 213 ASP cc_start: 0.7888 (m-30) cc_final: 0.6888 (m-30) REVERT: B 331 MET cc_start: 0.6812 (mmm) cc_final: 0.6562 (mmm) REVERT: B 343 TYR cc_start: 0.8204 (p90) cc_final: 0.7910 (p90) REVERT: C 150 LYS cc_start: 0.8387 (mttt) cc_final: 0.7886 (mmtm) REVERT: C 166 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7894 (m) REVERT: D 131 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6616 (mm-40) REVERT: D 135 PHE cc_start: 0.7436 (t80) cc_final: 0.7161 (t80) REVERT: D 153 GLN cc_start: 0.5482 (tt0) cc_final: 0.5126 (pt0) REVERT: D 159 LYS cc_start: 0.6319 (tptt) cc_final: 0.5851 (tttp) REVERT: D 194 TYR cc_start: 0.7058 (m-80) cc_final: 0.6580 (m-80) REVERT: E 153 GLN cc_start: 0.7626 (mp10) cc_final: 0.7403 (mp10) REVERT: E 194 TYR cc_start: 0.7512 (m-80) cc_final: 0.7275 (m-80) REVERT: E 245 GLN cc_start: 0.5773 (mt0) cc_final: 0.4991 (pp30) REVERT: E 251 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.5259 (mt) REVERT: F 255 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6759 (mm) REVERT: F 300 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7433 (mt) REVERT: F 308 LYS cc_start: 0.7231 (mttt) cc_final: 0.6575 (ptmm) REVERT: F 330 PHE cc_start: 0.7126 (m-80) cc_final: 0.6839 (m-80) outliers start: 50 outliers final: 42 residues processed: 222 average time/residue: 0.1349 time to fit residues: 45.9964 Evaluate side-chains 226 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 117 optimal weight: 20.0000 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154737 restraints weight = 19029.436| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.92 r_work: 0.3219 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17555 Z= 0.091 Angle : 0.488 7.432 24108 Z= 0.240 Chirality : 0.046 0.185 2824 Planarity : 0.003 0.046 2873 Dihedral : 7.937 62.816 2857 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 13.74 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1990 helix: 1.27 (0.25), residues: 499 sheet: 0.60 (0.28), residues: 348 loop : -0.69 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.015 0.001 TYR E 180 PHE 0.013 0.001 PHE F 303 TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (17555) covalent geometry : angle 0.48848 / 0.24 (24108) hydrogen bonds : bond 0.02802 / 1.83 ( 655) hydrogen bonds : angle 4.47241 / 3.22 ( 1829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8350 (mt-10) REVERT: A 110 LYS cc_start: 0.9116 (mttt) cc_final: 0.8603 (mmtm) REVERT: A 139 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7395 (mtp180) REVERT: B 105 MET cc_start: 0.8406 (mmm) cc_final: 0.7393 (mpp) REVERT: B 168 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 209 GLN cc_start: 0.7992 (tp40) cc_final: 0.7014 (tm-30) REVERT: B 213 ASP cc_start: 0.7920 (m-30) cc_final: 0.6959 (m-30) REVERT: B 331 MET cc_start: 0.6801 (mmm) cc_final: 0.6558 (mmm) REVERT: B 343 TYR cc_start: 0.8146 (p90) cc_final: 0.7898 (p90) REVERT: C 150 LYS cc_start: 0.8403 (mttt) cc_final: 0.7857 (mmtm) REVERT: C 166 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7839 (m) REVERT: D 131 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6575 (mm-40) REVERT: D 135 PHE cc_start: 0.7338 (t80) cc_final: 0.7104 (t80) REVERT: D 159 LYS cc_start: 0.6264 (tptt) cc_final: 0.5938 (tttp) REVERT: D 194 TYR cc_start: 0.6994 (m-80) cc_final: 0.6493 (m-80) REVERT: E 153 GLN cc_start: 0.7748 (mp10) cc_final: 0.7466 (mp10) REVERT: E 194 TYR cc_start: 0.7506 (m-80) cc_final: 0.7290 (m-80) REVERT: E 245 GLN cc_start: 0.5835 (mt0) cc_final: 0.5032 (pp30) REVERT: E 251 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5134 (mt) REVERT: E 265 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6276 (tt0) REVERT: F 219 MET cc_start: 0.6809 (mtt) cc_final: 0.6386 (mmm) REVERT: F 255 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6731 (mm) REVERT: F 272 MET cc_start: 0.7888 (ttp) cc_final: 0.7578 (ttt) REVERT: F 300 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7309 (mt) REVERT: F 308 LYS cc_start: 0.7173 (mttt) cc_final: 0.6515 (ptmm) REVERT: F 330 PHE cc_start: 0.7104 (m-80) cc_final: 0.6811 (m-80) outliers start: 48 outliers final: 34 residues processed: 230 average time/residue: 0.1296 time to fit residues: 46.0861 Evaluate side-chains 219 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.199612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143799 restraints weight = 19233.851| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.51 r_work: 0.3056 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17555 Z= 0.227 Angle : 0.578 7.805 24108 Z= 0.288 Chirality : 0.049 0.193 2824 Planarity : 0.004 0.044 2873 Dihedral : 8.193 63.089 2857 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.77 % Allowed : 13.51 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1990 helix: 0.97 (0.24), residues: 499 sheet: 0.46 (0.28), residues: 348 loop : -0.79 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 127 TYR 0.015 0.001 TYR E 180 PHE 0.014 0.002 PHE A 269 TRP 0.012 0.002 TRP C 87 HIS 0.005 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (17555) covalent geometry : angle 0.57816 / 0.29 (24108) hydrogen bonds : bond 0.03661 / 2.45 ( 655) hydrogen bonds : angle 4.85408 / 3.48 ( 1829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.604 Fit side-chains REVERT: A 110 LYS cc_start: 0.9085 (mttt) cc_final: 0.8500 (mmtm) REVERT: A 139 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7621 (mtp180) REVERT: B 105 MET cc_start: 0.8533 (mmm) cc_final: 0.7295 (mpp) REVERT: B 125 ASP cc_start: 0.8796 (t0) cc_final: 0.8583 (t70) REVERT: B 168 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 209 GLN cc_start: 0.7962 (tp40) cc_final: 0.7002 (tm-30) REVERT: B 213 ASP cc_start: 0.7861 (m-30) cc_final: 0.6885 (m-30) REVERT: B 331 MET cc_start: 0.6896 (mmm) cc_final: 0.6641 (mmm) REVERT: B 343 TYR cc_start: 0.8171 (p90) cc_final: 0.7863 (p90) REVERT: C 150 LYS cc_start: 0.8347 (mttt) cc_final: 0.7844 (mmtm) REVERT: C 166 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (m) REVERT: C 299 LEU cc_start: 0.8321 (tp) cc_final: 0.8089 (tp) REVERT: D 131 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6442 (mm-40) REVERT: D 153 GLN cc_start: 0.5498 (tt0) cc_final: 0.5122 (pt0) REVERT: D 194 TYR cc_start: 0.7059 (m-80) cc_final: 0.6532 (m-80) REVERT: D 285 GLN cc_start: 0.6011 (tt0) cc_final: 0.5400 (mp10) REVERT: E 153 GLN cc_start: 0.7771 (mp10) cc_final: 0.7516 (mp10) REVERT: E 245 GLN cc_start: 0.5724 (mt0) cc_final: 0.4924 (pp30) REVERT: E 251 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5690 (mt) REVERT: F 22 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: F 219 MET cc_start: 0.6795 (mtt) cc_final: 0.6389 (mmm) REVERT: F 255 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6789 (mm) REVERT: F 272 MET cc_start: 0.7953 (ttp) cc_final: 0.7587 (ttt) REVERT: F 300 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7437 (mt) REVERT: F 305 GLU cc_start: 0.8270 (tt0) cc_final: 0.7877 (pp20) REVERT: F 308 LYS cc_start: 0.7325 (mttt) cc_final: 0.6574 (ptmm) REVERT: F 330 PHE cc_start: 0.7270 (m-80) cc_final: 0.6929 (m-80) outliers start: 49 outliers final: 40 residues processed: 216 average time/residue: 0.1340 time to fit residues: 44.3862 Evaluate side-chains 221 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 67 optimal weight: 10.0000 chunk 74 optimal weight: 0.0770 chunk 168 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 92 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.208922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156081 restraints weight = 19108.173| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.76 r_work: 0.3225 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17555 Z= 0.084 Angle : 0.506 10.890 24108 Z= 0.249 Chirality : 0.046 0.179 2824 Planarity : 0.003 0.046 2873 Dihedral : 7.988 63.122 2857 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 14.19 