Starting phenix.real_space_refine on Sat Jul 4 00:32:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj2_25915/07_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_25915/07_2026/7tj2_25915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj2_25915/07_2026/7tj2_25915.cif" } 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-dev-6108/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: {'RNA': 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: {'RNA': 31} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna3p': 30} Time building chain proxies: 3.19, per 1000 atoms: 0.19 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: 1.45 Conformation dependent library (CDL) restraints added in 616.9 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: 2.09 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: 2.42 Time building geometry restraints manager: 1.92 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: 23723 1.12 - 2.24: 271 2.24 - 3.35: 104 3.35 - 4.47: 9 4.47 - 5.59: 1 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=" 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=" C2' G G 8 " pdb=" C1' G G 8 " pdb=" N9 G G 8 " ideal model delta sigma weight residual 112.00 114.13 -2.13 1.50e+00 4.44e-01 2.02e+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 - 18.04: 10075 18.04 - 36.09: 243 36.09 - 54.13: 32 54.13 - 72.18: 14 72.18 - 90.22: 3 Dihedral angle restraints: 10367 sinusoidal: 4560 harmonic: 5807 Sorted by residual: dihedral pdb=" CA CYS F 334 " pdb=" C CYS F 334 " pdb=" N LYS F 335 " pdb=" CA LYS F 335 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" O5' U H 31 " pdb=" C5' U H 31 " pdb=" C4' U H 31 " pdb=" C3' U H 31 " ideal model delta sinusoidal sigma weight residual 55.00 113.85 -58.85 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN B 310 " pdb=" CA GLN B 310 " pdb=" CB GLN B 310 " pdb=" CG GLN B 310 " ideal model delta sinusoidal sigma weight residual 180.00 -121.71 -58.29 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1703 0.026 - 0.052: 629 0.052 - 0.078: 254 0.078 - 0.103: 124 0.103 - 0.129: 114 Chirality restraints: 2824 Sorted by residual: chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE F 80 " pdb=" N ILE F 80 " pdb=" C ILE F 80 " pdb=" CB ILE F 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE E 80 " pdb=" N ILE E 80 " pdb=" C ILE E 80 " pdb=" CB ILE E 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.220 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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= 0.075 Angle : 0.370 5.591 24108 Z= 0.191 Chirality : 0.041 0.129 2824 Planarity : 0.003 0.027 2873 Dihedral : 8.616 90.221 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 0.00171 / 0.07 (17555) covalent geometry : angle 0.37004 / 0.19 (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 : 0.570 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: 0.1232 time to fit residues: 75.4586 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 : 0.655 ------------------------------------------------------------------------------- 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: 40.0000 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 = 0.4294 r_free = 0.4294 target = 0.203469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131355 restraints weight = 19180.203| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.19 r_work: 0.3244 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17555 Z= 0.213 Angle : 0.554 9.676 24108 Z= 0.293 Chirality : 0.046 0.369 2824 Planarity : 0.004 0.068 2873 Dihedral : 7.148 91.999 2868 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.11 % Allowed : 8.82 % Favored : 88.07 % 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: 0.00 (0.19), residues: 1990 helix: 0.78 (0.24), residues: 509 sheet: 0.53 (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 0.012 0.002 TRP C 87 HIS 0.004 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (17555) covalent geometry : angle 0.55412 / 0.29 (24108) hydrogen bonds : bond 0.04309 / 2.85 ( 655) hydrogen bonds : angle 5.66990 / 4.07 ( 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 272 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.634 Fit side-chains REVERT: A 47 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8294 (mmtm) REVERT: A 110 LYS cc_start: 0.9085 (mttt) cc_final: 