Starting phenix.real_space_refine on Thu Jul 2 13:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbe_38215/07_2026/8xbe_38215.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.533 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 1 5.49 5 S 67 5.16 5 C 5702 2.51 5 N 1513 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s 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: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "D" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'KW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.16 Number of scatterers: 8937 At special positions: 0 Unit cell: (128.455, 122.87, 91.594, 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 67 16.00 P 1 15.00 O 1654 8.00 N 1513 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.03 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: 0.54 Conformation dependent library (CDL) restraints added in 340.2 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 39.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.899A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.694A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.892A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.718A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.568A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.481A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 removed outlier: 4.263A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.674A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.668A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 352 removed outlier: 4.114A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.583A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.824A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 81 removed outlier: 3.587A pdb=" N LEU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.755A pdb=" N LEU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.928A pdb=" N TYR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 157 removed outlier: 4.341A pdb=" N TYR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 4.378A pdb=" N GLN A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 252 removed outlier: 4.105A pdb=" N ALA A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 294 removed outlier: 3.999A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 3.542A pdb=" N PHE A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 331 removed outlier: 3.734A pdb=" N ILE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 331 through 342 Processing sheet with id=AA1, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.518A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.759A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.441A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.303A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.629A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.706A pdb=" N THR C 102 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 113 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 122 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 153 removed outlier: 5.119A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 160 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.030A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.708A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.793A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 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: 0.91 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1579 1.33 - 1.45: 2409 1.45 - 1.57: 5027 1.57 - 1.70: 3 1.70 - 1.82: 98 Bond restraints: 9116 Sorted by residual: bond pdb=" C20 KW0 A 401 " pdb=" O4 KW0 A 401 " ideal model delta sigma weight residual 1.414 1.468 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C GLU S 222 " pdb=" N TYR S 223 " ideal model delta sigma weight residual 1.333 1.273 0.060 2.74e-02 1.33e+03 4.81e+00 bond pdb=" C22 KW0 A 401 " pdb=" C23 KW0 A 401 " ideal model delta sigma weight residual 1.512 1.469 0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" O4 KW0 A 401 " pdb=" P1 KW0 A 401 " ideal model delta sigma weight residual 1.647 1.606 0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C16 KW0 A 401 " pdb=" C17 KW0 A 401 " ideal model delta sigma weight residual 1.535 1.496 0.039 2.00e-02 2.50e+03 3.76e+00 ... (remaining 9111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12148 2.20 - 4.40: 155 4.40 - 6.59: 15 6.59 - 8.79: 4 8.79 - 10.99: 3 Bond angle restraints: 12325 Sorted by residual: angle pdb=" CA CYS C 103 " pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 114.40 125.39 -10.99 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C ALA C 113 " pdb=" N CYS C 114 " pdb=" CA CYS C 114 " ideal model