Starting phenix.real_space_refine on Fri Oct 10 15:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4p_36889/10_2025/8k4p_36889.cif" } resolution = 2.81 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= -0.001 sd= 0.047 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 54 5.16 5 C 4600 2.51 5 N 1250 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7231 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2345 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1867 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Time building chain proxies: 1.91, per 1000 atoms: 0.26 Number of scatterers: 7231 At special positions: 0 Unit cell: (78.2, 102.85, 136.85, 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 54 16.00 O 1327 8.00 N 1250 7.00 C 4600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 196 " distance=2.04 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: 0.72 Conformation dependent library (CDL) restraints added in 416.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 44.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.633A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.657A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.693A pdb=" N LEU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 149 removed outlier: 4.024A pdb=" N CYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 183 removed outlier: 4.305A pdb=" N GLY A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 221 through 239 removed outlier: 3.626A pdb=" N VAL A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 279 removed outlier: 3.815A pdb=" N GLY A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 287 through 318 removed outlier: 3.789A pdb=" N LEU A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Proline residue: A 311 - end of helix removed outlier: 4.025A pdb=" N GLY A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.520A pdb=" N ARG A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 removed outlier: 3.659A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.529A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.739A pdb=" N GLU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.195A pdb=" N TYR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.875A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.512A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.862A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.656A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.871A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.658A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.136A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.551A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.961A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.647A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.790A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 190 removed outlier: 6.249A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1020 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: 0.93 Time building geometry restraints manager: 0.95 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: 1363 1.33 - 1.45: 1837 1.45 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7367 Sorted by residual: bond pdb=" CA ARG C 24 " pdb=" C ARG C 24 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.37e-02 5.33e+03 9.33e+00 bond pdb=" CA MET C 18 " pdb=" CB MET C 18 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.66e-02 3.63e+03 7.70e+00 bond pdb=" CA LYS C 280 " pdb=" C LYS C 280 " ideal model delta sigma weight residual 1.524 1.506 0.018 7.00e-03 2.04e+04 6.89e+00 bond pdb=" C MET C 18 " pdb=" O MET C 18 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.26e-02 6.30e+03 6.81e+00 bond pdb=" C ARG C 24 " pdb=" O ARG C 24 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.29e-02 6.01e+03 6.77e+00 ... (remaining 7362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 9736 1.61 - 3.23: 189 3.23 - 4.84: 33 4.84 - 6.46: 7 6.46 - 8.07: 4 Bond angle restraints: 9969 Sorted by residual: angle pdb=" N ARG A 185 " pdb=" CA ARG A 185 " pdb=" C ARG A 185 " ideal model delta sigma weight residual 110.43 103.69 6.74 1.31e+00 5.83e-01 2.65e+01 angle pdb=" C SER A 285 " pdb=" N CYS A 286 " pdb=" CA CYS A 286 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C LYS C 280 " pdb=" CA LYS C 280 " pdb=" CB LYS C 280 " ideal model delta sigma weight residual 111.65 106.72 4.93 1.44e+00 4.82e-01 1.17e+01 angle pdb=" O LEU C 23 " pdb=" C LEU C 