Starting phenix.real_space_refine on Fri Jul 3 02:43:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f7r_28908/07_2026/8f7r_28908.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 98 5.16 5 C 7615 2.51 5 N 1900 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11697 Number of models: 1 Model: "" Number of chains: 11 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: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Classifications: {'peptide': 4} Link IDs: {'PCIS': 1, 'TRANS': 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Modifications used: {'COO': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: Q Time building chain proxies: 2.82, per 1000 atoms: 0.24 Number of scatterers: 11697 At special positions: 0 Unit cell: (104.8, 108, 147.2, 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 98 16.00 O 2084 8.00 N 1900 7.00 C 7615 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 643.2 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 48.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 68 through 98 Processing helix chain 'R' and resid 103 through 122 removed outlier: 3.915A pdb=" N THR R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.852A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.889A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.512A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.212A 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 264 removed outlier: 3.632A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix 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: 4.041A 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 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.895A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) 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 217 removed outlier: 3.738A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.850A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.655A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.679A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.554A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.609A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 98 Processing helix chain 'M' and resid 103 through 122 removed outlier: 3.914A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.851A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.890A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.512A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.212A 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 264 removed outlier: 3.631A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix 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: 4.041A 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 Processing helix chain 'F' and resid 339 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: 3.535A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.657A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.876A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.680A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.799A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.763A 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: 3.985A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.476A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.726A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.245A 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: 3.586A 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: 3.805A 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: 6.583A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.602A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 653 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3509 1.34 - 1.46: 2327 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11977 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C5 CLR M 405 " pdb=" C6 CLR M 405 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C10 CLR M 401 " pdb=" C9 CLR M 401 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 11972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15627 