delta sigma weight residual 121.86 114.90 6.96 1.58e+00 4.01e-01 1.94e+01 angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 112.83 108.68 4.15 9.90e-01 1.02e+00 1.76e+01 angle pdb=" CA PRO S 14 " pdb=" N PRO S 14 " pdb=" CD PRO S 14 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" C LEU C 261 " pdb=" N MET C 262 " pdb=" CA MET C 262 " ideal model delta sigma weight residual 121.85 115.30 6.55 1.77e+00 3.19e-01 1.37e+01 ... (remaining 12320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.38: 5279 30.38 - 60.77: 142 60.77 - 91.15: 17 91.15 - 121.53: 1 121.53 - 151.91: 1 Dihedral angle restraints: 5440 sinusoidal: 2141 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 132.57 -39.57 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" C15 KW0 A 401 " pdb=" C16 KW0 A 401 " pdb=" C17 KW0 A 401 " pdb=" C18 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 190.27 38.36 151.91 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 5437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1305 0.082 - 0.164: 94 0.164 - 0.246: 2 0.246 - 0.328: 0 0.328 - 0.410: 1 Chirality restraints: 1402 Sorted by residual: chirality pdb=" C20 KW0 A 401 " pdb=" C19 KW0 A 401 " pdb=" C21 KW0 A 401 " pdb=" O4 KW0 A 401 " both_signs ideal model delta sigma weight residual False -2.15 -2.56 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA CYS C 103 " pdb=" N CYS C 103 " pdb=" C CYS C 103 " pdb=" CB CYS C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 1399 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KW0 A 401 " -0.069 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C11 KW0 A 401 " 0.029 2.00e-02 2.50e+03 pdb=" C8 KW0 A 401 " -0.028 2.00e-02 2.50e+03 pdb=" C9 KW0 A 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.066 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO S 14 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO S 75 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.046 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 151 2.67 - 3.23: 8572 3.23 - 3.79: 13436 3.79 - 4.34: 18896 4.34 - 4.90: 30872 Nonbonded interactions: 71927 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.118 3.040 nonbonded pdb=" OE1 GLN C 176 " pdb=" OG1 THR C 179 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 147 " pdb=" OG SER C 160 " model vdw 2.151 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.233 3.040 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.254 3.120 ... (remaining 71922 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 0.084 9121 Z= 0.160 Angle : 0.645 10.992 12335 Z= 0.361 Chirality : 0.045 0.410 1402 Planarity : 0.005 0.097 1546 Dihedral : 13.987 151.913 3299 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.41 (0.25), residues: 1121 helix: 0.66 (0.26), residues: 398 sheet: -0.06 (0.32), residues: 277 loop : -1.20 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 67 TYR 0.027 0.001 TYR S 178 PHE 0.012 0.001 PHE C 234 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9116) covalent geometry : angle 0.64055 / 0.36 (12325) SS BOND : bond 0.00743 / 0.30 ( 5) SS BOND : angle 2.70761 / 1.46 ( 10) hydrogen bonds : bond 0.21767 / 14.75 ( 449) hydrogen bonds : angle 7.40671 / 5.17 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7281 (mp0) cc_final: 0.6870 (mp0) REVERT: S 67 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8273 (ttm110) REVERT: S 73 ASP cc_start: 0.7178 (t0) cc_final: 0.6750 (t0) REVERT: S 160 THR cc_start: 0.7972 (t) cc_final: 0.7745 (t) REVERT: S 218 MET cc_start: 0.8441 (ttp) cc_final: 0.8074 (ttt) REVERT: B 269 ASN cc_start: 0.7617 (m-40) cc_final: 0.7327 (m-40) REVERT: C 280 LYS cc_start: 0.8643 (tttp) cc_final: 0.8427 (ttmm) REVERT: C 303 ASP cc_start: 0.6849 (m-30) cc_final: 0.6628 (m-30) REVERT: A 72 ASN cc_start: 0.7622 (m110) cc_final: 0.6967 (m110) REVERT: A 240 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7356 (mtpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1017 time to fit residues: 31.3977 Evaluate side-chains 195 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 255 ASN C 176 GLN C 239 ASN C 340 ASN A 114 HIS A 306 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.148259 restraints weight = 10613.469| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.19 r_work: 0.3361 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9121 Z= 0.154 Angle : 0.613 11.575 12335 Z= 0.327 Chirality : 0.044 0.216 1402 Planarity : 0.005 0.063 1546 Dihedral : 8.379 173.727 1270 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.85 % Allowed : 9.26 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.16 (0.25), residues: 1121 helix: 1.31 (0.26), residues: 409 sheet: -0.27 (0.31), residues: 275 loop : -1.32 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 