23 " pdb=" N ARG C 24 " ideal model delta sigma weight residual 122.12 118.92 3.20 1.06e+00 8.90e-01 9.13e+00 angle pdb=" CA ILE A 282 " pdb=" CB ILE A 282 " pdb=" CG1 ILE A 282 " ideal model delta sigma weight residual 110.40 115.28 -4.88 1.70e+00 3.46e-01 8.23e+00 ... (remaining 9964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3707 17.13 - 34.26: 504 34.26 - 51.38: 140 51.38 - 68.51: 32 68.51 - 85.64: 12 Dihedral angle restraints: 4395 sinusoidal: 1724 harmonic: 2671 Sorted by residual: dihedral pdb=" CA LEU C 268 " pdb=" C LEU C 268 " pdb=" N ASN C 269 " pdb=" CA ASN C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 195 " pdb=" C MET A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE A 112 " pdb=" C ILE A 112 " pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 801 0.038 - 0.076: 262 0.076 - 0.114: 70 0.114 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA VAL A 310 " pdb=" N VAL A 310 " pdb=" C VAL A 310 " pdb=" CB VAL A 310 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA TRP A 154 " pdb=" N TRP A 154 " pdb=" C TRP A 154 " pdb=" CB TRP A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE C 265 " pdb=" N ILE C 265 " pdb=" C ILE C 265 " pdb=" CB ILE C 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1146 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 310 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 311 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 242 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LYS A 242 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS A 242 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 243 " -0.010 2.00e-02 2.50e+03 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 124 2.68 - 3.23: 6676 3.23 - 3.79: 10460 3.79 - 4.34: 14814 4.34 - 4.90: 24949 Nonbonded interactions: 57023 Sorted by model distance: nonbonded pdb=" OG SER A 99 " pdb=" OE2 GLU A 121 " model vdw 2.120 3.040 nonbonded pdb=" OD1 ASN A 61 " pdb=" OG SER A 93 " model vdw 2.145 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 176 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" O CYS A 196 " model vdw 2.246 3.120 ... (remaining 57018 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: 2.510 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: 8.400 Find NCS groups from input model: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.003 0.046 7368 Z= 0.158 Angle : 0.580 8.070 9971 Z= 0.326 Chirality : 0.041 0.189 1149 Planarity : 0.004 0.061 1255 Dihedral : 17.491 85.640 2664 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 27.88 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.27), residues: 908 helix: 1.07 (0.27), residues: 369 sheet: 1.15 (0.38), residues: 174 loop : -1.66 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.010 0.001 TYR A 128 PHE 0.013 0.001 PHE A 329 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7367) covalent geometry : angle 0.57933 ( 9969) SS BOND : bond 0.00931 ( 1) SS BOND : angle 2.27828 ( 2) hydrogen bonds : bond 0.17358 ( 348) hydrogen bonds : angle 5.95712 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.4125 (ttt) cc_final: 0.3760 (ppp) REVERT: C 18 MET cc_start: 0.7522 (ttp) cc_final: 0.7259 (ttp) REVERT: C 24 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7175 (ptp90) REVERT: C 29 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7482 (tttm) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.6206 time to fit residues: 69.0509 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 332 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127975 restraints weight = 8240.723| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.34 r_work: 0.3275 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7368 Z= 0.259 Angle : 0.664 9.047 9971 Z= 0.353 Chirality : 0.046 0.175 1149 Planarity : 0.005 0.047 1255 Dihedral : 6.340 59.557 1023 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.73 % Allowed : 21.42 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.27), residues: 908 helix: 1.21 (0.27), residues: 385 sheet: 1.08 (0.39), residues: 162 loop : -1.97 (0.26), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 183 TYR 0.016 0.001 TYR A 128 PHE 0.022 0.002 PHE A 134 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 7367) covalent geometry : angle 0.66316 ( 9969) SS BOND : bond 0.01241 ( 1) SS BOND : angle 2.80537 ( 2) hydrogen bonds : bond 0.06431 ( 348) hydrogen bonds : angle 4.42004 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 83 