1.94 - 3.88: 556 3.88 - 5.83: 92 5.83 - 7.77: 19 7.77 - 9.71: 5 Bond angle restraints: 16299 Sorted by residual: angle pdb=" N PRO A 288 " pdb=" CA PRO A 288 " pdb=" CB PRO A 288 " ideal model delta sigma weight residual 103.44 109.80 -6.36 1.12e+00 7.97e-01 3.22e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA PHE P 4 " pdb=" CB PHE P 4 " pdb=" CG PHE P 4 " ideal model delta sigma weight residual 113.80 116.70 -2.90 1.00e+00 1.00e+00 8.39e+00 angle pdb=" CA PHE Q 4 " pdb=" CB PHE Q 4 " pdb=" CG PHE Q 4 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.29e+00 ... (remaining 16294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.61: 6227 9.61 - 19.23: 660 19.23 - 28.84: 72 28.84 - 38.45: 33 38.45 - 48.06: 7 Dihedral angle restraints: 6999 sinusoidal: 2780 harmonic: 4219 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+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 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1706 0.092 - 0.183: 162 0.183 - 0.275: 15 0.275 - 0.367: 11 0.367 - 0.459: 9 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C14 CLR M 401 " pdb=" C13 CLR M 401 " pdb=" C15 CLR M 401 " pdb=" C8 CLR M 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C14 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C15 CLR R 405 " pdb=" C8 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1900 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 236 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 334 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO R 335 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 334 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO M 335 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 335 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 335 " 0.029 5.00e-02 4.00e+02 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2361 2.79 - 3.32: 10374 3.32 - 3.84: 19371 3.84 - 4.37: 21806 4.37 - 4.90: 39164 Nonbonded interactions: 93076 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.260 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.261 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.282 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.329 3.040 ... (remaining 93071 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' } ncs_group { reference = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.005 0.121 11982 Z= 0.270 Angle : 0.840 9.710 16305 Z= 0.443 Chirality : 0.065 0.459 1903 Planarity : 0.006 0.064 1962 Dihedral : 7.821 43.643 4262 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 1421 helix: 0.10 (0.16), residues: 653 sheet: 0.12 (0.31), residues: 276 loop : -1.47 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.022 0.002 TYR R 108 PHE 0.022 0.002 PHE R 349 TRP 0.024 0.003 TRP E 111 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (11977) covalent geometry : angle 0.83930 / 0.44 (16299) SS BOND : bond 0.00415 / 0.21 ( 3) SS BOND : angle 1.87917 / 1.12 ( 6) hydrogen bonds : bond 0.15595 / 10.51 ( 653) hydrogen bonds : angle 6.58147 / 4.75 ( 1890) Misc. bond : bond 0.12118 / 6.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 SER cc_start: 0.7480 (t) cc_final: 0.7261 (m) REVERT: R 195 ILE cc_start: 0.8729 (mt) cc_final: 0.8447 (mm) REVERT: R 200 ILE cc_start: 0.8162 (tp) cc_final: 0.7721 (tp) REVERT: R 212 TYR cc_start: 0.6749 (m-80) cc_final: 0.6296 (m-80) REVERT: A 305 CYS cc_start: 0.6977 (t) cc_final: 0.6498 (t) REVERT: B 198 LEU cc_start: 0.7504 (pp) cc_final: 0.7156 (mt) REVERT: C 18 GLN cc_start: 0.6833 (tp40) cc_final: 0.6279 (mm110) REVERT: E 80 PHE cc_start: 0.6714 (m-80) cc_final: 0.6347 (m-10) REVERT: E 220 LEU cc_start: 0.8039 (tp) cc_final: 0.7828 (tt) REVERT: M 328 TYR cc_start: 0.7241 (m-80) cc_final: 0.6413 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1141 time to fit residues: 45.7727 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 106 ASN A 188 HIS B 91 HIS B 183 HIS B 266 HIS E 168 HIS E 184 GLN M 126 GLN M 173 HIS M 190 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.194734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159829 