52 TYR 0.024 0.001 TYR S 178 PHE 0.020 0.002 PHE A 318 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9116) covalent geometry : angle 0.61055 / 0.33 (12325) SS BOND : bond 0.00751 / 0.31 ( 5) SS BOND : angle 2.07785 / 1.21 ( 10) hydrogen bonds : bond 0.05150 / 3.49 ( 449) hydrogen bonds : angle 5.00597 / 3.44 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: S 18 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.7878 (tpp-160) REVERT: S 67 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8479 (ttm110) REVERT: S 76 LYS cc_start: 0.6701 (mmtp) cc_final: 0.6466 (mttp) REVERT: S 146 SER cc_start: 0.8256 (t) cc_final: 0.8020 (m) REVERT: S 218 MET cc_start: 0.8620 (ttt) cc_final: 0.8362 (ttt) REVERT: B 14 GLU cc_start: 0.8099 (tt0) cc_final: 0.7826 (tt0) REVERT: A 104 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6812 (mp) REVERT: A 110 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6748 (tpt170) REVERT: A 153 TYR cc_start: 0.8052 (t80) cc_final: 0.7815 (t80) REVERT: A 157 ASN cc_start: 0.7397 (t0) cc_final: 0.7102 (t0) outliers start: 18 outliers final: 13 residues processed: 206 average time/residue: 0.0943 time to fit residues: 26.2475 Evaluate side-chains 202 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN C 176 GLN C 340 ASN A 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.186887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144589 restraints weight = 10543.507| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.16 r_work: 0.3321 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9121 Z= 0.187 Angle : 0.630 10.562 12335 Z= 0.332 Chirality : 0.045 0.221 1402 Planarity : 0.004 0.045 1546 Dihedral : 7.045 121.917 1270 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 2.06 % Allowed : 13.17 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.14 (0.25), residues: 1121 helix: 1.52 (0.26), residues: 408 sheet: -0.32 (0.31), residues: 276 loop : -1.50 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 52 TYR 0.026 0.002 TYR S 178 PHE 0.019 0.002 PHE A 318 TRP 0.015 0.002 TRP S 47 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 9116) covalent geometry : angle 0.62778 / 0.33 (12325) SS BOND : bond 0.00816 / 0.34 ( 5) SS BOND : angle 2.11931 / 1.14 ( 10) hydrogen bonds : bond 0.04497 / 3.03 ( 449) hydrogen bonds : angle 4.86460 / 3.33 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.321 Fit side-chains REVERT: S 18 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.7876 (tpp-160) REVERT: S 19 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7366 (mtmm) REVERT: S 76 LYS cc_start: 0.6639 (mmtp) cc_final: 0.6367 (mttp) REVERT: S 160 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 14 GLU cc_start: 0.8132 (tt0) cc_final: 0.7768 (tt0) REVERT: B 320 TYR cc_start: 0.7297 (m-80) cc_final: 0.6958 (m-10) REVERT: C 262 MET cc_start: 0.7471 (tpt) cc_final: 0.7116 (tpt) REVERT: A 104 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 110 ARG cc_start: 0.7252 (ttt180) cc_final: 0.7003 (tpt170) REVERT: A 240 LYS cc_start: 0.7534 (mtpt) cc_final: 0.7237 (mtpt) REVERT: A 312 MET cc_start: 0.7597 (mmt) cc_final: 0.7195 (mmt) outliers start: 20 outliers final: 16 residues processed: 190 average time/residue: 0.0859 time to fit residues: 22.6679 Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN A 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.183523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143161 restraints weight = 10810.847| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.09 r_work: 0.3293 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9121 Z= 0.235 Angle : 0.677 10.745 12335 Z= 0.356 Chirality : 0.047 0.237 1402 Planarity : 0.005 0.045 1546 Dihedral : 6.696 93.427 1270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 4.12 % Allowed : 14.30 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.38 (0.25), residues: 1121 helix: 1.38 (0.26), residues: 408 sheet: -0.53 (0.31), residues: 286 loop : -1.64 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 52 TYR 0.029 0.002 TYR S 178 PHE 0.019 0.002 PHE A 318 TRP 0.018 0.002 TRP S 47 HIS 0.006 0.002 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 ( 9116) covalent geometry : angle 0.67032 / 0.35 (12325) SS BOND : bond 0.01091 / 0.44 ( 5) SS BOND : angle 3.51866 / 1.94 ( 10) hydrogen bonds : bond 0.04566 / 3.08 ( 449) hydrogen bonds : angle 4.98700 / 3.41 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: S 19 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7357 (mtmm) REVERT: S 76 LYS cc_start: 0.6711 (mmtp) cc_final: 0.6458 (mttp) REVERT: S 80 PHE cc_start: 0.6904 (m-10) cc_final: 0.6638 (m-10) REVERT: S 179 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6899 (mpt180) REVERT: B 