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.8436 (t0) cc_final: 0.8201 (t0) REVERT: A 121 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: A 190 VAL cc_start: 0.2165 (OUTLIER) cc_final: 0.1814 (t) REVERT: A 203 MET cc_start: 0.4224 (ttt) cc_final: 0.3781 (ppp) REVERT: A 273 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7213 (tt) REVERT: C 18 MET cc_start: 0.8009 (ttp) cc_final: 0.7741 (ttp) REVERT: C 24 ARG cc_start: 0.7722 (ptm160) cc_final: 0.7245 (ptp90) REVERT: C 233 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7581 (p) outliers start: 61 outliers final: 24 residues processed: 129 average time/residue: 0.5833 time to fit residues: 79.2761 Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN A 303 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131670 restraints weight = 8142.676| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.18 r_work: 0.3349 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7368 Z= 0.122 Angle : 0.514 6.746 9971 Z= 0.275 Chirality : 0.040 0.154 1149 Planarity : 0.004 0.044 1255 Dihedral : 5.703 57.191 1012 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.08 % Allowed : 22.94 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.27), residues: 908 helix: 1.76 (0.27), residues: 384 sheet: 1.20 (0.38), residues: 165 loop : -2.00 (0.26), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.009 0.001 TYR A 128 PHE 0.019 0.001 PHE A 134 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7367) covalent geometry : angle 0.51260 ( 9969) SS BOND : bond 0.00920 ( 1) SS BOND : angle 2.59723 ( 2) hydrogen bonds : bond 0.04441 ( 348) hydrogen bonds : angle 3.92041 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: B 258 ASP cc_start: 0.8354 (t0) cc_final: 0.8130 (t0) REVERT: A 106 MET cc_start: 0.6808 (tpt) cc_final: 0.6281 (tmm) REVERT: A 121 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5738 (tp30) REVERT: A 190 VAL cc_start: 0.1927 (OUTLIER) cc_final: 0.1610 (t) REVERT: A 203 MET cc_start: 0.4395 (ttt) cc_final: 0.3903 (ppp) REVERT: A 244 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8110 (mm-40) REVERT: A 247 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7271 (mtm-85) REVERT: A 273 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7207 (tt) REVERT: C 18 MET cc_start: 0.7741 (ttp) cc_final: 0.7418 (tmm) REVERT: C 24 ARG cc_start: 0.7381 (ptm160) cc_final: 0.6999 (ptp90) REVERT: C 233 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7554 (p) outliers start: 48 outliers final: 18 residues processed: 118 average time/residue: 0.5967 time to fit residues: 74.1451 Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 327 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.174232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122619 restraints weight = 8253.897| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.20 r_work: 0.3312 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7368 Z= 0.146 Angle : 0.531 6.759 9971 Z= 0.283 Chirality : 0.041 0.158 1149 Planarity : 0.004 0.045 1255 Dihedral : 5.568 58.578 1010 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.08 % Allowed : 22.43 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.28), residues: 908 helix: 1.92 (0.28), residues: 384 sheet: 1.16 (0.38), residues: 165 loop : -1.99 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.012 0.001 TYR A 128 PHE 0.017 0.002 PHE A 134 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7367) covalent geometry : angle 0.52990 ( 9969) SS BOND : bond 0.00894 ( 1) SS BOND : angle 2.30671 ( 2) hydrogen bonds : bond 0.04660 ( 348) hydrogen bonds : angle 3.87775 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.8344 (t0) cc_final: 0.8127 (t0) REVERT: B 336 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8483 (mt) REVERT: A 106 MET cc_start: 0.6838 (tpt) cc_final: 0.6328 (tmm) REVERT: A 121 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5679 (tp30) REVERT: A 183 ARG cc_start: 0.4964 (ttm-80) cc_final: 0.4332 (ttm170) REVERT: A 190 VAL cc_start: 0.1644 (OUTLIER) cc_final: 0.1375 (t) REVERT: A 203 MET cc_start: 0.4284 (ttt) cc_final: 0.3842 (ppp) REVERT: A 242 LYS cc_start: 0.8064 (tttt) cc_final: 0.7861 (tttm) REVERT: A 247 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7278 (mtm-85) REVERT: C 18 MET cc_start: 0.7861 (ttp) cc_final: 0.7446 (tmm) REVERT: C 24 ARG cc_start: 0.7383 (ptm160) cc_final: 0.6982 (ptp90) REVERT: C 233 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7464 (p) outliers