0.8505 (mmtm) REVERT: A 265 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 297 ASP cc_start: 0.8824 (t0) cc_final: 0.8607 (t0) REVERT: B 105 MET cc_start: 0.8516 (mmm) cc_final: 0.7381 (mpp) REVERT: B 209 GLN cc_start: 0.7843 (tp40) cc_final: 0.7440 (pp30) REVERT: B 213 ASP cc_start: 0.7973 (m-30) cc_final: 0.7593 (m-30) REVERT: B 331 MET cc_start: 0.6891 (mmm) cc_final: 0.6310 (mmm) REVERT: B 343 TYR cc_start: 0.8172 (p90) cc_final: 0.7654 (p90) REVERT: C 75 ASN cc_start: 0.8818 (m-40) cc_final: 0.8609 (m-40) REVERT: C 150 LYS cc_start: 0.8385 (mttt) cc_final: 0.7875 (mmtm) REVERT: C 166 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7887 (m) REVERT: D 105 MET cc_start: 0.7432 (mmm) cc_final: 0.6927 (mpt) REVERT: D 194 TYR cc_start: 0.7182 (m-80) cc_final: 0.6672 (m-80) REVERT: D 297 ASP cc_start: 0.6622 (t0) cc_final: 0.6400 (t70) REVERT: E 245 GLN cc_start: 0.5738 (mt0) cc_final: 0.4907 (pp30) REVERT: F 154 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8266 (Cg_exo) REVERT: F 194 TYR cc_start: 0.8349 (m-80) cc_final: 0.8097 (m-80) REVERT: F 195 PHE cc_start: 0.8048 (m-80) cc_final: 0.7843 (m-10) REVERT: F 273 ASP cc_start: 0.7846 (t70) cc_final: 0.7600 (t70) REVERT: F 300 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7371 (mp) REVERT: F 305 GLU cc_start: 0.7849 (tt0) cc_final: 0.7372 (mt-10) REVERT: F 308 LYS cc_start: 0.7131 (mttt) cc_final: 0.6754 (ptmm) REVERT: F 330 PHE cc_start: 0.7213 (m-80) cc_final: 0.7002 (m-80) outliers start: 55 outliers final: 32 residues processed: 256 average time/residue: 0.1280 time to fit residues: 50.0368 Evaluate side-chains 218 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 28 ILE 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 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 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 115 THR 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 281 ILE 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: 20.0000 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 189 GLN C 19 GLN C 176 GLN D 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131064 restraints weight = 19209.044| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3312 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2484 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= 0.112 Angle : 0.460 8.575 24108 Z= 0.245 Chirality : 0.043 0.251 2824 Planarity : 0.003 0.040 2873 Dihedral : 6.846 96.002 2860 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.26 % Allowed : 10.46 % Favored : 87.28 % 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: 0.05 (0.19), residues: 1990 helix: 0.94 (0.24), residues: 509 sheet: 0.58 (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 225 TYR 0.015 0.001 TYR E 180 PHE 0.012 0.001 PHE E 280 TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (17555) covalent geometry : angle 0.46003 / 0.24 (24108) hydrogen bonds : bond 0.03439 / 2.27 ( 655) hydrogen bonds : angle 5.07887 / 3.65 ( 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 245 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.503 Fit side-chains REVERT: A 47 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8324 (mmtp) REVERT: A 110 LYS cc_start: 0.9109 (mttt) cc_final: 0.8556 (mmtm) REVERT: A 139 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7553 (mtp180) REVERT: A 297 ASP cc_start: 0.8690 (t0) cc_final: 0.8489 (t0) REVERT: B 47 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8600 (mmtp) REVERT: B 105 MET cc_start: 0.8495 (mmm) cc_final: 0.7433 (mpp) REVERT: B 209 GLN cc_start: 0.7839 (tp40) cc_final: 0.7411 (pp30) REVERT: B 213 ASP cc_start: 0.8049 (m-30) cc_final: 0.7659 (m-30) REVERT: B 331 MET cc_start: 0.6871 (mmm) cc_final: 0.6466 (mmm) REVERT: B 343 TYR cc_start: 0.8190 (p90) cc_final: 0.7779 (p90) REVERT: C 150 LYS cc_start: 0.8402 (mttt) cc_final: 0.7957 (mmtm) REVERT: C 166 VAL cc_start: 0.8230 (p) cc_final: 0.7906 (m) REVERT: D 105 MET cc_start: 0.7317 (mmm) cc_final: 0.6990 (mpp) REVERT: D 194 TYR cc_start: 0.7206 (m-80) cc_final: 0.6721 (m-80) REVERT: E 245 GLN cc_start: 0.5773 (mt0) cc_final: 0.4983 (pp30) REVERT: E 251 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5325 (mt) REVERT: F 194 TYR cc_start: 0.8339 (m-80) cc_final: 0.8129 (m-80) REVERT: F 299 LEU cc_start: 0.7285 (tt) cc_final: 0.7083 (tt) REVERT: F 300 