restraints weight = 13444.720| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.95 r_work: 0.3738 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11982 Z= 0.161 Angle : 0.566 6.183 16305 Z= 0.298 Chirality : 0.041 0.155 1903 Planarity : 0.005 0.051 1962 Dihedral : 4.535 41.254 1655 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.43 % Allowed : 6.34 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1421 helix: 1.71 (0.18), residues: 660 sheet: 0.25 (0.31), residues: 286 loop : -1.00 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.015 0.002 TYR E 191 PHE 0.019 0.002 PHE E 27 TRP 0.022 0.002 TRP B 332 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11977) covalent geometry : angle 0.56538 / 0.30 (16299) SS BOND : bond 0.00555 / 0.28 ( 3) SS BOND : angle 1.50457 / 0.77 ( 6) hydrogen bonds : bond 0.04102 / 2.70 ( 653) hydrogen bonds : angle 4.85109 / 3.50 ( 1890) Misc. bond : bond 0.00052 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8286 (tpp) cc_final: 0.7793 (tpt) REVERT: R 188 ILE cc_start: 0.8584 (mt) cc_final: 0.8383 (mp) REVERT: R 195 ILE cc_start: 0.8786 (mt) cc_final: 0.8135 (mm) REVERT: R 198 SER cc_start: 0.8555 (t) cc_final: 0.8081 (p) REVERT: R 212 TYR cc_start: 0.7032 (m-80) cc_final: 0.6316 (m-80) REVERT: R 272 GLU cc_start: 0.7184 (tp30) cc_final: 0.6324 (tp30) REVERT: A 197 LYS cc_start: 0.8650 (mttt) cc_final: 0.8187 (mmtt) REVERT: A 244 HIS cc_start: 0.8288 (m90) cc_final: 0.7805 (m90) REVERT: A 305 CYS cc_start: 0.8317 (t) cc_final: 0.7641 (t) REVERT: A 308 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 309 ASP cc_start: 0.7218 (m-30) cc_final: 0.6982 (m-30) REVERT: B 172 GLU cc_start: 0.7381 (tp30) cc_final: 0.6952 (tm-30) REVERT: C 18 GLN cc_start: 0.6963 (tp40) cc_final: 0.6367 (mm110) REVERT: E 55 SER cc_start: 0.7742 (m) cc_final: 0.7147 (p) REVERT: E 80 PHE cc_start: 0.6877 (m-80) cc_final: 0.6297 (m-10) REVERT: E 220 LEU cc_start: 0.8287 (tp) cc_final: 0.8021 (tt) REVERT: M 124 PRO cc_start: 0.6509 (Cg_exo) cc_final: 0.6164 (Cg_endo) outliers start: 18 outliers final: 11 residues processed: 242 average time/residue: 0.1043 time to fit residues: 35.7119 Evaluate side-chains 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 139 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 299 HIS B 75 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN M 299 HIS M 321 HIS ** M 330 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 = 0.4223 r_free = 0.4223 target = 0.191127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156660 restraints weight = 13512.939| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.98 r_work: 0.3725 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11982 Z= 0.121 Angle : 0.505 5.973 16305 Z= 0.265 Chirality : 0.039 0.138 1903 Planarity : 0.004 0.046 1962 Dihedral : 4.315 27.725 1655 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.22 % Allowed : 8.56 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1421 helix: 2.33 (0.19), residues: 657 sheet: 0.27 (0.31), residues: 290 loop : -0.68 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.014 0.001 TYR E 191 PHE 0.020 0.001 PHE E 27 TRP 0.018 0.002 TRP Q 3 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11977) covalent geometry : angle 0.50460 / 0.27 (16299) SS BOND : bond 0.00422 / 0.22 ( 3) SS BOND : angle 0.68869 / 0.35 ( 6) hydrogen bonds : bond 0.03626 / 2.36 ( 653) hydrogen bonds : angle 4.55497 / 3.29 ( 1890) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8280 (tpp) cc_final: 0.7699 (tpt) REVERT: R 147 SER cc_start: 0.8082 (t) cc_final: 0.7855 (m) REVERT: R 195 ILE cc_start: 0.8749 (mt) cc_final: 0.8059 (mm) REVERT: R 198 SER cc_start: 0.8606 (t) cc_final: 0.8071 (p) REVERT: R 212 TYR cc_start: 0.6966 (m-80) cc_final: 0.6181 (m-80) REVERT: R 340 PHE cc_start: 0.7294 (m-10) cc_final: 0.6015 (t80) REVERT: A 197 LYS cc_start: 0.8648 (mttt) cc_final: 0.8216 (mmtt) REVERT: A 244 HIS cc_start: 0.8149 (m90) cc_final: 0.7646 (m-70) REVERT: A 298 GLU cc_start: 0.5854 (tt0) cc_final: 0.5184 (pt0) REVERT: A 305 CYS cc_start: 0.8171 (t) cc_final: 0.7834 (t) REVERT: A 308 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: B 153 ASP cc_start: 0.8034 (t0) cc_final: 0.7755 (t70) REVERT: B 172 GLU cc_start: 0.7555 (tp30) cc_final: 0.7127 (tm-30) REVERT: B 239 ASN cc_start: 0.7801 (m-40) cc_final: 0.7090 (p0) REVERT: C 18 GLN cc_start: 0.6961 (tp40) cc_final: 0.6348 (mm110) REVERT: E 55 SER cc_start: 0.7885 (m) cc_final: 0.7320 (p) REVERT: E 80 PHE cc_start: 0.6902 (m-80) cc_final: 0.6557 (m-80) REVERT: E 141 MET cc_start: 0.7445 (mmm) cc_final: 0.7092 (mmm) REVERT: E 161 ARG cc_start: 0.7031 (mmm160) cc_final: 0.6482 (mpp80) REVERT: E 220 LEU cc_start: 0.8209 (tp) cc_final: 0.7893 (tt) REVERT: M 205 MET cc_start: 0.7357 (ttp) cc_final: 0.7018 (ttp) outliers start: 28 outliers final: 19 residues processed: 227 average time/residue: 0.1052 time to fit residues: 33.6891 Evaluate side-chains 202 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN B 230 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 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 = 0.4191 r_free = 0.4191 target = 0.187836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154321 restraints weight = 13458.490| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.02 r_work: 0.3670 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11982 Z= 0.127 Angle : 0.497 5.558 16305 Z= 0.259 Chirality : 0.039 0.139 1903 Planarity : 0.004 0.046 1962 Dihedral : 4.294 26.514 1655 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.38 % Allowed : 10.47 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1421 helix: 2.51 (0.19), residues: 659 sheet: 0.31 (0.31), residues: 297 loop : -0.59 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.014 0.001 TYR E 191 PHE 0.021 0.001 PHE B 278 TRP 0.015 0.002 TRP M 320 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11977) covalent geometry : angle 0.49677 / 0.26 (16299) SS BOND : bond 0.00313 / 0.15 ( 3) SS BOND : angle 0.74940 / 0.38 ( 6) hydrogen bonds : bond 0.03457 / 2.25 ( 653) hydrogen bonds : angle 4.42987 / 3.20 ( 1890) Misc. bond : bond 0.00009 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8265 (tpp) cc_final: 0.7953 (tpt) REVERT: R 132 MET cc_start: 0.7768 (ptp) cc_final: 0.7438 (ptp) REVERT: R 147 SER cc_start: 0.8123 (t) cc_final: 0.7905 (m) REVERT: R 195 ILE cc_start: 0.8745 (mt) cc_final: 0.8043 (mm) REVERT: R 198 SER cc_start: 0.8643 (t) cc_final: 0.8103 (p) REVERT: R 212 TYR cc_start: 0.6940 (m-80) cc_final: 0.6143 (m-80) REVERT: R 340 PHE cc_start: 0.7429 (m-10) cc_final: 0.6057 (t80) REVERT: A 197 LYS cc_start: 0.8690 (mttt) cc_final: 0.8403 (mttm) REVERT: A 244 HIS cc_start: 0.7989 (m90) cc_final: 0.7419 (m90) REVERT: A 298 GLU cc_start: 0.5882 (tt0) cc_final: 0.5246 (pt0) REVERT: A 305 CYS cc_start: 0.8159 (t) cc_final: 0.7860 (t) REVERT: A 306 GLN cc_start: 0.7212 (tp40) cc_final: 0.6937 (mm110) REVERT: A 308 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: B 82 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: B 172 GLU cc_start: 0.7595 (tp30) cc_final: 0.7204 (tm-30) REVERT: B 214 ARG cc_start: 0.7374 (mpp80) cc_final: 0.7065 (mmm-85) REVERT: E 55 SER cc_start: 0.7891 (m) cc_final: 0.7312 (p) REVERT: E 141 MET cc_start: 0.7500 (mmm) cc_final: 0.7043 (mmm) REVERT: E 161 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6492 (mpp80) REVERT: E 181 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8219 (mtm-85) REVERT: E 221 GLU cc_start: 0.7620 (tt0) cc_final: 0.7338 (tt0) REVERT: E 231 MET cc_start: 0.7402 (ttt) cc_final: 0.7089 (ttm) REVERT: M 92 MET cc_start: 0.6401 (mmt) cc_final: 0.5857 (mmt) REVERT: M 234 LEU cc_start: 0.8541 (tp) cc_final: 0.8151 (tp) outliers start: 30 outliers final: 20 residues processed: 217 average time/residue: 0.1073 time to fit residues: 32.6318 Evaluate side-chains 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 137 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153795 restraints weight = 13312.075| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.86 r_work: 0.3676 