14 GLU cc_start: 0.8463 (tt0) cc_final: 0.8121 (tt0) REVERT: B 23 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 320 TYR cc_start: 0.7672 (m-10) cc_final: 0.7280 (m-10) REVERT: C 7 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4602 (pp) REVERT: C 262 MET cc_start: 0.7638 (tpt) cc_final: 0.7357 (tpt) REVERT: A 104 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.7022 (mp) REVERT: A 148 ILE cc_start: 0.8810 (mt) cc_final: 0.8582 (mt) REVERT: A 153 TYR cc_start: 0.8233 (t80) cc_final: 0.7880 (t80) REVERT: A 157 ASN cc_start: 0.7421 (t0) cc_final: 0.7170 (t0) REVERT: A 312 MET cc_start: 0.7912 (mmt) cc_final: 0.7526 (mmt) REVERT: A 330 MET cc_start: 0.6170 (mmp) cc_final: 0.5799 (mmt) outliers start: 40 outliers final: 24 residues processed: 206 average time/residue: 0.0984 time to fit residues: 27.9256 Evaluate side-chains 205 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 230 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.186381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144912 restraints weight = 10593.677| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.19 r_work: 0.3332 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9121 Z= 0.145 Angle : 0.606 13.286 12335 Z= 0.316 Chirality : 0.044 0.235 1402 Planarity : 0.004 0.041 1546 Dihedral : 6.368 85.672 1270 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 3.29 % Allowed : 16.67 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1121 helix: 1.68 (0.26), residues: 407 sheet: -0.46 (0.30), residues: 286 loop : -1.63 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 52 TYR 0.027 0.002 TYR S 178 PHE 0.015 0.002 PHE A 79 TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 9116) covalent geometry : angle 0.60266 / 0.31 (12325) SS BOND : bond 0.00949 / 0.38 ( 5) SS BOND : angle 2.45849 / 1.43 ( 10) hydrogen bonds : bond 0.03949 / 2.65 ( 449) hydrogen bonds : angle 4.76923 / 3.26 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: S 18 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.7925 (tpp-160) REVERT: S 19 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7360 (mtmm) REVERT: S 76 LYS cc_start: 0.6551 (mmtp) cc_final: 0.6326 (mttp) REVERT: S 179 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6609 (mpt-90) REVERT: B 14 GLU cc_start: 0.8107 (tt0) cc_final: 0.7688 (tt0) REVERT: B 23 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (mp) REVERT: C 7 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4626 (pp) REVERT: A 85 LYS cc_start: 0.8257 (tppt) cc_final: 0.7743 (tppt) REVERT: A 104 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6736 (mp) REVERT: A 273 ILE cc_start: 0.7748 (mm) cc_final: 0.7523 (mm) REVERT: A 312 MET cc_start: 0.7625 (mmt) cc_final: 0.7190 (mmt) outliers start: 32 outliers final: 21 residues processed: 204 average time/residue: 0.1016 time to fit residues: 28.5031 Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.178438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136962 restraints weight = 10707.768| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.16 r_work: 0.3213 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 9121 Z= 0.400 Angle : 0.826 11.538 12335 Z= 0.433 Chirality : 0.053 0.291 1402 Planarity : 0.005 0.051 1546 Dihedral : 6.847 81.471 1270 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 4.42 % Allowed : 16.67 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.87 (0.25), residues: 1121 helix: 0.87 (0.25), residues: 406 sheet: -0.71 (0.31), residues: 287 loop : -1.87 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 110 TYR 0.032 0.003 TYR S 178 PHE 0.021 0.003 PHE A 79 TRP 0.030 0.003 TRP C 211 HIS 0.007 0.002 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.40 ( 9116) covalent geometry : angle 0.82138 / 0.43 (12325) SS BOND : bond 0.01398 / 0.58 ( 5) SS BOND : angle 3.10306 / 1.81 ( 10) hydrogen bonds : bond 0.05245 / 3.60 ( 449) hydrogen bonds : angle 5.33700 / 3.65 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.352 Fit side-chains REVERT: S 179 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6974 (mpt180) REVERT: B 14 GLU cc_start: 0.8293 (tt0) cc_final: 0.7945 (tt0) REVERT: B 243 MET cc_start: 0.6382 (tpp) cc_final: 0.5757 (tpp) REVERT: B 320 TYR cc_start: 0.7747 (m-10) cc_final: 0.7229 (m-10) REVERT: C 130 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 308 LEU cc_start: 0.8832 (mp) cc_final: 0.8597 (mp) REVERT: A 104 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6838 (mp) REVERT: A 312 MET cc_start: 0.7997 (mmt) cc_final: 0.7538 (mmt) REVERT: A 330 MET cc_start: 0.6054 (mmp) cc_final: 0.5685 (mmt) outliers start: 43 outliers final: 29 residues processed: 214 average time/residue: 0.0973 time to fit residues: 28.9497 Evaluate side-chains 