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1990 helix: 1.22 (0.24), residues: 499 sheet: 0.77 (0.28), residues: 338 loop : -0.75 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.016 0.001 TYR E 180 PHE 0.030 0.001 PHE F 214 TRP 0.009 0.001 TRP A 87 HIS 0.002 0.000 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.08 (17555) covalent geometry : angle 0.50569 / 0.25 (24108) hydrogen bonds : bond 0.02798 / 1.83 ( 655) hydrogen bonds : angle 4.47311 / 3.22 ( 1829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9102 (mttt) cc_final: 0.8601 (mmtm) REVERT: A 139 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7605 (mtp180) REVERT: B 105 MET cc_start: 0.8466 (mmm) cc_final: 0.7481 (mpp) REVERT: B 203 GLU cc_start: 0.7543 (mp0) cc_final: 0.7022 (pm20) REVERT: B 209 GLN cc_start: 0.8004 (tp40) cc_final: 0.7048 (tm-30) REVERT: B 213 ASP cc_start: 0.8028 (m-30) cc_final: 0.7152 (m-30) REVERT: B 331 MET cc_start: 0.7009 (mmm) cc_final: 0.6782 (mmm) REVERT: B 342 PHE cc_start: 0.8698 (t80) cc_final: 0.8489 (t80) REVERT: B 343 TYR cc_start: 0.8231 (p90) cc_final: 0.8019 (p90) REVERT: C 150 LYS cc_start: 0.8253 (mttt) cc_final: 0.7795 (mmtm) REVERT: C 166 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7878 (m) REVERT: C 299 LEU cc_start: 0.8425 (tp) cc_final: 0.8091 (tp) REVERT: D 131 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6720 (mm-40) REVERT: D 135 PHE cc_start: 0.7440 (t80) cc_final: 0.7142 (t80) REVERT: D 159 LYS cc_start: 0.6172 (tptt) cc_final: 0.5211 (tttp) REVERT: D 194 TYR cc_start: 0.6968 (m-80) cc_final: 0.6465 (m-80) REVERT: D 285 GLN cc_start: 0.5898 (tt0) cc_final: 0.5359 (mp10) REVERT: E 107 ASP cc_start: 0.7982 (m-30) cc_final: 0.7751 (m-30) REVERT: E 153 GLN cc_start: 0.7714 (mp10) cc_final: 0.7371 (mp10) REVERT: E 200 ASN cc_start: 0.6925 (t0) cc_final: 0.6602 (t0) REVERT: E 245 GLN cc_start: 0.5708 (mt0) cc_final: 0.4968 (pp30) REVERT: E 251 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5128 (mt) REVERT: E 265 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6274 (tt0) REVERT: F 22 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: F 164 ASN cc_start: 0.7537 (t0) cc_final: 0.7295 (m-40) REVERT: F 219 MET cc_start: 0.6863 (mtt) cc_final: 0.6477 (mmm) REVERT: F 255 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6809 (mm) REVERT: F 272 MET cc_start: 0.7882 (ttp) cc_final: 0.7608 (ttt) REVERT: F 300 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7350 (mt) REVERT: F 308 LYS cc_start: 0.7277 (mttt) cc_final: 0.6463 (ptmm) REVERT: F 330 PHE cc_start: 0.7210 (m-80) cc_final: 0.6903 (m-80) outliers start: 38 outliers final: 30 residues processed: 218 average time/residue: 0.1360 time to fit residues: 45.4885 Evaluate side-chains 209 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 184 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 110 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.211324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157957 restraints weight = 19258.740| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.97 r_work: 0.3290 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17555 Z= 0.081 Angle : 0.498 9.759 24108 Z= 0.243 Chirality : 0.046 0.178 2824 Planarity : 0.003 0.046 2873 Dihedral : 7.866 64.388 2857 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 14.41 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1990 helix: 1.36 (0.24), residues: 504 sheet: 0.89 (0.29), residues: 321 loop : -0.64 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.015 0.001 TYR E 180 PHE 0.024 0.001 PHE F 259 TRP 0.010 0.001 TRP F 333 HIS 0.002 0.000 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (17555) covalent geometry : angle 0.49825 / 0.24 (24108) hydrogen bonds : bond 0.02611 / 1.71 ( 655) hydrogen bonds : angle 4.33897 / 3.14 ( 1829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4729.62 seconds wall clock time: 81 minutes 49.49 seconds (4909.49 seconds total)