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11982 Z= 0.117 Angle : 0.492 6.200 16305 Z= 0.255 Chirality : 0.038 0.131 1903 Planarity : 0.003 0.044 1962 Dihedral : 4.303 27.939 1655 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.30 % Allowed : 11.42 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1421 helix: 2.57 (0.19), residues: 660 sheet: 0.42 (0.31), residues: 295 loop : -0.55 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.014 0.001 TYR E 191 PHE 0.019 0.001 PHE M 125 TRP 0.022 0.002 TRP Q 3 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11977) covalent geometry : angle 0.49223 / 0.26 (16299) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 0.63408 / 0.32 ( 6) hydrogen bonds : bond 0.03360 / 2.18 ( 653) hydrogen bonds : angle 4.34529 / 3.15 ( 1890) Misc. bond : bond 0.00001 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8259 (tpp) cc_final: 0.7944 (tpt) REVERT: R 132 MET cc_start: 0.7874 (ptp) cc_final: 0.7656 (ptp) REVERT: R 147 SER cc_start: 0.8107 (t) cc_final: 0.7897 (m) REVERT: R 195 ILE cc_start: 0.8746 (mt) cc_final: 0.8028 (mm) REVERT: R 198 SER cc_start: 0.8700 (t) cc_final: 0.8160 (p) REVERT: R 212 TYR cc_start: 0.6808 (m-80) cc_final: 0.6102 (m-80) REVERT: R 340 PHE cc_start: 0.7419 (m-10) cc_final: 0.6020 (t80) REVERT: A 197 LYS cc_start: 0.8660 (mttt) cc_final: 0.8352 (mttm) REVERT: A 298 GLU cc_start: 0.5872 (tt0) cc_final: 0.5161 (pt0) REVERT: A 305 CYS cc_start: 0.8161 (t) cc_final: 0.7920 (t) REVERT: A 306 GLN cc_start: 0.7170 (tp40) cc_final: 0.6913 (mm110) REVERT: B 82 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: B 172 GLU cc_start: 0.7549 (tp30) cc_final: 0.7169 (tm-30) REVERT: B 214 ARG cc_start: 0.7402 (mpp80) cc_final: 0.7091 (mmm-85) REVERT: E 55 SER cc_start: 0.7775 (m) cc_final: 0.7212 (p) REVERT: E 141 MET cc_start: 0.7567 (mmm) cc_final: 0.7075 (mmm) REVERT: E 161 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6496 (mpp80) REVERT: E 231 MET cc_start: 0.7370 (ttt) cc_final: 0.7062 (ttm) REVERT: M 92 MET cc_start: 0.6442 (mmt) cc_final: 0.5755 (mmt) REVERT: M 231 GLU cc_start: 0.7608 (tt0) cc_final: 0.7360 (tp30) outliers start: 29 outliers final: 21 residues processed: 202 average time/residue: 0.1107 time to fit residues: 31.9426 Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153413 restraints weight = 13392.717| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.85 r_work: 0.3679 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11982 Z= 0.112 Angle : 0.481 7.335 16305 Z= 0.248 Chirality : 0.038 0.130 1903 Planarity : 0.003 0.044 1962 Dihedral : 4.250 30.100 1655 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.54 % Allowed : 11.50 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.22), residues: 1421 helix: 2.63 (0.19), residues: 660 sheet: 0.44 (0.31), residues: 295 loop : -0.48 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.013 0.001 TYR E 191 PHE 0.015 0.001 PHE E 27 TRP 0.014 0.002 TRP M 320 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11977) covalent geometry : angle 0.48109 / 0.25 (16299) SS BOND : bond 0.00269 / 0.13 ( 3) SS BOND : angle 0.63132 / 0.32 ( 6) hydrogen bonds : bond 0.03272 / 2.11 ( 653) hydrogen bonds : angle 4.28077 / 3.11 ( 1890) Misc. bond : bond 0.00008 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8284 (tpp) cc_final: 0.7965 (tpt) REVERT: R 195 ILE cc_start: 0.8767 (mt) cc_final: 0.8056 (mm) REVERT: R 198 SER cc_start: 0.8738 (t) cc_final: 0.8195 (p) REVERT: R 212 TYR cc_start: 0.6718 (m-80) cc_final: 0.6045 (m-80) REVERT: R 283 MET cc_start: 0.7547 (tpp) cc_final: 0.6826 (mtt) REVERT: R 340 PHE cc_start: 0.7414 (m-10) cc_final: 0.6029 (t80) REVERT: A 197 LYS cc_start: 0.8647 (mttt) cc_final: 0.8375 (mttm) REVERT: A 298 GLU cc_start: 0.5881 (tt0) cc_final: 0.5181 (pt0) REVERT: A 305 CYS cc_start: 0.8149 (t) cc_final: 0.7885 (t) REVERT: A 308 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 82 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: B 172 GLU cc_start: 0.7557 (tp30) cc_final: 0.7205 (tm-30) REVERT: B 214 ARG cc_start: 0.7416 (mpp80) cc_final: 0.7119 (mmm-85) REVERT: B 292 PHE cc_start: 0.7118 (m-80) cc_final: 0.6892 (m-10) REVERT: E 55 SER cc_start: 0.7777 (m) cc_final: 0.7219 (p) REVERT: E 141 MET cc_start: 0.7586 (mmm) cc_final: 0.7085 (mmm) REVERT: E 161 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6515 (mpp80) REVERT: E 181 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: E 231 MET cc_start: 0.7468 (ttt) cc_final: 0.7131 (ttm) REVERT: M 231 GLU cc_start: 0.7625 (tt0) cc_final: 0.7403 (tp30) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 0.1200 time to fit residues: 34.2560 Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 173 HIS A 306 GLN E 168 HIS ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153200 restraints weight = 13322.141| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.86 r_work: 0.3688 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11982 Z= 0.106 Angle : 0.473 6.456 16305 Z= 0.244 Chirality : 0.038 0.132 1903 Planarity : 0.003 0.043 1962 Dihedral : 4.205 31.382 1655 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.70 % Allowed : 11.58 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1421 helix: 2.68 (0.19), residues: 660 sheet: 0.46 (0.31), residues: 295 loop : -0.44 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.013 0.001 TYR E 95 PHE 0.014 0.001 PHE E 27 TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS E 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11977) covalent geometry : angle 0.47341 / 0.24 (16299) SS BOND : bond 0.00291 / 0.14 ( 3) SS BOND : angle 0.64201 / 0.33 ( 6) hydrogen bonds : bond 0.03195 / 2.06 ( 653) hydrogen bonds : angle 4.19927 / 3.05 ( 1890) Misc. bond : bond 0.00004 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8231 (tpp) cc_final: 0.7893 (tpt) REVERT: R 195 ILE cc_start: 0.8750 (mt) cc_final: 0.8023 (mm) REVERT: R 198 SER cc_start: 0.8708 (t) cc_final: 0.8150 (p) REVERT: R 212 TYR cc_start: 0.6594 (m-80) cc_final: 0.5940 (m-80) REVERT: R 283 MET cc_start: 0.7479 (tpp) cc_final: 0.6795 (mtt) REVERT: R 340 PHE cc_start: 0.7390 (m-10) cc_final: 0.6038 (t80) REVERT: A 197 LYS cc_start: 0.8636 (mttt) cc_final: 0.8335 (mttm) REVERT: A 298 GLU cc_start: 0.5864 (tt0) cc_final: 0.5128 (pt0) REVERT: A 305 CYS cc_start: 0.8071 (t) cc_final: 0.7813 (t) REVERT: A 308 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: B 82 TRP cc_start: 0.7469 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: B 292 PHE cc_start: 0.7052 (m-80) cc_final: 0.6675 (m-10) REVERT: E 55 SER cc_start: 0.7744 (m) cc_final: 0.7217 (p) REVERT: E 73 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.5397 (t70) REVERT: E 141 MET cc_start: 0.7554 (mmm) cc_final: 0.7010 (mmm) REVERT: E 161 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6492 (mpp80) REVERT: E 231 MET cc_start: 0.7456 (ttt) cc_final: 0.7157 (ttm) REVERT: M 231 GLU cc_start: 0.7576 (tt0) cc_final: 0.7323 (tp30) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 0.1033 time to fit residues: 30.7804 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN B 230 ASN E 187 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149554 restraints weight = 13469.644| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.08 r_work: 0.3634 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11982 Z= 0.129 Angle : 0.511 6.271 16305 Z= 0.265 Chirality : 0.039 0.135 1903 Planarity : 0.003 0.044 1962 Dihedral : 4.321 31.685 1655 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.78 % Allowed : 11.82 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.22), residues: 1421 helix: 2.61 (0.19), residues: 660 sheet: 0.52 (0.31), residues: 294 loop : -0.50 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.013 0.001 TYR E 95 PHE 0.016 0.001 PHE B 278 TRP 0.018 0.002 TRP E 47 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11977) covalent geometry : angle 0.51056 / 0.26 (16299) SS BOND : bond 0.00265 / 0.13 ( 3) SS BOND : angle 0.67732 / 0.35 ( 6) hydrogen bonds : bond 0.03344 / 2.16 ( 653) hydrogen bonds : angle 4.26171 / 3.11 ( 1890) Misc. bond : bond 0.00003 