Starting phenix.real_space_refine on Sat May 2 20:03:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3z_66515/05_2026/9x3z_66515.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5351 2.51 5 N 1425 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8360 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1960 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2538 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1691 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 409 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Time building chain proxies: 1.80, per 1000 atoms: 0.22 Number of scatterers: 8360 At special positions: 0 Unit cell: (89.64, 114.54, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1526 8.00 N 1425 7.00 C 5351 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: 0.77 Conformation dependent library (CDL) restraints added in 530.0 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.7% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.531A pdb=" N TRP R 37 " --> pdb=" O PRO R 33 " (cutoff:3.500A) Proline residue: R 44 - end of helix Processing helix chain 'R' and resid 64 through 93 removed outlier: 3.562A pdb=" N VAL R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR R 69 " --> pdb=" O PRO R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.679A pdb=" N VAL R 134 " --> pdb=" O ARG R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 143 Processing helix chain 'R' and resid 147 through 171 Processing helix chain 'R' and resid 182 through 197 Processing helix chain 'R' and resid 198 through 216 Processing helix chain 'R' and resid 226 through 241 Processing helix chain 'R' and resid 241 through 255 removed outlier: 4.638A pdb=" N ARG R 245 " --> pdb=" O ALA R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 281 Proline residue: R 277 - end of helix Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.539A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.010A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.589A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.588A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.544A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.576A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.506A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.540A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.519A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.823A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.636A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 162 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.566A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.508A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.613A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.845A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.319A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.444A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.444A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1323 1.31 - 1.43: 2412 1.43 - 1.56: 4719 1.56 - 1.68: 0 1.68 - 1.81: 85 Bond restraints: 8539 Sorted by residual: bond pdb=" CA GLN L 16 " pdb=" C GLN L 16 " ideal model delta sigma weight residual 1.525 1.433 0.092 2.10e-02 2.27e+03 1.90e+01 bond pdb=" C GLN L 16 " pdb=" O GLN L 16 " ideal model delta sigma weight residual 1.231 1.181 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C MET S 83 " pdb=" O MET S 83 " ideal model delta sigma weight residual 1.235 1.209 0.026 1.18e-02 7.18e+03 4.69e+00 bond pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta sigma weight residual 1.530 1.488 0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" CD GLN L 16 " pdb=" NE2 GLN L 16 " ideal model delta sigma weight residual 1.328 1.288 0.040 2.10e-02 2.27e+03 3.68e+00 ... (remaining 8534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 11579 6.83 - 13.66: 0 13.66 - 20.49: 0 20.49 - 27.32: 0 27.32 - 34.15: 1 Bond angle restraints: 11580 Sorted by residual: angle pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" C GLN L 16 " ideal model delta sigma weight residual 111.00 76.85 34.15 2.80e+00 1.28e-01 1.49e+02 angle pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta sigma weight residual 110.50 117.27 -6.77 1.70e+00 3.46e-01 1.58e+01 angle pdb=" N VAL R 134 " pdb=" CA VAL R 134 " pdb=" C VAL R 134 " ideal model delta sigma weight residual 112.96 109.40 3.56 1.00e+00 1.00e+00 1.27e+01 angle pdb=" N ILE B 275 " pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 113.20 110.38 2.82 9.60e-01 1.09e+00 8.66e+00 angle pdb=" O PRO L 15 " pdb=" C PRO L 15 " pdb=" N GLN L 16 " ideal model delta sigma weight residual 122.64 118.68 3.96 1.35e+00 5.49e-01 