207 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN B 188 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.184540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.145575 restraints weight = 10700.481| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.01 r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9121 Z= 0.166 Angle : 0.672 15.926 12335 Z= 0.347 Chirality : 0.045 0.270 1402 Planarity : 0.004 0.042 1546 Dihedral : 6.330 76.724 1270 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 3.09 % Allowed : 19.75 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.53 (0.25), residues: 1121 helix: 1.35 (0.26), residues: 406 sheet: -0.64 (0.31), residues: 278 loop : -1.80 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.032 0.002 TYR S 178 PHE 0.015 0.002 PHE C 151 TRP 0.018 0.002 TRP S 47 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9116) covalent geometry : angle 0.66035 / 0.34 (12325) SS BOND : bond 0.00951 / 0.38 ( 5) SS BOND : angle 4.40370 / 2.20 ( 10) hydrogen bonds : bond 0.04155 / 2.80 ( 449) hydrogen bonds : angle 4.99571 / 3.42 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.336 Fit side-chains REVERT: S 18 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8134 (tpp80) REVERT: S 179 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6751 (mpt180) REVERT: B 14 GLU cc_start: 0.8406 (tt0) cc_final: 0.8053 (tt0) REVERT: B 243 MET cc_start: 0.6352 (tpp) cc_final: 0.5740 (tpp) REVERT: C 118 ASP cc_start: 0.8383 (p0) cc_final: 0.8078 (p0) REVERT: C 130 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 104 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 277 ILE cc_start: 0.6938 (pt) cc_final: 0.6495 (pt) REVERT: A 312 MET cc_start: 0.7935 (mmt) cc_final: 0.7455 (mmt) REVERT: A 326 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6091 (mtp) REVERT: A 330 MET cc_start: 0.5993 (mmp) cc_final: 0.5471 (mmt) outliers start: 30 outliers final: 23 residues processed: 197 average time/residue: 0.0928 time to fit residues: 25.6755 Evaluate side-chains 198 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN B 188 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.188617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.150145 restraints weight = 10579.896| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.02 r_work: 0.3387 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9121 Z= 0.124 Angle : 0.627 15.043 12335 Z= 0.322 Chirality : 0.043 0.280 1402 Planarity : 0.004 0.039 1546 Dihedral : 5.799 63.640 1270 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 2.57 % Allowed : 20.47 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.25), residues: 1121 helix: 1.71 (0.26), residues: 406 sheet: -0.54 (0.31), residues: 271 loop : -1.69 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.027 0.001 TYR S 178 PHE 0.017 0.001 PHE B 354 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9116) covalent geometry : angle 0.61631 / 0.32 (12325) SS BOND : bond 0.00843 / 0.33 ( 5) SS BOND : angle 4.13286 / 2.06 ( 10) hydrogen bonds : bond 0.03667 / 2.44 ( 449) hydrogen bonds : angle 4.72915 / 3.23 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.332 Fit side-chains REVERT: B 14 GLU cc_start: 0.8305 (tt0) cc_final: 0.7941 (tt0) REVERT: C 156 GLN cc_start: 0.8234 (pt0) cc_final: 0.8023 (mt0) REVERT: C 280 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8229 (ttmt) REVERT: C 322 ASP cc_start: 0.8721 (t0) cc_final: 0.8517 (m-30) REVERT: A 85 LYS cc_start: 0.8292 (tppt) cc_final: 0.8005 (ttpt) REVERT: A 104 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6796 (mp) REVERT: A 201 SER cc_start: 0.7448 (m) cc_final: 0.7064 (t) REVERT: A 273 ILE cc_start: 0.7935 (mm) cc_final: 0.7716 (mm) REVERT: A 277 ILE cc_start: 0.6978 (pt) cc_final: 0.6582 (pt) REVERT: A 312 MET cc_start: 0.7762 (mmt) cc_final: 0.7230 (mmt) REVERT: A 326 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5931 (mtp) REVERT: A 330 MET cc_start: 0.5934 (mmp) cc_final: 0.5408 (mmt) outliers start: 25 outliers final: 22 residues processed: 199 average time/residue: 0.0968 time to fit residues: 26.5287 Evaluate side-chains 201 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.0170 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN B 188 HIS C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.191033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.151545 restraints weight = 10606.657| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.12 r_work: 0.3410 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9121 Z= 0.108 Angle : 0.608 14.841 12335 Z= 0.311 Chirality : 0.042 0.273 1402 Planarity : 0.003 0.040 1546 Dihedral : 5.411 62.060 1270 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.06 % Allowed : 