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8293 (tpp) cc_final: 0.7944 (tpt) REVERT: R 195 ILE cc_start: 0.8752 (mt) cc_final: 0.8041 (mm) REVERT: R 198 SER cc_start: 0.8741 (t) cc_final: 0.8212 (p) REVERT: R 205 MET cc_start: 0.7387 (ttm) cc_final: 0.7134 (ttm) REVERT: R 212 TYR cc_start: 0.6550 (m-80) cc_final: 0.5944 (m-80) REVERT: R 283 MET cc_start: 0.7554 (tpp) cc_final: 0.6892 (mtt) REVERT: R 340 PHE cc_start: 0.7533 (m-10) cc_final: 0.6078 (t80) REVERT: A 18 MET cc_start: 0.8391 (tpp) cc_final: 0.8147 (tpt) REVERT: A 21 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7482 (ttm110) REVERT: A 197 LYS cc_start: 0.8672 (mttt) cc_final: 0.8399 (mttm) REVERT: A 298 GLU cc_start: 0.5754 (tt0) cc_final: 0.5193 (pt0) REVERT: A 305 CYS cc_start: 0.8087 (t) cc_final: 0.7843 (t) REVERT: A 308 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 82 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: B 292 PHE cc_start: 0.7401 (m-80) cc_final: 0.6961 (m-10) REVERT: C 62 ARG cc_start: 0.6187 (mtm-85) cc_final: 0.5599 (mtt180) REVERT: E 38 ARG cc_start: 0.7413 (ptp90) cc_final: 0.7203 (ptp90) REVERT: E 141 MET cc_start: 0.7607 (mmm) cc_final: 0.7052 (mmm) REVERT: E 161 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6546 (mpp80) REVERT: E 193 MET cc_start: 0.6381 (mmm) cc_final: 0.5795 (ttp) REVERT: E 231 MET cc_start: 0.7528 (ttt) cc_final: 0.7216 (ttm) REVERT: M 163 MET cc_start: 0.8034 (ttm) cc_final: 0.7749 (mtm) REVERT: M 231 GLU cc_start: 0.7554 (tt0) cc_final: 0.7313 (tp30) REVERT: M 234 LEU cc_start: 0.8532 (tp) cc_final: 0.8178 (tp) outliers start: 35 outliers final: 30 residues processed: 201 average time/residue: 0.1218 time to fit residues: 34.6371 Evaluate side-chains 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149831 restraints weight = 13363.727| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.99 r_work: 0.3638 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11982 Z= 0.121 Angle : 0.500 6.591 16305 Z= 0.259 Chirality : 0.039 0.132 1903 Planarity : 0.003 0.047 1962 Dihedral : 4.312 32.322 1655 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.85 % Allowed : 11.97 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1421 helix: 2.59 (0.19), residues: 662 sheet: 0.52 (0.31), residues: 295 loop : -0.44 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.012 0.001 TYR E 191 PHE 0.015 0.001 PHE B 278 TRP 0.018 0.002 TRP E 47 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11977) covalent geometry : angle 0.50018 / 0.26 (16299) SS BOND : bond 0.00274 / 0.13 ( 3) SS BOND : angle 0.65911 / 0.34 ( 6) hydrogen bonds : bond 0.03290 / 2.13 ( 653) hydrogen bonds : angle 4.26155 / 3.11 ( 1890) Misc. bond : bond 0.00010 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8194 (tpp) cc_final: 0.7811 (tpt) REVERT: R 195 ILE cc_start: 0.8729 (mt) cc_final: 0.8006 (mm) REVERT: R 198 SER cc_start: 0.8724 (t) cc_final: 0.8174 (p) REVERT: R 205 MET cc_start: 0.7361 (ttm) cc_final: 0.7100 (ttm) REVERT: R 212 TYR cc_start: 0.6491 (m-80) cc_final: 0.5912 (m-80) REVERT: R 283 MET cc_start: 0.7463 (tpp) cc_final: 0.6851 (mtt) REVERT: R 340 PHE cc_start: 0.7557 (m-10) cc_final: 0.6069 (t80) REVERT: A 197 LYS cc_start: 0.8625 (mttt) cc_final: 0.8393 (mttm) REVERT: A 298 GLU cc_start: 0.5689 (tt0) cc_final: 0.5050 (pt0) REVERT: A 305 CYS cc_start: 0.8075 (t) cc_final: 0.7349 (t) REVERT: A 308 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: B 82 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: B 134 ARG cc_start: 0.7072 (ptt-90) cc_final: 0.6296 (ttt90) REVERT: B 292 PHE cc_start: 0.7444 (m-80) cc_final: 0.7031 (m-10) REVERT: E 141 MET cc_start: 0.7601 (mmm) cc_final: 0.7018 (mmm) REVERT: E 161 ARG cc_start: 0.7077 (mmm160) cc_final: 0.6531 (mpp80) REVERT: E 181 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8449 (mtm-85) REVERT: E 193 MET cc_start: 0.6361 (mmm) cc_final: 0.5852 (ttp) REVERT: E 231 MET cc_start: 0.7503 (ttt) cc_final: 0.7270 (ttm) REVERT: M 163 MET cc_start: 0.8032 (ttm) cc_final: 0.7756 (mtm) REVERT: M 231 GLU cc_start: 0.7519 (tt0) cc_final: 