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7535 (mt) REVERT: F 305 GLU cc_start: 0.8054 (tt0) cc_final: 0.7523 (mt-10) REVERT: F 308 LYS cc_start: 0.7200 (mttt) cc_final: 0.6748 (ptmm) REVERT: F 330 PHE cc_start: 0.7217 (m-80) cc_final: 0.6975 (m-80) outliers start: 40 outliers final: 24 residues processed: 235 average time/residue: 0.1256 time to fit residues: 44.6322 Evaluate side-chains 212 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 156 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 125 ASP Chi-restraints excluded: chain C residue 156 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 97 ILE Chi-restraints excluded: chain E residue 28 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 199 ARG 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: 6.9990 chunk 74 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150680 restraints weight = 19222.722| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 4.03 r_work: 0.3140 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17555 Z= 0.144 Angle : 0.471 7.537 24108 Z= 0.251 Chirality : 0.044 0.194 2824 Planarity : 0.004 0.041 2873 Dihedral : 6.903 95.687 2857 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.39 % Allowed : 10.46 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.05 (0.24), residues: 499 sheet: 0.49 (0.28), residues: 348 loop : -0.68 (0.18), 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 0.011 0.001 PHE A 269 TRP 0.011 0.001 TRP F 333 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (17555) covalent geometry : angle 0.47121 / 0.25 (24108) hydrogen bonds : bond 0.03360 / 2.23 ( 655) hydrogen bonds : angle 4.93283 / 3.54 ( 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 258 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.636 Fit side-chains REVERT: A 110 LYS cc_start: 0.9108 (mttt) cc_final: 0.8549 (mmtm) REVERT: A 139 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7490 (mtp180) REVERT: A 265 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: A 297 ASP cc_start: 0.8711 (t0) cc_final: 0.8458 (t0) REVERT: B 105 MET cc_start: 0.8522 (mmm) cc_final: 0.7324 (mpp) REVERT: B 125 ASP cc_start: 0.8676 (t0) cc_final: 0.8361 (t70) REVERT: B 174 LYS cc_start: 0.8134 (tttp) cc_final: 0.7925 (tttp) REVERT: B 209 GLN cc_start: 0.7893 (tp40) cc_final: 0.6910 (tm-30) REVERT: B 213 ASP cc_start: 0.7961 (m-30) cc_final: 0.7023 (m-30) REVERT: B 331 MET cc_start: 0.6846 (mmm) cc_final: 0.6462 (mmm) REVERT: B 343 TYR cc_start: 0.8195 (p90) cc_final: 0.7826 (p90) REVERT: C 150 LYS cc_start: 0.8420 (mttt) cc_final: 0.7954 (mmtm) REVERT: C 166 VAL cc_start: 0.8239 (p) cc_final: 0.7928 (m) REVERT: D 105 MET cc_start: 0.7308 (mmm) cc_final: 0.7069 (mpp) REVERT: D 194 TYR cc_start: 0.7003 (m-80) cc_final: 0.6500 (m-80) REVERT: D 272 MET cc_start: 0.7206 (ttp) cc_final: 0.6797 (ttt) REVERT: E 245 GLN cc_start: 0.5623 (mt0) cc_final: 0.4880 (pp30) REVERT: E 251 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5285 (mt) REVERT: F 194 TYR cc_start: 0.8216 (m-80) cc_final: 0.7923 (m-80) REVERT: F 255 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6870 (mm) REVERT: F 300 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7412 (mt) REVERT: F 306 ILE cc_start: 0.7557 (mt) cc_final: 0.7339 (pt) REVERT: F 308 LYS cc_start: 0.7196 (mttt) cc_final: 0.6703 (ptmm) REVERT: F 330 PHE cc_start: 0.7182 (m-80) cc_final: 0.6871 (m-80) outliers start: 60 outliers final: 38 residues processed: 240 average time/residue: 0.1218 time to fit residues: 44.4106 Evaluate side-chains 223 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP 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 40 ASP 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 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 252 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 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 146 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 171 optimal weight: 0.0070 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN C 338 HIS E 176 GLN F 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.207218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154760 restraints weight = 19144.854| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 4.06 r_work: 0.3210 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17555 Z= 0.091 Angle : 0.440 9.020 24108 Z= 0.232 Chirality : 0.042 0.174 2824 Planarity : 0.003 0.043 2873 Dihedral : 6.756 97.922 2857 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 12.32 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.19), residues: 1990 helix: 1.26 (0.24), residues: 499 sheet: 0.54 (0.28), residues: 348 loop : -0.68 (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 0.012 0.001 PHE F 241 TRP 0.009 0.001 TRP F 333 HIS 0.004 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (17555) covalent geometry : angle 0.44048 / 0.23 (24108) hydrogen bonds : bond 0.02862 / 1.87 ( 655) hydrogen bonds : angle 4.62246 / 3.33 ( 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 261 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.656 Fit side-chains REVERT: A 110 LYS cc_start: 0.9114 (mttt) cc_final: 0.8591 (mmtm) REVERT: A 139 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7491 (mtp180) REVERT: A 265 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: A 297 ASP cc_start: 0.8602 (t0) cc_final: 0.8361 (t0) REVERT: B 47 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8573 (mmtp) REVERT: B 105 MET cc_start: 0.8413 (mmm) cc_final: 0.7361 (mpp) REVERT: B 173 VAL cc_start: 0.8431 (m) cc_final: 0.8138 (p) REVERT: B 209 GLN cc_start: 0.7906 (tp40) cc_final: 0.6911 (tm-30) REVERT: B 213 ASP cc_start: 0.7966 (m-30) cc_final: 0.7021 (m-30) REVERT: B 331 MET cc_start: 0.6798 (mmm) cc_final: 0.6335 (mmm) REVERT: B 343 TYR cc_start: 0.8176 (p90) cc_final: 0.7866 (p90) REVERT: C 40 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: C 150 LYS cc_start: 0.8410 (mttt) cc_final: 0.7942 (mmtm) REVERT: C 166 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7903 (m) REVERT: D 131 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6585 (mm-40) REVERT: D 153 GLN cc_start: 0.5625 (tt0) cc_final: 0.5329 (pt0) REVERT: D 194 TYR cc_start: 0.7004 (m-80) cc_final: 0.6515 (m-80) REVERT: D 272 MET cc_start: 0.7077 (ttp) cc_final: 0.6711 (ttt) REVERT: E 245 GLN cc_start: 0.5803 (mt0) cc_final: 0.5009 (pp30) REVERT: E 251 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.5073 (mt) REVERT: F 164 ASN cc_start: 0.7521 (t0) cc_final: 0.7267 (m-40) REVERT: F 214 PHE cc_start: 0.7411 (t80) cc_final: 0.7155 (t80) REVERT: F 300 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7372 (mt) REVERT: F 306 ILE cc_start: 0.7500 (mt) cc_final: 0.7290 (pt) REVERT: F 308 LYS cc_start: 0.7176 (mttt) cc_final: 0.6666 (ptmm) REVERT: F 330 PHE cc_start: 0.7147 (m-80) cc_final: 0.6800 (m-80) outliers start: 47 outliers final: 31 residues processed: 248 average time/residue: 0.1223 time to fit residues: 46.4661 Evaluate side-chains 222 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 265 GLU 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 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 291 CYS 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 40 ASP 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 49 THR Chi-restraints excluded: chain E residue 72 ILE 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 252 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 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: 7.9990 chunk 188 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 199 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 ASN D 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150443 restraints weight = 19000.483| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.13 r_work: 0.3121 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17555 Z= 0.183 Angle : 0.499 8.214 24108 Z= 0.261 Chirality : 0.044 0.169 2824 Planarity : 0.004 0.044 2873 Dihedral : 6.960 96.358 2857 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.17 % Allowed : 12.89 % Favored : 83.95 % 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: 1.13 (0.24), residues: 499 sheet: 0.48 (0.28), residues: 348 loop : -0.74 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 127 TYR 0.014 0.001 TYR E 180 PHE 0.015 0.001 PHE B 303 TRP 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (17555) covalent geometry : angle 0.49914 / 0.26 (24108) hydrogen bonds : bond 0.03422 / 2.26 ( 655) hydrogen bonds : angle 4.84252 / 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 245 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.625 Fit side-chains REVERT: A 110 LYS cc_start: 0.9142 (mttt) cc_final: 0.8604 (mmtm) REVERT: A 139 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7497 (mtp180) REVERT: A 265 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7818 (tp30) REVERT: A 297 ASP cc_start: 0.8738 (t0) cc_final: 0.8467 (t0) REVERT: B 105 MET cc_start: 0.8541 (mmm) cc_final: 0.7512 (mpp) REVERT: B 173 VAL cc_start: 0.8531 (m) cc_final: 0.8284 (p) REVERT: B 209 GLN cc_start: 0.7971 (tp40) cc_final: 0.7019 (tm-30) REVERT: B 213 ASP cc_start: 0.7932 (m-30) cc_final: 0.6993 (m-30) REVERT: B 331 MET cc_start: 0.6919 (mmm) cc_final: 0.6581 (mmm) REVERT: B 343 TYR cc_start: 0.8226 (p90) cc_final: 0.7880 (p90) REVERT: C 150 LYS cc_start: 0.8392 (mttt) cc_final: 0.7921 (mmtm) REVERT: C 166 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7963 (m) REVERT: C 219 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5755 (tmm) REVERT: C 249 LEU cc_start: 0.7458 (tp) cc_final: 0.7214 (tt) REVERT: D 131 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6573 (mm-40) REVERT: D 153 GLN cc_start: 0.5553 (tt0) cc_final: 0.5134 (pt0) REVERT: D 194 TYR cc_start: 0.7002 (m-80) cc_final: 0.6488 (m-80) REVERT: E 153 GLN cc_start: 0.7700 (mp10) cc_final: 0.7459 (mp10) REVERT: E 245 GLN cc_start: 0.5778 (mt0) cc_final: 0.4982 (pp30) REVERT: E 251 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5226 (mt) REVERT: F 214 PHE cc_start: 0.7419 (t80) cc_final: 0.7206 (t80) REVERT: F 255 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6760 (mm) REVERT: F 300 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7413 (mt) REVERT: F 308 LYS cc_start: 0.7201 (mttt) cc_final: 0.6654 (ptmm) REVERT: F 330 PHE cc_start: 0.7269 (m-80) cc_final: 0.6972 (m-80) outliers start: 56 outliers final: 44 residues processed: 229 average time/residue: 0.1309 time to fit residues: 45.8071 Evaluate side-chains 231 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 99 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 291 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 40 ASP 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 17 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 188 GLN 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 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: 7.9990 chunk 201 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 184 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 188 GLN F 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.206222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154480 restraints weight = 19036.092| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.98 r_work: 0.3194 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3254 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= 0.089 Angle : 0.446 7.773 24108 Z= 0.234 Chirality : 0.042 0.157 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.822 98.090 2857 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.94 % Allowed : 13.40 % 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: 0.01 (0.19), residues: 1990 helix: 1.25 (0.24), residues: 499 sheet: 0.56 (0.28), residues: 348 loop : -0.73 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.016 0.001 TYR E 180 PHE 0.016 0.001 PHE B 342 TRP 0.009 0.001 TRP F 333 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (17555) covalent geometry : angle 0.44616 / 0.23 (24108) hydrogen bonds : bond 0.02851 / 1.87 ( 655) hydrogen bonds : angle 4.54167 / 3.27 ( 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 255 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.645 Fit side-chains REVERT: A 110 LYS cc_start: 0.9129 (mttt) cc_final: 0.8598 (mmtm) REVERT: A 139 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7464 (mtp180) REVERT: A 297 ASP cc_start: 0.8626 (t0) cc_final: 0.8382 (t0) REVERT: B 105 MET cc_start: 0.8459 (mmm) cc_final: 0.7424 (mpp) REVERT: B 125 ASP cc_start: 0.8573 (t0) cc_final: 0.8298 (t70) REVERT: B 173 VAL cc_start: 0.8497 (m) cc_final: 0.8267 (p) REVERT: B 209 GLN cc_start: 0.7956 (tp40) cc_final: 0.6973 (tm-30) REVERT: B 213 ASP cc_start: 0.7929 (m-30) cc_final: 0.6984 (m-30) REVERT: B 331 MET cc_start: 0.6784 (mmm) cc_final: 0.6525 (mmm) REVERT: B 343 TYR cc_start: 0.8155 (p90) cc_final: 0.7893 (p90) REVERT: C 150 LYS cc_start: 0.8391 (mttt) cc_final: 0.7888 (mmtm) REVERT: C 166 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7884 (m) REVERT: C 219 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5762 (tmm) REVERT: D 131 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6588 (mm-40) REVERT: D 153 GLN cc_start: 0.5537 (tt0) cc_final: 0.5181 (pt0) REVERT: D 194 TYR cc_start: 0.6980 (m-80) cc_final: 0.6488 (m-80) REVERT: E 194 TYR cc_start: 0.7470 (m-80) cc_final: 0.7264 (m-80) REVERT: E 245 GLN cc_start: 0.5783 (mt0) cc_final: 0.5023 (pp30) REVERT: F 22 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: F 164 ASN cc_start: 0.7525 (t0) cc_final: 0.7280 (m-40) REVERT: F 219 MET cc_start: 0.6838 (mtt) cc_final: 0.6449 (mmm) REVERT: F 255 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6741 (mm) REVERT: F 300 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7311 (mt) REVERT: F 305 GLU cc_start: 0.8243 (tt0) cc_final: 0.7632 (mt-10) REVERT: F 308 LYS cc_start: 0.7197 (mttt) cc_final: 0.6640 (ptmm) REVERT: F 330 PHE cc_start: 0.7141 (m-80) cc_final: 0.6862 (m-80) outliers start: 52 outliers final: 38 residues processed: 240 average time/residue: 0.1347 time to fit residues: 49.3607 Evaluate side-chains 229 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 99 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 291 CYS 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 49 THR Chi-restraints excluded: chain D residue 188 GLN 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 276 VAL 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 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: 0.8980 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 0.0010 chunk 136 optimal weight: 0.0060 chunk 25 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.8604 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.206205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153214 restraints weight = 19050.743| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.85 r_work: 0.3211 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17555 Z= 0.099 Angle : 0.457 9.566 24108 Z= 0.238 Chirality : 0.042 0.158 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.841 97.672 2857 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.60 % Allowed : 13.91 % Favored : 83.49 % 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: 1.35 (0.25), residues: 499 sheet: 0.58 (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 B 342 TRP 0.009 0.001 TRP C 87 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (17555) covalent geometry : angle 0.45705 / 0.24 (24108) hydrogen bonds : bond 0.02853 / 1.88 ( 655) hydrogen bonds : angle 4.53046 / 3.26 ( 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 239 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9107 (mttt) cc_final: 0.8596 (mmtm) REVERT: A 139 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7397 (mtp180) REVERT: A 297 ASP cc_start: 0.8605 (t0) cc_final: 0.8362 (t0) REVERT: B 105 MET cc_start: 0.8428 (mmm) cc_final: 0.7425 (mpp) REVERT: B 125 ASP cc_start: 0.8544 (t0) cc_final: 0.8272 (t70) REVERT: B 168 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 209 GLN cc_start: 0.8007 (tp40) cc_final: 0.7019 (tm-30) REVERT: B 213 ASP cc_start: 0.7896 (m-30) cc_final: 0.6888 (m-30) REVERT: B 331 MET cc_start: 0.6801 (mmm) cc_final: 0.6439 (mmm) REVERT: B 343 TYR cc_start: 0.8068 (p90) cc_final: 0.7829 (p90) REVERT: C 150 LYS cc_start: 0.8414 (mttt) cc_final: 0.7899 (mmtm) REVERT: C 166 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7904 (m) REVERT: C 219 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5790 (tmm) REVERT: D 131 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6583 (mm-40) REVERT: D 194 TYR cc_start: 0.6986 (m-80) cc_final: 0.6543 (m-80) REVERT: E 245 GLN cc_start: 0.5792 (mt0) cc_final: 0.5034 (pp30) REVERT: F 22 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: F 164 ASN cc_start: 0.7485 (t0) cc_final: 0.7252 (m-40) REVERT: F 219 MET cc_start: 0.6769 (mtt) cc_final: 0.6407 (pmm) REVERT: F 255 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6804 (mm) REVERT: F 300 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7340 (mt) REVERT: F 308 LYS cc_start: 0.7242 (mttt) cc_final: 0.6624 (ptmm) REVERT: F 330 PHE cc_start: 0.7109 (m-80) cc_final: 0.6861 (m-80) outliers start: 46 outliers final: 37 residues processed: 228 average time/residue: 0.1346 time to fit residues: 47.0589 Evaluate side-chains 226 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 99 