21.71 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.02 (0.26), residues: 1121 helix: 1.98 (0.27), residues: 402 sheet: -0.44 (0.32), residues: 264 loop : -1.53 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.024 0.001 TYR S 178 PHE 0.016 0.001 PHE C 151 TRP 0.025 0.001 TRP C 82 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9116) covalent geometry : angle 0.59683 / 0.31 (12325) SS BOND : bond 0.00622 / 0.26 ( 5) SS BOND : angle 4.05916 / 1.95 ( 10) hydrogen bonds : bond 0.03470 / 2.28 ( 449) hydrogen bonds : angle 4.61462 / 3.15 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.344 Fit side-chains REVERT: S 18 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.7760 (tpp-160) REVERT: S 65 LYS cc_start: 0.8431 (tptp) cc_final: 0.7672 (tppt) REVERT: S 93 MET cc_start: 0.7215 (mtt) cc_final: 0.6570 (tpp) REVERT: C 280 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8089 (ttmt) REVERT: A 104 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6616 (mp) REVERT: A 201 SER cc_start: 0.7432 (m) cc_final: 0.6980 (t) REVERT: A 273 ILE cc_start: 0.7881 (mm) cc_final: 0.7640 (mm) REVERT: A 277 ILE cc_start: 0.7164 (pt) cc_final: 0.6798 (pt) REVERT: A 312 MET cc_start: 0.7410 (mmt) cc_final: 0.6869 (mmt) REVERT: A 330 MET cc_start: 0.5895 (mmp) cc_final: 0.5412 (mmt) outliers start: 20 outliers final: 16 residues processed: 205 average time/residue: 0.0989 time to fit residues: 28.0651 Evaluate side-chains 197 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 136 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN B 188 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.184436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144671 restraints weight = 10677.171| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.09 r_work: 0.3322 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9121 Z= 0.184 Angle : 0.685 14.981 12335 Z= 0.348 Chirality : 0.046 0.291 1402 Planarity : 0.004 0.066 1546 Dihedral : 5.627 59.603 1270 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 2.26 % Allowed : 21.81 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.25), residues: 1121 helix: 1.73 (0.26), residues: 402 sheet: -0.68 (0.31), residues: 279 loop : -1.58 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 252 TYR 0.025 0.002 TYR S 178 PHE 0.018 0.002 PHE B 354 TRP 0.015 0.002 TRP B 258 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 9116) covalent geometry : angle 0.67404 / 0.34 (12325) SS BOND : bond 0.00902 / 0.37 ( 5) SS BOND : angle 4.42961 / 2.18 ( 10) hydrogen bonds : bond 0.03938 / 2.65 ( 449) hydrogen bonds : angle 4.81555 / 3.29 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.303 Fit side-chains REVERT: S 18 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7702 (tpp-160) REVERT: S 19 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7379 (mtmm) REVERT: S 65 LYS cc_start: 0.8524 (tptp) cc_final: 0.7819 (tppt) REVERT: B 14 GLU cc_start: 0.8180 (tt0) cc_final: 0.7783 (tt0) REVERT: C 118 ASP cc_start: 0.8126 (p0) cc_final: 0.7897 (p0) REVERT: A 104 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6754 (mp) REVERT: A 252 ARG cc_start: 0.5003 (ttp80) cc_final: 0.4667 (tmt-80) REVERT: A 312 MET cc_start: 0.7687 (mmt) cc_final: 0.7111 (mmt) outliers start: 22 outliers final: 21 residues processed: 195 average time/residue: 0.0834 time to fit residues: 22.6138 Evaluate side-chains 200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 136 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 130 GLN B 188 HIS A 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.186536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.146516 restraints weight = 10515.653| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.02 r_work: 0.3353 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9121 Z= 0.151 Angle : 0.668 15.516 12335 Z= 0.338 Chirality : 0.045 0.297 1402 Planarity : 0.004 0.065 1546 Dihedral : 5.528 57.665 1270 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 2.47 % Allowed : 22.02 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.26 (0.25), residues: 1121 helix: 1.65 (0.26), residues: 408 sheet: -0.67 (0.31), residues: 279 loop : -1.59 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 252 TYR 0.026 0.002 TYR S 178 PHE 0.024 0.002 PHE B 354 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9116) covalent geometry : angle 0.65502 / 0.33 (12325) SS BOND : bond 0.00784 / 0.32 ( 5) SS BOND : angle 4.57087 / 2.23 ( 10) hydrogen bonds : bond 0.03782 / 2.52 ( 449) hydrogen bonds : angle 4.78833 / 3.27 ( 1269) =============================================================================== Job complete usr+sys time: 2202.58 seconds wall clock time: 38 minutes 38.46 seconds (2318.46 seconds total)