0.7276 (tp30) outliers start: 36 outliers final: 29 residues processed: 201 average time/residue: 0.1038 time to fit residues: 29.4355 Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 101 MET Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.0060 chunk 127 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 GLN A 306 GLN E 187 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144265 restraints weight = 13675.276| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.92 r_work: 0.3587 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11982 Z= 0.169 Angle : 0.564 9.215 16305 Z= 0.291 Chirality : 0.041 0.145 1903 Planarity : 0.004 0.044 1962 Dihedral : 4.733 34.369 1655 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 12.45 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.22), residues: 1421 helix: 2.34 (0.20), residues: 661 sheet: 0.44 (0.31), residues: 293 loop : -0.53 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 313 TYR 0.015 0.002 TYR R 301 PHE 0.015 0.002 PHE B 278 TRP 0.023 0.002 TRP E 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (11977) covalent geometry : angle 0.56365 / 0.29 (16299) SS BOND : bond 0.00250 / 0.12 ( 3) SS BOND : angle 0.78474 / 0.41 ( 6) hydrogen bonds : bond 0.03647 / 2.37 ( 653) hydrogen bonds : angle 4.46533 / 3.26 ( 1890) Misc. bond : bond 0.00017 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8299 (tpp) cc_final: 0.7940 (tpt) REVERT: R 195 ILE cc_start: 0.8739 (mt) cc_final: 0.8034 (mm) REVERT: R 198 SER cc_start: 0.8778 (t) cc_final: 0.8252 (p) REVERT: R 205 MET cc_start: 0.7395 (ttm) cc_final: 0.7078 (ttm) REVERT: R 212 TYR cc_start: 0.6517 (m-80) cc_final: 0.5979 (m-80) REVERT: R 283 MET cc_start: 0.7498 (tpp) cc_final: 0.6910 (mtt) REVERT: A 21 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7481 (ttm110) REVERT: A 197 LYS cc_start: 0.8618 (mttt) cc_final: 0.8417 (mttm) REVERT: A 298 GLU cc_start: 0.5492 (tt0) cc_final: 0.4973 (pt0) REVERT: A 305 CYS cc_start: 0.8059 (t) cc_final: 0.7761 (t) REVERT: A 308 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: B 82 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.7190 (m-10) REVERT: B 134 ARG cc_start: 0.7045 (ptt-90) cc_final: 0.6390 (ttt180) REVERT: C 62 ARG cc_start: 0.5968 (mtm-85) cc_final: 0.5439 (mtt180) REVERT: E 141 MET cc_start: 0.7613 (mmm) cc_final: 0.7072 (mmm) REVERT: E 161 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6500 (mpp80) REVERT: E 193 MET cc_start: 0.6523 (mmm) cc_final: 0.5996 (ttp) REVERT: M 231 GLU cc_start: 0.7509 (tt0) cc_final: 0.7259 (tp30) outliers start: 33 outliers final: 27 residues processed: 216 average time/residue: 0.1076 time to fit residues: 32.3193 Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 101 MET Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 GLN R 214 GLN R 330 ASN A 306 GLN B 75 GLN ** M 106 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 = 0.4104 r_free = 0.4104 target = 0.179006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145318 restraints weight = 13523.502| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.96 r_work: 0.3591 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11982 Z= 0.143 Angle : 0.539 9.117 16305 Z= 0.277 Chirality : 0.040 0.140 1903 Planarity : 0.004 0.044 1962 Dihedral : 4.651 32.783 1655 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.54 % Allowed : 13.40 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1421 helix: 2.37 (0.20), residues: 661 sheet: 0.35 (0.31), residues: 296 loop : -0.46 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.012 0.001 TYR R 301 PHE 0.015 0.001 PHE B 278 TRP 0.024 0.002 TRP E 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (11977) covalent geometry : angle 0.53839 / 0.28 (16299) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 0.89532 / 0.45 ( 6) hydrogen bonds : bond 0.03477 / 2.25 ( 653) hydrogen bonds : angle 4.43572 / 3.24 ( 1890) Misc. bond : bond 0.00012 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.40 seconds wall clock time: 54 minutes 19.93 seconds (3259.93 seconds total)