8.59e+00 ... (remaining 11575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4537 17.90 - 35.79: 370 35.79 - 53.69: 82 53.69 - 71.58: 17 71.58 - 89.48: 12 Dihedral angle restraints: 5018 sinusoidal: 1904 harmonic: 3114 Sorted by residual: dihedral pdb=" C GLN L 16 " pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta harmonic sigma weight residual -122.60 -107.17 -15.43 0 2.50e+00 1.60e-01 3.81e+01 dihedral pdb=" CA LEU B 122 " pdb=" C LEU B 122 " pdb=" N ASP B 123 " pdb=" CA ASP B 123 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP B 295 " pdb=" C ASP B 295 " pdb=" N ASP B 296 " pdb=" CA ASP B 296 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 829 0.031 - 0.062: 331 0.062 - 0.093: 99 0.093 - 0.125: 60 0.125 - 0.156: 6 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CA ILE R 32 " pdb=" N ILE R 32 " pdb=" C ILE R 32 " pdb=" CB ILE R 32 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1322 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO A 299 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 15 " -0.013 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C PRO L 15 " 0.042 2.00e-02 2.50e+03 pdb=" O PRO L 15 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN L 16 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO S 75 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.027 5.00e-02 4.00e+02 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1227 2.75 - 3.29: 7810 3.29 - 3.83: 14096 3.83 - 4.36: 17227 4.36 - 4.90: 29845 Nonbonded interactions: 70205 Sorted by model distance: nonbonded pdb=" OH TYR R 116 " pdb=" O ALA R 241 " model vdw 2.218 3.040 nonbonded pdb=" O ASP S 74 " pdb=" ND2 ASN S 77 " model vdw 2.316 3.120 nonbonded pdb=" O ASP B 200 " pdb=" OG1 THR B 201 " model vdw 2.329 3.040 nonbonded pdb=" NH2 ARG S 202 " pdb=" OD2 ASP S 223 " model vdw 2.357 3.120 nonbonded pdb=" OE2 GLU R 167 " pdb=" NH2 ARG R 245 " model vdw 2.372 3.120 ... (remaining 70200 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.004 0.092 8539 Z= 0.192 Angle : 0.658 34.147 11580 Z= 0.347 Chirality : 0.041 0.156 1325 Planarity : 0.005 0.080 1453 Dihedral : 14.892 89.479 3008 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.56 % Allowed : 12.72 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1047 helix: 2.86 (0.26), residues: 370 sheet: 0.98 (0.30), residues: 275 loop : -0.38 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.015 0.002 TYR A 306 PHE 0.017 0.002 PHE B 156 TRP 0.014 0.002 TRP A 211 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8539) covalent geometry : angle 0.65800 (11580) hydrogen bonds : bond 0.15597 ( 444) hydrogen bonds : angle 5.88682 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8200 (tt0) cc_final: 0.7916 (tt0) REVERT: A 230 TYR cc_start: 0.8129 (m-10) cc_final: 0.7925 (m-80) REVERT: A 235 GLU cc_start: 0.7566 (tt0) cc_final: 0.7162 (mp0) REVERT: A 250 ARG cc_start: 0.8112 (ptp90) cc_final: 0.7819 (ptp-110) REVERT: B 134 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7479 (tpt-90) REVERT: S 18 ARG cc_start: 0.7909 (tpt-90) cc_final: 0.7496 (ttt180) REVERT: S 117 LEU cc_start: 0.8571 (tp) cc_final: 0.8302 (tp) outliers start: 5 outliers final: 1 residues processed: 186 average time/residue: 0.6195 time to fit residues: 121.6338 Evaluate side-chains 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 271 HIS S 39 GLN S 77 ASN S 179 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116990 restraints weight = 9590.395| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.96 r_work: 0.3383 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8539 Z= 0.173 Angle : 0.600 7.212 11580 Z= 0.323 Chirality : 0.044 0.179 1325 Planarity : 0.004 0.061 1453 Dihedral : 4.854 21.457 1166 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.35 % Allowed : 13.84 % Favored : 82.81 % 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: 1.78 (0.26), residues: 1047 helix: 2.81 (0.26), residues: 369 sheet: 1.11 (0.30), residues: 279 loop : -0.34 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.016 0.002 TYR S 190 PHE 0.018 0.002 PHE B 156 TRP 0.015 0.002 TRP A 211 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8539) covalent geometry : angle 0.59959 (11580) hydrogen bonds : bond 0.05372 ( 444) hydrogen bonds : angle 4.60682 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.318 Fit side-chains REVERT: R 52 ILE cc_start: 0.8034 (mt) cc_final: 0.7790 (mp) REVERT: R 185 ARG cc_start: 0.6262 (mmt90) cc_final: 0.5718 (mmt180) REVERT: R 252 TYR cc_start: 0.7604 (m-10) cc_final: 0.7378 (m-10) REVERT: A 235 GLU cc_start: 0.7900 (tt0) cc_final: 0.7024 (mp0) REVERT: A 250 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7976 (ptp-110) REVERT: B 134 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7768 (tpt-90) REVERT: B 180 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: B 222 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7618 (pmm) REVERT: B 232 SER cc_start: 0.8959 (t) cc_final: 0.8709 (t) REVERT: B 308 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: B 319 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8235 (ttt180) REVERT: G 28 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7052 (pt) outliers start: 30 outliers final: 14 residues processed: 155 average time/residue: 0.6897 time to fit residues: 112.5641 Evaluate side-chains 149 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 271 HIS B 273 ASN S 39 GLN S 82 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120635 restraints weight = 9539.933| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.94 r_work: 0.3460 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8539 Z= 0.113 Angle : 0.515 6.766 11580 Z= 0.277 Chirality : 0.042 0.152 1325 Planarity : 0.004 0.052 1453 Dihedral : 4.389 17.799 1165 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.79 % Allowed : 14.96 % Favored : 82.25 % 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: 2.03 (0.26), residues: 1047 helix: 3.15 (0.25), residues: 364 sheet: 1.21 (0.30), residues: 271 loop : -0.23 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.018 0.001 TYR R 168 PHE 0.015 0.001 PHE A 189 TRP 0.013 0.001 TRP A 211 HIS 0.002 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8539) covalent geometry : angle 0.51526 (11580) hydrogen bonds : bond 0.04346 ( 444) hydrogen bonds : angle 4.28348 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: R 52 ILE cc_start: 0.8034 (mt) cc_final: 0.7797 (mp) REVERT: R 185 ARG cc_start: 0.6194 (mmt90) cc_final: 0.5628 (mmt180) REVERT: A 235 GLU cc_start: 0.7862 (tt0) cc_final: 0.7029 (mp0) REVERT: A 250 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7741 (ptp-110) REVERT: B 19 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6957 (mm) REVERT: B 27 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7305 (mtt180) REVERT: B 134 ARG cc_start: 0.7993 (tpt-90) cc_final: 0.7715 (tpt-90) REVERT: B 180 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: B 222 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7614 (pmm) REVERT: B 232 SER cc_start: 0.8956 (t) cc_final: 0.8711 (t) REVERT: B 319 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8209 (ttt180) outliers start: 25 outliers final: 11 residues processed: 155 average time/residue: 0.6146 time to fit residues: 100.9036 Evaluate side-chains 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 6 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 271 HIS S 39 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121571 restraints weight = 9728.660| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.96 r_work: 0.3450 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8539 Z= 0.119 Angle : 0.516 6.899 11580 Z= 0.277 Chirality : 0.042 0.148 1325 Planarity : 0.004 0.047 1453 Dihedral : 4.337 18.080 1165 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 15.18 % Favored : 82.03 % 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: 2.08 (0.26), residues: 1047 helix: 3.23 (0.25), residues: 364 sheet: 1.17 (0.30), residues: 274 loop : -0.20 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.019 0.001 TYR R 168 PHE 0.016 0.001 PHE A 189 TRP 0.013 0.001 TRP A 211 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8539) covalent geometry : angle 0.51589 (11580) hydrogen bonds : bond 0.04345 ( 444) hydrogen bonds : angle 4.22946 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.291 Fit side-chains REVERT: R 52 ILE cc_start: 0.8058 (mt) cc_final: 0.7803 (mp) REVERT: R 185 ARG cc_start: 0.6241 (mmt90) cc_final: 0.5646 (mmt180) REVERT: R 203 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7273 (tmt) REVERT: A 235 GLU cc_start: 0.7948 (tt0) cc_final: 0.7091 (mp0) REVERT: A 242 SER cc_start: 0.8971 (t) cc_final: 0.8758 (t) REVERT: A 250 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7784 (ptp-110) REVERT: B 19 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7007 (mm) REVERT: B 22 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: B 27 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7397 (mtt180) REVERT: B 134 ARG cc_start: 0.8003 (tpt-90) cc_final: 0.7722 (tpt-90) REVERT: B 180 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: B 232 SER cc_start: 0.8907 (t) cc_final: 0.8664 (t) REVERT: B 239 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: B 319 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8225 (ttt180) REVERT: S 18 ARG cc_start: 0.7815 (tpt-90) cc_final: 0.7513 (tpt170) outliers start: 25 outliers final: 11 residues processed: 150 average time/residue: 0.6002 time to fit residues: 95.3813 Evaluate side-chains 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 HIS R 50 ASN R 263 HIS B 271 HIS S 82 GLN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.159238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115277 restraints weight = 9611.494| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.96 r_work: 0.3334 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8539 Z= 0.219 Angle : 0.621 7.928 11580 Z= 0.333 Chirality : 0.046 0.189 1325 Planarity : 0.005 0.046 1453 Dihedral : 4.870 19.405 1165 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.91 % Allowed : 13.73 % Favored : 82.37 % 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: 1.66 (0.26), residues: 1047 helix: 2.75 (0.26), residues: 370 sheet: 0.92 (0.30), residues: 273 loop : -0.32 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 87 TYR 0.019 0.002 TYR R 168 PHE 0.020 0.002 PHE L 13 TRP 0.016 0.002 TRP A 211 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8539) covalent geometry : angle 0.62114 (11580) hydrogen bonds : bond 0.05602 ( 444) hydrogen bonds : angle 4.59581 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.315 Fit side-chains REVERT: R 52 ILE cc_start: 0.8077 (mt) cc_final: 0.7811 (mp) REVERT: R 63 ARG cc_start: 0.6562 (ttm-80) cc_final: 0.6228 (ttm-80) REVERT: R 185 ARG cc_start: 0.6210 (mmt90) cc_final: 0.5509 (mmt180) REVERT: R 203 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7429 (tmt) REVERT: A 235 GLU cc_start: 0.7887 (tt0) cc_final: 0.6998 (mp0) REVERT: A 250 ARG cc_start: 0.8243 (ptp90) cc_final: 0.7839 (ptp-110) REVERT: B 19 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6893 (mm) REVERT: B 134 ARG cc_start: 0.8055 (tpt-90) cc_final: 0.7733 (tpt-90) REVERT: B 180 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: B 219 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7485 (mpt180) REVERT: B 232 SER cc_start: 0.8898 (t) cc_final: 0.8650 (t) REVERT: B 308 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 319 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8238 (ttt180) REVERT: G 28 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7148 (pt) outliers start: 35 outliers final: 12 residues processed: 149 average time/residue: 0.6080 time to fit residues: 95.9676 Evaluate side-chains 148 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN B 271 HIS B 273 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115733 restraints weight = 9577.803| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.96 r_work: 0.3405 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8539 Z= 0.199 Angle : 0.601 7.728 11580 Z= 0.322 Chirality : 0.045 0.186 1325 Planarity : 0.005 0.044 1453 Dihedral : 4.842 18.721 1165 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.35 % Allowed : 15.29 % Favored : 81.36 % 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: 1.58 (0.26), residues: 1047 helix: 2.68 (0.26), residues: 370 sheet: 0.86 (0.30), residues: 273 loop : -0.35 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 144 TYR 0.020 0.002 TYR R 168 PHE 0.020 0.002 PHE L 13 TRP 0.016 0.002 TRP A 211 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8539) covalent geometry : angle 0.60062 (11580) hydrogen bonds : bond 0.05360 ( 444) hydrogen bonds : angle 4.53111 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.396 Fit side-chains REVERT: R 52 ILE cc_start: 0.8074 (mt) cc_final: 0.7803 (mp) REVERT: R 63 ARG cc_start: 0.6628 (ttm-80) cc_final: 0.6312 (ttm-80) REVERT: R 185 ARG cc_start: 0.6197 (mmt90) cc_final: 0.5544 (mmt180) REVERT: R 203 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7528 (tmt) REVERT: R 263 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: A 235 GLU cc_start: 0.7920 (tt0) cc_final: 0.7043 (mp0) REVERT: A 250 ARG cc_start: 0.8200 (ptp90) cc_final: 0.7822 (ptp-110) REVERT: B 19 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6994 (mm) REVERT: B 134 ARG cc_start: 0.8045 (tpt-90) cc_final: 0.7658 (tpt-90) REVERT: B 180 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: B 219 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7514 (mpt180) REVERT: B 232 SER cc_start: 0.8867 (t) cc_final: 0.8622 (t) REVERT: B 308 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: B 319 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8236 (ttt180) outliers start: 30 outliers final: 12 residues processed: 145 average time/residue: 0.5925 time to fit residues: 91.2484 Evaluate side-chains 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117804 