Starting phenix.real_space_refine on Wed Jul 30 04:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.map" model { file = "/net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efo_28086/07_2025/8efo_28086.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.003 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 100 5.16 5 C 7618 2.51 5 N 1900 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" 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: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {'8QY': 1, 'CLR': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 137 Unusual residues: {'8QY': 1, 'CLR': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.45, per 1000 atoms: 0.64 Number of scatterers: 11708 At special positions: 0 Unit cell: (104, 110.24, 149.76, 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 100 16.00 O 2090 8.00 N 1900 7.00 C 7618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 49.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'R' and resid 67 through 98 removed outlier: 3.503A pdb=" N VAL R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.613A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.509A pdb=" N ILE R 144 " --> pdb=" O ILE R 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.514A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.166A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 243 Processing helix chain 'R' and resid 243 through 264 Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.574A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.528A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.754A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.811A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.576A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.713A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.946A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'M' and resid 67 through 98 removed outlier: 3.503A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 133 removed outlier: 3.613A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.510A pdb=" N ILE M 144 " --> pdb=" O ILE M 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.513A pdb=" N LEU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 4.166A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 243 Processing helix chain 'M' and resid 243 through 264 Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 339 removed outlier: 3.573A pdb=" N HIS M 321 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 removed outlier: 3.528A pdb=" N CYS M 348 " --> pdb=" O ASN M 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.039A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.508A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.861A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.782A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.247A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.629A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.535A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.492A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.902A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AB7, first strand: chain 'M' and resid 208 through 213 667 hydrogen bonds defined for protein. 1932 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: 3.70 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2738 1.33 - 1.46: 2741 1.46 - 1.58: 6358 1.58 - 1.70: 0 1.70 - 1.83: 149 Bond restraints: 11986 Sorted by residual: bond pdb=" C19 8QY M 401 " pdb=" O20 8QY M 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" C19 8QY R 401 " pdb=" O20 8QY R 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C02 8QY M 401 " pdb=" N12 8QY M 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C02 8QY R 401 " pdb=" N12 8QY R 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.94e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15623 1.92 - 3.84: 580 3.84 - 5.76: 84 5.76 - 7.68: 22 7.68 - 9.60: 1 Bond angle restraints: 16310 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 120.63 126.54 -5.91 1.61e+00 3.86e-01 1.35e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 128.08 -4.61 1.53e+00 4.27e-01 9.08e+00 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.23 114.59 -4.36 1.45e+00 4.76e-01 9.03e+00 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 7045 11.90 - 23.80: 405 23.80 - 35.71: 74 35.71 - 47.61: 34 47.61 - 59.51: 23 Dihedral angle restraints: 7581 sinusoidal: 3368 harmonic: 4213 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS R 142 " pdb=" SG CYS R 142 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 124.29 -31.29 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 