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 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 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 252 LEU Chi-restraints excluded: chain E residue 276 VAL 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 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: 0.9980 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 23 optimal weight: 0.0870 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.202339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148971 restraints weight = 19208.666| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.48 r_work: 0.3107 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17555 Z= 0.104 Angle : 0.457 8.483 24108 Z= 0.238 Chirality : 0.042 0.156 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.886 97.905 2857 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.49 % Allowed : 13.96 % 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: 0.08 (0.19), residues: 1990 helix: 1.31 (0.24), residues: 499 sheet: 0.65 (0.28), residues: 348 loop : -0.71 (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 0.022 0.001 PHE F 259 TRP 0.010 0.001 TRP F 333 HIS 0.003 0.000 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (17555) covalent geometry : angle 0.45728 / 0.24 (24108) hydrogen bonds : bond 0.02859 / 1.89 ( 655) hydrogen bonds : angle 4.49895 / 3.24 ( 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 239 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9137 (mttt) cc_final: 0.8546 (mmtm) REVERT: A 139 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7409 (mtp180) REVERT: A 297 ASP cc_start: 0.8707 (t0) cc_final: 0.8381 (t0) REVERT: B 105 MET cc_start: 0.8384 (mmm) cc_final: 0.7222 (mpp) REVERT: B 125 ASP cc_start: 0.8468 (t0) cc_final: 0.8139 (t70) REVERT: B 168 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8026 (pp) REVERT: B 209 GLN cc_start: 0.8004 (tp40) cc_final: 0.7034 (tm-30) REVERT: B 213 ASP cc_start: 0.7763 (m-30) cc_final: 0.6819 (m-30) REVERT: B 340 GLU cc_start: 0.6735 (tm-30) cc_final: 0.5823 (mt-10) REVERT: C 150 LYS cc_start: 0.8394 (mttt) cc_final: 0.7773 (mmtm) REVERT: C 166 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7756 (m) REVERT: C 219 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5780 (tmm) REVERT: D 131 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6338 (mm-40) REVERT: D 194 TYR cc_start: 0.7264 (m-80) cc_final: 0.6609 (m-80) REVERT: D 195 PHE cc_start: 0.7107 (m-80) cc_final: 0.6229 (m-10) REVERT: D 272 MET cc_start: 0.7139 (ttp) cc_final: 0.6716 (ttm) REVERT: D 285 GLN cc_start: 0.5853 (tt0) cc_final: 0.5347 (mp10) REVERT: E 153 GLN cc_start: 0.7763 (mp10) cc_final: 0.7467 (mp10) REVERT: E 245 GLN cc_start: 0.5763 (mt0) cc_final: 0.4996 (pp30) REVERT: F 22 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: F 164 ASN cc_start: 0.7247 (t0) cc_final: 0.7013 (m-40) REVERT: F 255 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6789 (mm) REVERT: F 300 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7293 (mt) REVERT: F 305 GLU cc_start: 0.8257 (tt0) cc_final: 0.7592 (mt-10) REVERT: F 308 LYS cc_start: 0.7079 (mttt) cc_final: 0.6593 (ptmm) REVERT: F 330 PHE cc_start: 0.7080 (m-80) cc_final: 0.6819 (m-80) outliers start: 44 outliers final: 37 residues processed: 227 average time/residue: 0.1212 time to fit residues: 42.6798 Evaluate side-chains 232 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 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 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 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 252 LEU Chi-restraints excluded: chain E residue 276 VAL 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 292 VAL 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: 0.9990 chunk 74 optimal weight: 0.0980 chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.202127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147972 restraints weight = 19048.338| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.27 r_work: 0.3080 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3470 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= 0.113 Angle : 0.466 9.016 24108 Z= 0.242 Chirality : 0.043 0.161 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.949 97.848 2857 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.43 % Allowed : 