restraints weight = 9665.805| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.93 r_work: 0.3405 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8539 Z= 0.190 Angle : 0.595 7.592 11580 Z= 0.319 Chirality : 0.045 0.181 1325 Planarity : 0.004 0.043 1453 Dihedral : 4.818 18.788 1165 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.57 % Allowed : 15.62 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.26), residues: 1047 helix: 2.68 (0.26), residues: 370 sheet: 0.83 (0.30), residues: 273 loop : -0.42 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 144 TYR 0.020 0.002 TYR R 168 PHE 0.021 0.002 PHE L 13 TRP 0.016 0.002 TRP A 211 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8539) covalent geometry : angle 0.59534 (11580) hydrogen bonds : bond 0.05298 ( 444) hydrogen bonds : angle 4.52857 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.281 Fit side-chains REVERT: R 52 ILE cc_start: 0.8100 (mt) cc_final: 0.7834 (mp) REVERT: R 63 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.6372 (ttm-80) REVERT: R 113 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7749 (tt) REVERT: R 185 ARG cc_start: 0.6272 (mmt90) cc_final: 0.5637 (mmt180) REVERT: R 203 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7588 (tmt) REVERT: R 263 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7311 (t-90) REVERT: A 235 GLU cc_start: 0.7979 (tt0) cc_final: 0.7171 (mp0) REVERT: A 250 ARG cc_start: 0.8230 (ptp90) cc_final: 0.7856 (ptp-110) REVERT: B 19 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7126 (mm) REVERT: B 22 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 134 ARG cc_start: 0.8045 (tpt-90) cc_final: 0.7743 (tpt-90) REVERT: B 180 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: B 219 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7527 (mpt180) REVERT: B 308 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: B 319 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8292 (ttt180) outliers start: 32 outliers final: 14 residues processed: 145 average time/residue: 0.5873 time to fit residues: 90.2696 Evaluate side-chains 149 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN B 244 ASN B 271 HIS B 273 ASN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121000 restraints weight = 9625.081| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.96 r_work: 0.3468 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8539 Z= 0.106 Angle : 0.502 7.554 11580 Z= 0.270 Chirality : 0.041 0.146 1325 Planarity : 0.004 0.041 1453 Dihedral : 4.285 17.252 1165 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.23 % Allowed : 16.96 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.26), residues: 1047 helix: 3.17 (0.25), residues: 363 sheet: 0.98 (0.31), residues: 265 loop : -0.29 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.017 0.001 TYR R 168 PHE 0.021 0.001 PHE R 82 TRP 0.013 0.001 TRP A 211 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8539) covalent geometry : angle 0.50199 (11580) hydrogen bonds : bond 0.04016 ( 444) hydrogen bonds : angle 4.15566 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.364 Fit side-chains REVERT: R 52 ILE cc_start: 0.8009 (mt) cc_final: 0.7761 (mp) REVERT: R 63 ARG cc_start: 0.6606 (ttm-80) cc_final: 0.6279 (ttm-80) REVERT: R 185 ARG cc_start: 0.6139 (mmt90) cc_final: 0.5447 (mmt180) REVERT: R 263 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: A 235 GLU cc_start: 0.7927 (tt0) cc_final: 0.7097 (mp0) REVERT: A 250 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7741 (ptp-110) REVERT: B 22 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: B 134 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7656 (tpt-90) REVERT: B 219 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7467 (mpt180) REVERT: B 239 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 319 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8200 (ttt180) REVERT: S 159 CYS cc_start: 0.8444 (p) cc_final: 0.7933 (t) outliers start: 20 outliers final: 8 residues processed: 142 average time/residue: 0.6167 time to fit residues: 92.8407 Evaluate side-chains 141 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN B 271 HIS B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118944 restraints weight = 9570.395| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.97 r_work: 0.3429 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8539 Z= 0.156 Angle : 0.568 7.755 11580 Z= 0.302 Chirality : 0.044 0.313 1325 Planarity : 0.004 0.041 1453 Dihedral : 4.568 18.165 1165 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.68 % Allowed : 16.85 % Favored : 80.47 % 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: 