7578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1695 0.086 - 0.172: 169 0.172 - 0.259: 24 0.259 - 0.345: 10 0.345 - 0.431: 10 Chirality restraints: 1908 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1905 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " -0.008 2.00e-02 2.50e+03 1.37e-02 4.71e+00 pdb=" CG TRP E 111 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ILE B 232 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 232 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 233 " 0.011 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1734 2.77 - 3.30: 11006 3.30 - 3.84: 19649 3.84 - 4.37: 23130 4.37 - 4.90: 40050 Nonbonded interactions: 95569 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.241 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.323 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.331 3.040 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.336 3.040 ... (remaining 95564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'R' and (resid 66 through 352 or resid 401 through 405)) } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.160 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 0.052 11989 Z= 0.224 Angle : 0.852 9.597 16316 Z= 0.452 Chirality : 0.065 0.431 1908 Planarity : 0.005 0.053 1965 Dihedral : 9.172 59.509 4848 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1423 helix: -0.48 (0.16), residues: 629 sheet: 0.09 (0.30), residues: 263 loop : -0.95 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 111 HIS 0.010 0.002 HIS E 35 PHE 0.020 0.002 PHE B 234 TYR 0.022 0.002 TYR M 254 ARG 0.008 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.25504 ( 667) hydrogen bonds : angle 8.36308 ( 1932) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.18907 ( 6) covalent geometry : bond 0.00436 (11986) covalent geometry : angle 0.85155 (16310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 231 GLU cc_start: 0.7684 (tt0) cc_final: 0.7461 (tt0) REVERT: A 272 ASP cc_start: 0.7709 (p0) cc_final: 0.7439 (p0) REVERT: A 290 TYR cc_start: 0.6417 (t80) cc_final: 0.6061 (t80) REVERT: B 44 GLN cc_start: 0.6884 (mt0) cc_final: 0.6420 (pp30) REVERT: B 188 MET cc_start: 0.7762 (mmm) cc_final: 0.7537 (mmm) outliers start: 0 outliers final: 1 residues processed: 371 average time/residue: 1.2185 time to fit residues: 488.3822 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 128 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN C 18 GLN E 77 ASN M 106 ASN M 126 GLN M 173 HIS M 185 ASN M 225 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135554 restraints weight = 15561.526| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.84 r_work: 0.3541 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11989 Z= 0.133 Angle : 0.567 8.418 16316 Z= 0.300 Chirality : 0.042 0.152 1908 Planarity : 0.004 0.040 1965 Dihedral : 7.988 54.278 2249 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.70 % Allowed : 13.49 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1423 helix: 1.64 (0.18), residues: 657 sheet: 0.19 (0.29), residues: 285 loop : -0.68 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.001 PHE A 189 TYR 0.021 0.002 TYR E 191 ARG 0.005 0.000 ARG R 278 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 667) hydrogen bonds : angle 5.18183 ( 1932) SS BOND : bond 0.00691 ( 3) SS BOND : angle 0.54962 ( 6) covalent geometry : bond 0.00282 (11986) covalent geometry : angle 0.56703 (16310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 68 ILE cc_start: 0.7491 (mp) cc_final: 0.7251 (mm) REVERT: R 97 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: R 140 ILE cc_start: 0.8049 (tp) cc_final: 0.7663 (tt) REVERT: R 231 GLU cc_start: 0.8405 (tt0) cc_final: 0.8123 (tt0) REVERT: A 225 VAL cc_start: 0.7268 (p) cc_final: 0.7000 (m) REVERT: A 269 ASN cc_start: 0.8528 (m110) cc_final: 0.8231 (m110) REVERT: B 33 ILE cc_start: 0.6797 (mt) cc_final: 0.6383 (mt) REVERT: B 259 GLN cc_start: 0.6385 (mp10) cc_final: 0.5941 (mp10) REVERT: B 325 MET cc_start: 0.8193 (tpp) cc_final: 0.7833 (tpt) REVERT: B 331 SER cc_start: 0.8753 (t) cc_final: 0.8479 (t) REVERT: C 28 ILE cc_start: 0.7490 (pt) cc_final: 0.7155 (pp) REVERT: E 63 THR cc_start: 0.7828 (t) cc_final: 0.7519 (m) REVERT: M 67 MET cc_start: 0.5368 (tmt) cc_final: 0.4571 (ttm) REVERT: M 86 PHE cc_start: 0.7505 (t80) cc_final: 0.7048 (t80) REVERT: M 97 ARG cc_start: 0.6792 (tpt170) cc_final: 0.6148 (ttt180) REVERT: M 144 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7021 (mp) REVERT: M 278 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6333 (tpt170) REVERT: F 340 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7352 (t) REVERT: F 342 VAL cc_start: 0.8446 (t) cc_final: 0.8217 (p) outliers start: 34 outliers final: 10 residues processed: 255 average time/residue: 1.2116 time to fit residues: 334.3295 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 136 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 18 GLN E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122333 restraints weight = 15723.298| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.96 r_work: 0.3402 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11989 Z= 0.144 Angle : 0.549 10.135 16316 Z= 0.286 Chirality : 0.041 0.145 1908 Planarity : 0.004 0.038 1965 Dihedral : 7.681 56.950 2249 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.70 % Allowed : 15.16 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1423 helix: 2.13 (0.19), residues: 678 sheet: 0.09 (0.28), residues: 309 loop : -0.26 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.013 0.001 PHE A 196 TYR 0.025 0.002 TYR M 130 ARG 0.008 0.001 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 667) hydrogen bonds : angle 4.91670 ( 1932) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.74027 ( 6) covalent geometry : bond 0.00323 (11986) covalent geometry : angle 0.54927 (16310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6788 (ttm-80) REVERT: R 155 THR cc_start: 0.8772 (m) cc_final: 0.8544 (p) REVERT: R 231 GLU cc_start: 0.8467 (tt0) cc_final: 0.8163 (tt0) REVERT: R 282 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7345 (ttt-90) REVERT: A 21 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7674 (ttp-110) REVERT: A 53 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7147 (mtt) REVERT: A 269 ASN cc_start: 0.8560 (m110) cc_final: 0.8228 (m110) REVERT: A 276 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: B 259 GLN cc_start: 0.6710 (mp10) cc_final: 0.6226 (mp10) REVERT: B 325 MET cc_start: 0.8155 (tpp) cc_final: 0.7717 (tpt) REVERT: C 28 ILE cc_start: 0.7502 (pt) cc_final: 0.7126 (pp) REVERT: E 63 THR cc_start: 0.7991 (t) cc_final: 0.7716 (m) REVERT: E 234 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8518 (mt) REVERT: M 86 PHE cc_start: 0.7658 (t80) cc_final: 0.7081 (t80) REVERT: M 97 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6195 (ttt180) REVERT: M 144 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7058 (mp) REVERT: M 206 PHE cc_start: 0.7258 (m-80) cc_final: 0.7036 (m-10) REVERT: M 278 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6284 (tpt-90) REVERT: F 340 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7350 (t) REVERT: F 342 VAL cc_start: 0.8542 (t) cc_final: 0.8297 (p) outliers start: 34 outliers final: 11 residues processed: 223 average time/residue: 1.3861 time to fit residues: 332.4854 Evaluate side-chains 194 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN A 213 HIS B 259 GLN B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121015 restraints weight = 15620.289| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.95 r_work: 0.3363 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11989 Z= 0.138 Angle : 0.533 7.875 16316 Z= 0.278 Chirality : 0.040 0.155 1908 Planarity : 0.004 0.043 1965 Dihedral : 7.366 55.881 2249 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.81 % Allowed : 15.79 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1423 helix: 2.28 (0.19), residues: 676 sheet: 0.13 (0.30), residues: 283 loop : -0.23 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.016 0.002 TYR M 130 ARG 0.010 0.001 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 667) hydrogen bonds : angle 4.83860 ( 1932) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.58249 ( 6) covalent geometry : bond 0.00312 (11986) covalent geometry : angle 0.53303 (16310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7965 (m-10) cc_final: 0.7589 (m-10) REVERT: R 97 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6853 (ttm-80) REVERT: R 147 SER cc_start: 0.8750 (t) cc_final: 0.8466 (p) REVERT: R 155 THR cc_start: 0.8804 (m) cc_final: 0.8543 (p) REVERT: R 210 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8139 (p) REVERT: R 211 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: R 231 GLU cc_start: 0.8440 (tt0) cc_final: 0.8143 (tt0) REVERT: A 269 ASN cc_start: 0.8556 (m110) cc_final: 0.8157 (m110) REVERT: A 276 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: B 146 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8594 (tp) REVERT: B 259 GLN cc_start: 0.6866 (mp-120) cc_final: 0.6345 (mp10) REVERT: B 325 MET cc_start: 0.8180 (tpp) cc_final: 0.7788 (tpt) REVERT: B 331 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8688 (t) REVERT: C 28 ILE cc_start: 0.7561 (pt) cc_final: 0.7177 (pp) REVERT: E 63 THR