start: 48 outliers final: 23 residues processed: 119 average time/residue: 0.6037 time to fit residues: 75.5797 Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129606 restraints weight = 8224.434| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.22 r_work: 0.3326 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7368 Z= 0.155 Angle : 0.532 6.749 9971 Z= 0.285 Chirality : 0.041 0.157 1149 Planarity : 0.004 0.045 1255 Dihedral : 5.524 56.618 1010 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.70 % Allowed : 23.19 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 908 helix: 1.94 (0.28), residues: 385 sheet: 1.13 (0.39), residues: 165 loop : -1.97 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 333 TYR 0.012 0.001 TYR A 128 PHE 0.016 0.002 PHE A 134 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7367) covalent geometry : angle 0.53145 ( 9969) SS BOND : bond 0.00846 ( 1) SS BOND : angle 2.19065 ( 2) hydrogen bonds : bond 0.04678 ( 348) hydrogen bonds : angle 3.87895 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 82 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7752 (mtm180) REVERT: B 258 ASP cc_start: 0.8378 (t0) cc_final: 0.8158 (t0) REVERT: B 336 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 106 MET cc_start: 0.6955 (tpt) cc_final: 0.6459 (tmm) REVERT: A 121 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: A 175 LEU cc_start: 0.7549 (mt) cc_final: 0.7309 (mp) REVERT: A 183 ARG cc_start: 0.4974 (ttm-80) cc_final: 0.4500 (ttm170) REVERT: A 190 VAL cc_start: 0.1677 (OUTLIER) cc_final: 0.1425 (t) REVERT: A 203 MET cc_start: 0.4276 (ttt) cc_final: 0.3703 (ppp) REVERT: A 242 LYS cc_start: 0.8120 (tttt) cc_final: 0.7898 (tttm) REVERT: A 247 ARG cc_start: 0.8081 (ptm160) cc_final: 0.7338 (mtm-85) REVERT: C 18 MET cc_start: 0.7882 (ttp) cc_final: 0.7479 (tmm) REVERT: C 24 ARG cc_start: 0.7445 (ptm160) cc_final: 0.7058 (ptp90) REVERT: C 233 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7514 (p) REVERT: C 249 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8175 (tt) REVERT: C 298 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7195 (tm-30) outliers start: 45 outliers final: 23 residues processed: 116 average time/residue: 0.5912 time to fit residues: 72.3290 Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 2 optimal weight: 0.0170 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.175939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132201 restraints weight = 8207.753| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.18 r_work: 0.3363 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7368 Z= 0.111 Angle : 0.487 6.909 9971 Z= 0.261 Chirality : 0.040 0.140 1149 Planarity : 0.003 0.042 1255 Dihedral : 4.993 55.364 1008 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.07 % Allowed : 23.95 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.28), residues: 908 helix: 2.17 (0.28), residues: 386 sheet: 1.18 (0.38), residues: 166 loop : -1.93 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.009 0.001 TYR A 128 PHE 0.015 0.001 PHE A 134 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7367) covalent geometry : angle 0.48635 ( 9969) SS BOND : bond 0.00718 ( 1) SS BOND : angle 2.06777 ( 2) hydrogen bonds : bond 0.03924 ( 348) hydrogen bonds : angle 3.70189 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.276 Fit side-chains REVERT: B 258 ASP cc_start: 0.8346 (t0) cc_final: 0.8120 (t0) REVERT: B 336 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 106 MET cc_start: 0.6986 (tpt) cc_final: 0.6475 (tmm) REVERT: A 175 LEU cc_start: 0.7412 (mt) cc_final: 0.7140 (mp) REVERT: A 183 ARG cc_start: 0.5079 (ttm-80) cc_final: 0.4597 (ttm170) REVERT: A 190 VAL cc_start: 0.1695 (OUTLIER) cc_final: 0.1438 (t) REVERT: A 195 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.4102 (tpt) REVERT: A 203 MET cc_start: 0.4210 (ttt) cc_final: 0.3763 (ppp) REVERT: A 242 LYS cc_start: 0.8160 (tttt) cc_final: 0.7797 (tttp) REVERT: C 18 MET cc_start: 0.7833 (ttp) cc_final: 0.7446 (tmm) REVERT: C 24 ARG cc_start: 0.7328 (ptm160) cc_final: 0.6954 (ptp90) REVERT: C 233 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 249 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8126 (tt) REVERT: C 279 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7349 (mtpt) outliers start: 40 outliers final: 19 residues processed: 113 average time/residue: 0.6241 time to fit residues: 74.2039 Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130251 