14.08 % Favored : 83.49 % 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: 0.08 (0.19), residues: 1990 helix: 1.23 (0.24), residues: 504 sheet: 0.65 (0.28), residues: 348 loop : -0.68 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.022 0.001 TYR B 343 PHE 0.021 0.001 PHE D 195 TRP 0.013 0.001 TRP B 333 HIS 0.003 0.000 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (17555) covalent geometry : angle 0.46602 / 0.24 (24108) hydrogen bonds : bond 0.02927 / 1.94 ( 655) hydrogen bonds : angle 4.50852 / 3.24 ( 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 230 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9121 (mttt) cc_final: 0.8531 (mmtm) REVERT: A 139 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7478 (mtp180) REVERT: A 297 ASP cc_start: 0.8741 (t0) cc_final: 0.8427 (t0) REVERT: B 105 MET cc_start: 0.8410 (mmm) cc_final: 0.7243 (mpp) REVERT: B 125 ASP cc_start: 0.8568 (t0) cc_final: 0.8256 (t70) REVERT: B 168 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8064 (pp) REVERT: B 209 GLN cc_start: 0.7987 (tp40) cc_final: 0.7007 (tm-30) REVERT: B 213 ASP cc_start: 0.7784 (m-30) cc_final: 0.6833 (m-30) REVERT: B 340 GLU cc_start: 0.6740 (tm-30) cc_final: 0.5794 (mt-10) REVERT: C 150 LYS cc_start: 0.8361 (mttt) cc_final: 0.7756 (mmtm) REVERT: C 166 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7774 (m) REVERT: C 219 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5833 (tmm) REVERT: D 131 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6363 (mm-40) REVERT: D 194 TYR cc_start: 0.7256 (m-80) cc_final: 0.6590 (m-80) REVERT: D 195 PHE cc_start: 0.7151 (m-80) cc_final: 0.6265 (m-10) REVERT: D 272 MET cc_start: 0.7187 (ttp) cc_final: 0.6771 (ttm) REVERT: D 285 GLN cc_start: 0.5900 (tt0) cc_final: 0.5360 (mp10) REVERT: E 107 ASP cc_start: 0.8176 (m-30) cc_final: 0.7938 (m-30) REVERT: E 153 GLN cc_start: 0.7730 (mp10) cc_final: 0.7444 (mp10) REVERT: E 245 GLN cc_start: 0.5736 (mt0) cc_final: 0.4978 (pp30) REVERT: F 22 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: F 164 ASN cc_start: 0.7299 (t0) cc_final: 0.7059 (m-40) REVERT: F 219 MET cc_start: 0.6773 (mtt) cc_final: 0.6421 (mmt) REVERT: F 255 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6805 (mm) REVERT: F 300 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7335 (mt) REVERT: F 308 LYS cc_start: 0.7192 (mttt) cc_final: 0.6579 (ptmm) REVERT: F 330 PHE cc_start: 0.7299 (m-80) cc_final: 0.7030 (m-80) outliers start: 43 outliers final: 37 residues processed: 219 average time/residue: 0.1326 time to fit residues: 45.0305 Evaluate side-chains 229 residues out of total 1781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 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 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 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 252 LEU Chi-restraints excluded: chain E residue 276 VAL 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 292 VAL 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: 1.9990 chunk 3 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.0050 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 195 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 overall best weight: 1.0176 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.202414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148707 restraints weight = 19096.235| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.41 r_work: 0.3095 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17555 Z= 0.105 Angle : 0.456 8.816 24108 Z= 0.238 Chirality : 0.042 0.159 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.974 98.110 2857 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.49 % Allowed : 14.19 % Favored : 83.32 % 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: 0.09 (0.19), residues: 1990 helix: 1.23 (0.24), residues: 504 sheet: 0.67 (0.28), residues: 348 loop : -0.68 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.031 0.001 TYR B 343 PHE 0.020 0.001 PHE D 195 TRP 0.011 0.001 TRP B 333 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 (17555) covalent geometry : angle 0.45612 / 0.24 (24108) hydrogen bonds : bond 0.02855 / 1.89 ( 655) hydrogen bonds : angle 4.46441 / 3.21 ( 1829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.15 seconds wall clock time: 75 minutes 21.32 seconds (4521.32 seconds total)