cc_start: 0.8024 (t) cc_final: 0.7703 (m) REVERT: M 67 MET cc_start: 0.5437 (tmt) cc_final: 0.4841 (ttm) REVERT: M 86 PHE cc_start: 0.7697 (t80) cc_final: 0.7162 (t80) REVERT: M 97 ARG cc_start: 0.6710 (tpt170) cc_final: 0.6490 (ttt90) REVERT: M 120 THR cc_start: 0.8262 (m) cc_final: 0.8049 (p) REVERT: M 144 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7032 (mp) REVERT: M 206 PHE cc_start: 0.7255 (m-80) cc_final: 0.7018 (m-10) REVERT: M 278 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6364 (tpt-90) REVERT: F 340 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7381 (t) REVERT: F 341 ASP cc_start: 0.8105 (t0) cc_final: 0.7337 (m-30) REVERT: F 342 VAL cc_start: 0.8589 (t) cc_final: 0.8311 (p) outliers start: 48 outliers final: 16 residues processed: 225 average time/residue: 1.2358 time to fit residues: 300.8359 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 101 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN A 22 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 18 GLN E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121439 restraints weight = 15693.495| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.91 r_work: 0.3353 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11989 Z= 0.138 Angle : 0.530 8.869 16316 Z= 0.275 Chirality : 0.040 0.151 1908 Planarity : 0.004 0.036 1965 Dihedral : 7.130 56.224 2249 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.49 % Allowed : 17.14 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1423 helix: 2.41 (0.19), residues: 676 sheet: 0.05 (0.30), residues: 285 loop : -0.18 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.016 0.001 TYR M 130 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 667) hydrogen bonds : angle 4.80980 ( 1932) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.67191 ( 6) covalent geometry : bond 0.00313 (11986) covalent geometry : angle 0.53014 (16310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7990 (m-10) cc_final: 0.7643 (m-10) REVERT: R 146 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (mm) REVERT: R 210 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8219 (p) REVERT: R 211 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7628 (mtpp) REVERT: R 231 GLU cc_start: 0.8518 (tt0) cc_final: 0.8180 (tt0) REVERT: R 282 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7362 (ttt-90) REVERT: A 21 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7710 (ttp-110) REVERT: A 269 ASN cc_start: 0.8578 (m110) cc_final: 0.8259 (m110) REVERT: A 276 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: B 146 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 259 GLN cc_start: 0.6695 (mp-120) cc_final: 0.6168 (mp10) REVERT: B 325 MET cc_start: 0.8134 (tpp) cc_final: 0.7668 (tpt) REVERT: B 331 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8741 (t) REVERT: C 28 ILE cc_start: 0.7502 (pt) cc_final: 0.7125 (pp) REVERT: E 5 VAL cc_start: 0.7992 (m) cc_final: 0.7684 (p) REVERT: E 63 THR cc_start: 0.8069 (t) cc_final: 0.7754 (m) REVERT: M 86 PHE cc_start: 0.7747 (t80) cc_final: 0.7221 (t80) REVERT: M 97 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6272 (ttt180) REVERT: M 120 THR cc_start: 0.8381 (m) cc_final: 0.8164 (p) REVERT: M 144 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7044 (mp) REVERT: M 206 PHE cc_start: 0.7325 (m-80) cc_final: 0.7048 (m-10) REVERT: M 218 ASP cc_start: 0.7304 (t70) cc_final: 0.6447 (p0) REVERT: M 278 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6185 (tpp80) REVERT: F 340 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7365 (t) REVERT: F 341 ASP cc_start: 0.8085 (t0) cc_final: 0.7331 (m-30) REVERT: F 342 VAL cc_start: 0.8496 (t) cc_final: 0.8218 (p) outliers start: 44 outliers final: 20 residues processed: 240 average time/residue: 1.2175 time to fit residues: 316.4531 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 101 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 121 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 122 optimal weight: 0.0870 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 269 ASN B 156 GLN B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125032 restraints weight = 15807.066| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11989 Z= 0.108 Angle : 0.518 10.018 16316 Z= 0.267 Chirality : 0.039 0.148 1908 Planarity : 0.004 0.036 1965 Dihedral : 6.691 57.380 2249 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.22), residues: 1423 helix: 2.68 (0.19), residues: 663 sheet: 0.04 (0.29), residues: 289 loop : -0.12 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.000 HIS B 62 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR E 191 ARG 0.012 0.001 