restraints weight = 8293.734| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.27 r_work: 0.3324 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7368 Z= 0.138 Angle : 0.512 7.057 9971 Z= 0.272 Chirality : 0.041 0.152 1149 Planarity : 0.003 0.043 1255 Dihedral : 4.507 41.410 1003 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.94 % Allowed : 23.95 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 908 helix: 2.16 (0.28), residues: 386 sheet: 1.12 (0.38), residues: 166 loop : -1.91 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.011 0.001 TYR A 128 PHE 0.014 0.001 PHE C 189 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7367) covalent geometry : angle 0.51142 ( 9969) SS BOND : bond 0.00767 ( 1) SS BOND : angle 1.82415 ( 2) hydrogen bonds : bond 0.04310 ( 348) hydrogen bonds : angle 3.75543 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.293 Fit side-chains REVERT: B 46 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7755 (mtm180) REVERT: B 258 ASP cc_start: 0.8438 (t0) cc_final: 0.8220 (t0) REVERT: B 301 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7035 (mtpt) REVERT: B 336 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 106 MET cc_start: 0.6907 (tpt) cc_final: 0.6477 (tmm) REVERT: A 175 LEU cc_start: 0.7506 (mt) cc_final: 0.7212 (mp) REVERT: A 183 ARG cc_start: 0.5240 (ttm-80) cc_final: 0.4726 (ttm170) REVERT: A 190 VAL cc_start: 0.1549 (OUTLIER) cc_final: 0.1307 (t) REVERT: A 203 MET cc_start: 0.4337 (ttt) cc_final: 0.3790 (ppp) REVERT: A 242 LYS cc_start: 0.8185 (tttt) cc_final: 0.7819 (tttp) REVERT: C 18 MET cc_start: 0.7941 (ttp) cc_final: 0.7550 (tmm) REVERT: C 24 ARG cc_start: 0.7492 (ptm160) cc_final: 0.7126 (ptp90) REVERT: C 233 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7495 (p) REVERT: C 249 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8211 (tt) outliers start: 39 outliers final: 21 residues processed: 108 average time/residue: 0.5689 time to fit residues: 64.8259 Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 49 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.0270 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133622 restraints weight = 8270.755| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.18 r_work: 0.3382 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7368 Z= 0.095 Angle : 0.468 6.804 9971 Z= 0.249 Chirality : 0.039 0.140 1149 Planarity : 0.003 0.041 1255 Dihedral : 4.220 41.720 1003 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.80 % Allowed : 24.97 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.28), residues: 908 helix: 2.36 (0.28), residues: 386 sheet: 1.20 (0.38), residues: 166 loop : -1.87 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.008 0.001 TYR A 128 PHE 0.013 0.001 PHE C 189 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7367) covalent geometry : angle 0.46697 ( 9969) SS BOND : bond 0.00646 ( 1) SS BOND : angle 2.01645 ( 2) hydrogen bonds : bond 0.03458 ( 348) hydrogen bonds : angle 3.55534 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.293 Fit side-chains REVERT: B 46 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7684 (mtm180) REVERT: B 325 MET cc_start: 0.8966 (mmt) cc_final: 0.8536 (mmt) REVERT: A 106 MET cc_start: 0.6753 (tpt) cc_final: 0.6316 (tmm) REVERT: A 175 LEU cc_start: 0.7443 (mt) cc_final: 0.7165 (mp) REVERT: A 183 ARG cc_start: 0.5115 (ttm-80) cc_final: 0.4520 (ttm170) REVERT: A 190 VAL cc_start: 0.1582 (OUTLIER) cc_final: 0.1327 (t) REVERT: A 203 MET cc_start: 0.4412 (ttt) cc_final: 0.3755 (ppp) REVERT: A 242 LYS cc_start: 0.8126 (tttt) cc_final: 0.7735 (tttp) REVERT: C 18 MET cc_start: 0.7789 (ttp) cc_final: 0.7400 (tmm) REVERT: C 24 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6925 (ptp90) REVERT: C 233 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7421 (p) REVERT: C 249 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8100 (tt) REVERT: C 279 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7406 (mtpt) outliers start: 30 outliers final: 18 residues processed: 106 average time/residue: 0.5870 time to fit residues: 65.6909 Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129449 restraints weight = 8010.032| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.20 r_work: 0.3495 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7368 Z= 0.096 Angle : 0.464 7.090 9971 Z= 0.247 Chirality : 0.039 0.140 1149 Planarity : 0.003 0.040 1255 Dihedral : 4.066 40.718 1003 