1.74 (0.26), residues: 1047 helix: 2.97 (0.25), residues: 364 sheet: 0.85 (0.30), residues: 272 loop : -0.30 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.021 0.002 TYR R 251 PHE 0.017 0.002 PHE A 189 TRP 0.014 0.002 TRP A 211 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8539) covalent geometry : angle 0.56791 (11580) hydrogen bonds : bond 0.04827 ( 444) hydrogen bonds : angle 4.38616 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.200 Fit side-chains REVERT: R 52 ILE cc_start: 0.8035 (mt) cc_final: 0.7781 (mp) REVERT: R 63 ARG cc_start: 0.6766 (ttm-80) cc_final: 0.6419 (ttm-80) REVERT: R 185 ARG cc_start: 0.6132 (mmt90) cc_final: 0.5470 (mmt180) REVERT: R 203 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7502 (tmt) REVERT: R 263 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7129 (t-90) REVERT: A 235 GLU cc_start: 0.7929 (tt0) cc_final: 0.7097 (mp0) REVERT: A 250 ARG cc_start: 0.8157 (ptp90) cc_final: 0.7824 (ptp-110) REVERT: A 314 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7971 (ttp-110) REVERT: B 22 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: B 134 ARG cc_start: 0.8011 (tpt-90) cc_final: 0.7702 (tpt-90) REVERT: B 219 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7509 (mpt180) REVERT: B 319 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8213 (ttt180) outliers start: 24 outliers final: 14 residues processed: 144 average time/residue: 0.6034 time to fit residues: 92.2203 Evaluate side-chains 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN B 271 HIS B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122643 restraints weight = 9646.747| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.95 r_work: 0.3476 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8539 Z= 0.110 Angle : 0.521 10.048 11580 Z= 0.276 Chirality : 0.043 0.358 1325 Planarity : 0.004 0.041 1453 Dihedral : 4.265 17.416 1165 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.01 % Allowed : 17.19 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.26), residues: 1047 helix: 3.13 (0.25), residues: 364 sheet: 0.97 (0.31), residues: 265 loop : -0.29 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.017 0.001 TYR R 251 PHE 0.030 0.001 PHE R 82 TRP 0.012 0.001 TRP A 211 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8539) covalent geometry : angle 0.52056 (11580) hydrogen bonds : bond 0.04067 ( 444) hydrogen bonds : angle 4.16485 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.316 Fit side-chains REVERT: R 52 ILE cc_start: 0.8021 (mt) cc_final: 0.7773 (mp) REVERT: R 63 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.6296 (ttm-80) REVERT: R 185 ARG cc_start: 0.6081 (mmt90) cc_final: 0.5406 (mmt180) REVERT: R 263 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6921 (t-90) REVERT: A 235 GLU cc_start: 0.7873 (tt0) cc_final: 0.7041 (mp0) REVERT: A 250 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7770 (ptp-110) REVERT: B 22 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: B 134 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: B 219 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7456 (mpt180) REVERT: B 239 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: B 319 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8194 (ttt180) REVERT: S 159 CYS cc_start: 0.8466 (p) cc_final: 0.8000 (t) outliers start: 18 outliers final: 12 residues processed: 145 average time/residue: 0.5928 time to fit residues: 91.2352 Evaluate side-chains 148 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 263 HIS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN B 271 HIS B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115684 restraints weight = 9542.486| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.95 r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8539 Z= 0.245 Angle : 0.659 9.753 11580 Z= 0.348 Chirality : 0.048 0.330 1325 Planarity : 0.005 0.042 1453 Dihedral : 4.936 19.754 1165 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.34 % Allowed : 17.30 % Favored : 80.36 % 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: 1.42 (0.26), residues: 1047 helix: 2.53 (0.26), residues: 371 sheet: 0.82 (0.30), residues: 272 loop : -0.47 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 144 TYR 0.029 0.002 TYR R 252 PHE 0.020 0.002 PHE B 156 TRP 0.015 0.002 TRP A 211 HIS 0.010 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 8539) covalent geometry : angle 0.65894 (11580) hydrogen bonds : bond 0.05707 ( 444) hydrogen bonds : angle 4.62311 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4058.79 seconds wall clock time: 69 minutes 45.48 seconds (4185.48 seconds total)