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 667) hydrogen bonds : angle 4.61715 ( 1932) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.59710 ( 6) covalent geometry : bond 0.00235 (11986) covalent geometry : angle 0.51762 (16310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7967 (m-10) cc_final: 0.7697 (m-10) REVERT: R 146 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (mm) REVERT: R 155 THR cc_start: 0.8876 (m) cc_final: 0.8589 (p) REVERT: R 231 GLU cc_start: 0.8457 (tt0) cc_final: 0.8125 (tt0) REVERT: A 21 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7719 (ttp-110) REVERT: A 269 ASN cc_start: 0.8677 (m-40) cc_final: 0.8300 (m110) REVERT: A 276 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 197 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7218 (mmt180) REVERT: B 259 GLN cc_start: 0.6592 (mp-120) cc_final: 0.6153 (mp10) REVERT: B 325 MET cc_start: 0.8023 (tpp) cc_final: 0.7686 (tpt) REVERT: B 331 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8717 (t) REVERT: C 28 ILE cc_start: 0.7481 (pt) cc_final: 0.7118 (pp) REVERT: C 47 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7218 (mt-10) REVERT: C 62 ARG cc_start: 0.5239 (mtm-85) cc_final: 0.4208 (ttp-110) REVERT: E 63 THR cc_start: 0.8003 (t) cc_final: 0.7596 (m) REVERT: E 83 MET cc_start: 0.7652 (mtm) cc_final: 0.7169 (mtp) REVERT: M 86 PHE cc_start: 0.7738 (t80) cc_final: 0.7251 (t80) REVERT: M 97 ARG cc_start: 0.6807 (tpt170) cc_final: 0.6558 (ttt90) REVERT: M 120 THR cc_start: 0.8302 (m) cc_final: 0.8072 (p) REVERT: M 144 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6900 (mp) REVERT: M 206 PHE cc_start: 0.7266 (m-80) cc_final: 0.6953 (m-10) REVERT: M 209 THR cc_start: 0.6470 (m) cc_final: 0.6141 (p) REVERT: M 218 ASP cc_start: 0.7310 (t70) cc_final: 0.6448 (p0) REVERT: M 266 MET cc_start: 0.5539 (tmm) cc_final: 0.5296 (tpt) REVERT: M 278 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6204 (tpp80) REVERT: F 340 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7309 (t) REVERT: F 341 ASP cc_start: 0.7995 (t0) cc_final: 0.7228 (m-30) REVERT: F 342 VAL cc_start: 0.8476 (t) cc_final: 0.8196 (p) outliers start: 30 outliers final: 12 residues processed: 224 average time/residue: 1.3018 time to fit residues: 314.0641 Evaluate side-chains 210 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115461 restraints weight = 15869.474| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.88 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11989 Z= 0.214 Angle : 0.605 10.120 16316 Z= 0.313 Chirality : 0.043 0.160 1908 Planarity : 0.004 0.036 1965 Dihedral : 7.436 58.909 2249 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.57 % Allowed : 18.73 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1423 helix: 2.35 (0.19), residues: 676 sheet: -0.01 (0.29), residues: 290 loop : -0.28 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS B 62 PHE 0.017 0.002 PHE A 189 TYR 0.014 0.002 TYR E 191 ARG 0.005 0.001 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 667) hydrogen bonds : angle 4.99774 ( 1932) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.74396 ( 6) covalent geometry : bond 0.00500 (11986) covalent geometry : angle 0.60445 (16310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7930 (m-10) cc_final: 0.7701 (m-10) REVERT: R 211 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7689 (mtpp) REVERT: R 231 GLU cc_start: 0.8490 (tt0) cc_final: 0.8137 (tt0) REVERT: R 282 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7403 (ttt-90) REVERT: A 21 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7642 (ttp-110) REVERT: A 245 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: A 269 ASN cc_start: 0.8736 (m-40) cc_final: 0.8361 (m110) REVERT: A 276 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 325 MET cc_start: 0.8109 (tpp) cc_final: 0.7845 (tpt) REVERT: B 331 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8824 (t) REVERT: C 28 ILE cc_start: 0.7517 (pt) cc_final: 0.7158 (pp) REVERT: E 3 GLN cc_start: 0.7808 (mt0) cc_final: 0.7331 (mt0) REVERT: E 63 THR cc_start: 0.8090 (t) cc_final: 0.7749 (m) REVERT: M 97 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6604 (ttt90) REVERT: M 144 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6948 (mp) REVERT: M 184 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7245 (ttp-110) REVERT: M 206 PHE cc_start: 0.7286 (m-80) cc_final: 0.7063 (m-10) REVERT: M 209 THR cc_start: 0.6477 (m) cc_final: 0.6037 (p) REVERT: M 218 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7061 (t70) REVERT: M 278 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6162 (tpp80) REVERT: F 340 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7337 (t) REVERT: F 341 ASP cc_start: 0.8047 (t0) cc_final: 0.7347 (m-30) REVERT: F 342 VAL cc_start: 0.8458 (t) cc_final: 0.8176 (p) outliers start: 45 outliers final: 25 residues processed: 228 average time/residue: 1.3366 time to fit residues: 328.3446 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 205 MET Chi-restraints excluded: chain M residue 218 ASP Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 188 HIS B 259 GLN B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119524 restraints weight = 15768.540| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.87 r_work: 0.3352 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11989 Z= 0.128 Angle : 0.551 10.433 16316 Z= 0.284 Chirality : 0.040 0.146 1908 Planarity : 0.004 0.035 1965 Dihedral : 6.926 59.345 2249 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.78 % Allowed : 20.79 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1423 helix: 2.46 (0.19), residues: 676 sheet: 0.05 (0.31), residues: 265 loop : -0.38 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR M 130 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 667) hydrogen bonds : angle 4.75631 ( 1932) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.75350 ( 6) covalent geometry : bond 0.00287 (11986) covalent geometry : angle 0.55126 (16310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7884 (m-10) cc_final: 0.7670 (m-10) REVERT: R 231 GLU cc_start: 0.8444 (tt0) cc_final: 0.8087 (tt0) REVERT: A 21 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7559 (ttp-110) REVERT: A 269 ASN cc_start: 0.8675 (m-40) cc_final: 0.8296 (m110) REVERT: B 146 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8785 (tp) REVERT: B 325 MET cc_start: 0.7970 (tpp) cc_final: 0.7610 (tpt) REVERT: B 331 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8796 (t) REVERT: C 28 ILE cc_start: 0.7513 (pt) cc_final: 0.7199 (pp) REVERT: C 47 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7318 (mt-10) REVERT: E 3 GLN cc_start: 0.7796 (mt0) cc_final: 0.7419 (mt0) REVERT: E 63 THR cc_start: 0.7971 (t) cc_final: 0.7610 (m) REVERT: E 219 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.6572 (tpp-160) REVERT: M 86 PHE cc_start: 0.7779 (t80) cc_final: 0.7221 (t80) REVERT: M 97 ARG cc_start: 0.6814 (tpt170) cc_final: 0.6482 (ttt90) REVERT: M 144 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6883 (mp) REVERT: M 206 PHE cc_start: 0.7360 (m-80) cc_final: 0.7052 (m-10) REVERT: M 209 THR cc_start: 0.6519 (m) cc_final: 0.6233 (p) REVERT: M 218 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6993 (t70) REVERT: M 278 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6191 (tpp80) REVERT: F 340 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7267 (t) REVERT: F 341 ASP cc_start: 0.7849 (t0) cc_final: 0.7238 (m-30) REVERT: F 342 VAL cc_start: 0.8428 (t) cc_final: 0.8137 (p) outliers start: 35 outliers final: 19 residues processed: 214 average time/residue: 1.3185 time to fit residues: 304.1370 Evaluate side-chains 205 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 218 ASP Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 188 HIS B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118770 restraints weight = 15788.306| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.82 r_work: 0.3336 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11989 Z= 0.145 Angle : 0.568 10.940 16316 Z= 0.292 Chirality : 0.041 0.148 1908 Planarity : 0.004 0.055 1965 Dihedral : 6.893 55.144 2249 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.94 % Allowed : 20.79 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1423 helix: 2.44 (0.19), residues: 676 sheet: -0.02 (0.31), residues: 275 loop : -0.34 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR M 130 ARG 0.015 0.001 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 667) hydrogen bonds : angle 4.79101 ( 1932) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.81072 ( 6) covalent geometry : bond 0.00334 (11986) covalent geometry : angle 0.56767 (16310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 231 GLU cc_start: 0.8508 (tt0) cc_final: 0.8160 (tt0) REVERT: A 21 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7792 (ttp-110) REVERT: A 269 ASN cc_start: 0.8680 (m-40) cc_final: 0.8294 (m110) REVERT: B 44 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: B 325 MET cc_start: 0.8161 (tpp) cc_final: 0.7709 (tpt) REVERT: B 331 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8669 (t) REVERT: C 28 ILE cc_start: 0.7654 (pt) cc_final: 0.7349 (pp) REVERT: C 47 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 3 GLN cc_start: 0.7852 (mt0) cc_final: 0.7498 (mt0) REVERT: E 219 ARG cc_start: 0.6966 (mtm-85) cc_final: 0.6582 (tpp-160) REVERT: M 67 MET cc_start: 0.5452 (tmm) cc_final: 0.4978 (tmt) REVERT: M 97 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6531 (ttt90) REVERT: M 144 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7159 (mp) REVERT: M 206 PHE cc_start: 0.7354 (m-80) cc_final: 0.7119 (m-10) REVERT: M 209 THR cc_start: 0.6553 (m) cc_final: 0.6272 (p) REVERT: M 218 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7039 (t70) REVERT: M 278 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6284 (tpp80) REVERT: F 340 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7413 (t) REVERT: F 341 ASP cc_start: 0.7945 (t0) cc_final: 0.7353 (m-30) REVERT: F 342 VAL cc_start: 0.8557 (t) cc_final: 0.8295 (p) outliers start: 37 outliers final: 25 residues processed: 204 average time/residue: 1.3230 time to fit residues: 290.8697 Evaluate side-chains 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 218 ASP Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 188 HIS ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.148536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120216 restraints weight = 15661.373| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.80 r_work: 0.3353 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11989 Z= 0.130 Angle : 0.564 10.316 16316 Z= 0.288 Chirality : 0.040 0.147 1908 Planarity : 0.004 0.039 1965 Dihedral : 6.687 54.117 2249 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.02 % Allowed : 20.87 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1423 helix: 2.47 (0.19), residues: 676 sheet: -0.07 (0.31), residues: 268 loop : -0.38 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR M 130 ARG 0.012 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 667) hydrogen bonds : angle 4.72072 ( 1932) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.85362 ( 6) covalent geometry : bond 0.00295 (11986) covalent geometry : angle 0.56339 (16310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.8045 (m-10) cc_final: 0.7818 (m-10) REVERT: R 231 GLU cc_start: 0.8513 (tt0) cc_final: 0.8197 (tt0) REVERT: A 21 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7787 (ttp-110) REVERT: A 269 ASN cc_start: 0.8671 (m-40) cc_final: 0.8279 (m110) REVERT: B 44 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: B 331 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8646 (t) REVERT: C 28 ILE cc_start: 0.7667 (pt) cc_final: 0.7386 (pp) REVERT: C 47 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7239 (mt-10) REVERT: E 3 GLN cc_start: 0.7841 (mt0) cc_final: 0.7490 (mt0) REVERT: M 97 ARG cc_start: 0.6795 (tpt170) cc_final: 0.6523 (ttt90) REVERT: M 144 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7170 (mp) REVERT: M 206 PHE cc_start: 0.7285 (m-80) cc_final: 0.7035 (m-10) REVERT: M 209 THR cc_start: 0.6501 (m) cc_final: 0.6237 (p) REVERT: M 218 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7117 (t70) REVERT: M 266 MET cc_start: 0.6126 (tmt) cc_final: 0.5925 (tpt) REVERT: M 278 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6285 (tpp80) REVERT: F 340 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7417 (t) REVERT: F 341 ASP cc_start: 0.7786 (t0) cc_final: 0.7357 (m-30) REVERT: F 342 VAL cc_start: 0.8556 (t) cc_final: 0.8298 (p) outliers start: 38 outliers final: 24 residues processed: 202 average time/residue: 1.6203 time to fit residues: 352.2979 Evaluate side-chains 204 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 218 ASP Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 124 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 ASN A 22 ASN A 188 HIS ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116481 restraints weight = 15711.170| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.80 r_work: 0.3268 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11989 Z= 0.190 Angle : 0.627 10.244 16316 Z= 0.320 Chirality : 0.042 0.151 1908 Planarity : 0.004 0.068 1965 Dihedral : 7.171 57.311 2249 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.86 % Allowed : 21.03 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1423 helix: 2.36 (0.19), residues: 670 sheet: -0.23 (0.31), residues: 270 loop : -0.50 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.015 0.002 TYR M 130 ARG 0.012 0.001 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 667) hydrogen bonds : angle 4.94774 ( 1932) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.84180 ( 6) covalent geometry : bond 0.00442 (11986) covalent geometry : angle 0.62683 (16310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10387.60 seconds wall clock time: 179 minutes 29.75 seconds (10769.75 seconds total)