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.17 % Allowed : 25.22 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.28), residues: 908 helix: 2.51 (0.28), residues: 386 sheet: 1.11 (0.38), residues: 168 loop : -1.88 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.008 0.001 TYR A 128 PHE 0.013 0.001 PHE C 189 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7367) covalent geometry : angle 0.46351 ( 9969) SS BOND : bond 0.00659 ( 1) SS BOND : angle 1.87384 ( 2) hydrogen bonds : bond 0.03395 ( 348) hydrogen bonds : angle 3.49644 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.335 Fit side-chains REVERT: A 106 MET cc_start: 0.6649 (tpt) cc_final: 0.6407 (tmm) REVERT: A 175 LEU cc_start: 0.6969 (mt) cc_final: 0.6695 (mp) REVERT: A 183 ARG cc_start: 0.4956 (ttm-80) cc_final: 0.4470 (ttm170) REVERT: A 190 VAL cc_start: 0.1703 (OUTLIER) cc_final: 0.1410 (t) REVERT: A 203 MET cc_start: 0.4451 (ttt) cc_final: 0.3816 (ppp) REVERT: A 242 LYS cc_start: 0.7948 (tttt) cc_final: 0.7517 (tttp) REVERT: C 18 MET cc_start: 0.7303 (ttp) cc_final: 0.6862 (tmm) REVERT: C 24 ARG cc_start: 0.6933 (ptm160) cc_final: 0.6508 (ptp90) REVERT: C 233 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7281 (p) REVERT: C 249 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7661 (tt) REVERT: C 279 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7310 (mtpt) outliers start: 25 outliers final: 16 residues processed: 99 average time/residue: 0.6282 time to fit residues: 65.4824 Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.0000 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123553 restraints weight = 8147.939| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.28 r_work: 0.3340 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7368 Z= 0.096 Angle : 0.461 6.854 9971 Z= 0.245 Chirality : 0.039 0.141 1149 Planarity : 0.003 0.040 1255 Dihedral : 4.008 40.493 1003 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.79 % Allowed : 26.24 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.28), residues: 908 helix: 2.56 (0.28), residues: 386 sheet: 1.13 (0.38), residues: 168 loop : -1.86 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.009 0.001 TYR B 124 PHE 0.013 0.001 PHE C 189 TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7367) covalent geometry : angle 0.46075 ( 9969) SS BOND : bond 0.00632 ( 1) SS BOND : angle 1.85167 ( 2) hydrogen bonds : bond 0.03337 ( 348) hydrogen bonds : angle 3.46396 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.286 Fit side-chains REVERT: A 56 LEU cc_start: 0.8041 (mp) cc_final: 0.7840 (mp) REVERT: A 106 MET cc_start: 0.6713 (tpt) cc_final: 0.6489 (tmm) REVERT: A 175 LEU cc_start: 0.7201 (mt) cc_final: 0.6882 (mp) REVERT: A 183 ARG cc_start: 0.5026 (ttm-80) cc_final: 0.4540 (ttm170) REVERT: A 190 VAL cc_start: 0.1507 (OUTLIER) cc_final: 0.1226 (t) REVERT: A 203 MET cc_start: 0.4214 (ttt) cc_final: 0.3700 (ppp) REVERT: A 242 LYS cc_start: 0.8084 (tttt) cc_final: 0.7673 (tttp) REVERT: C 18 MET cc_start: 0.7748 (ttp) cc_final: 0.7319 (tmm) REVERT: C 24 ARG cc_start: 0.7284 (ptm160) cc_final: 0.6871 (ptp90) REVERT: C 233 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7422 (p) REVERT: C 249 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8018 (tt) REVERT: C 279 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7351 (mtpt) outliers start: 22 outliers final: 16 residues processed: 97 average time/residue: 0.6151 time to fit residues: 62.9085 Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133489 restraints weight = 8179.790| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.27 r_work: 0.3376 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7368 Z= 0.112 Angle : 0.481 6.827 9971 Z= 0.255 Chirality : 0.040 0.145 1149 Planarity : 0.003 0.041 1255 Dihedral : 4.085 40.501 1002 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.04 % Allowed : 25.73 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.28), residues: 908 helix: 2.52 (0.28), residues: 386 sheet: 1.18 (0.38), residues: 166 loop : -1.87 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.010 0.001 TYR A 128 PHE 0.014 0.001 PHE C 189 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7367) covalent geometry : angle 0.48073 ( 9969) SS BOND : bond 0.00662 ( 1) SS BOND : angle 1.77485 ( 2) hydrogen bonds : bond 0.03735 ( 348) hydrogen bonds : angle 3.54588 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.05 seconds wall clock time: 53 minutes 35.63 seconds (3215.63 seconds total)