Starting phenix.real_space_refine on Sat Aug 23 11:14:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7r_28908/08_2025/8f7r_28908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7r_28908/08_2025/8f7r_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_28908/08_2025/8f7r_28908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7r_28908/08_2025/8f7r_28908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7r_28908/08_2025/8f7r_28908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7r_28908/08_2025/8f7r_28908.map" } 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-2.0-5787/lib/python3.9/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: 3.44, per 1000 atoms: 0.29 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: 1.00 Conformation dependent library (CDL) restraints added in 569.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 2.01 Time building geometry restraints manager: 1.32 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 - 10.76: 6854 10.76 - 21.52: 596 21.52 - 32.28: 70 32.28 - 43.04: 33 43.04 - 53.81: 6 Dihedral angle restraints: 7559 sinusoidal: 3340 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 7556 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: 2.420 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.120 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 : 8.210 53.806 4822 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 aren 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 covalent geometry : bond 0.00425 (11977) covalent geometry : angle 0.83930 (16299) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.87917 ( 6) hydrogen bonds : bond 0.15595 ( 653) hydrogen bonds : angle 6.58147 ( 1890) Misc. bond : bond 0.12118 ( 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 : 0.373 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: 0.7505 (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: 0.7240 (m-80) cc_final: 0.6413 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1319 time to fit residues: 52.7070 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 : 0.462 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157717 restraints weight = 13333.013| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.12 r_work: 0.3736 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11982 Z= 0.163 Angle : 0.567 6.025 16305 Z= 0.298 Chirality : 0.041 0.150 1903 Planarity : 0.004 0.051 1962 Dihedral : 5.413 44.225 2215 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.35 % Allowed : 6.19 % Favored : 92.47 % 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 aren not related in a simple way. whole: 0.81 (0.21), residues: 1421 helix: 1.77 (0.19), residues: 656 sheet: 0.33 (0.31), residues: 284 loop : -1.07 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.016 0.002 TYR E 191 PHE 0.019 0.002 PHE E 27 TRP 0.021 0.002 TRP B 332 HIS 0.009 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00371 (11977) covalent geometry : angle 0.56596 (16299) SS BOND : bond 0.00685 ( 3) SS BOND : angle 1.45097 ( 6) hydrogen bonds : bond 0.04086 ( 653) hydrogen bonds : angle 4.86650 ( 1890) Misc. bond : bond 0.00037 ( 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 246 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8174 (tpp) cc_final: 0.7656 (tpt) REVERT: R 188 ILE cc_start: 0.8461 (mt) cc_final: 0.8242 (mp) REVERT: R 195 ILE cc_start: 0.8742 (mt) cc_final: 0.8056 (mm) REVERT: R 198 SER cc_start: 0.8465 (t) cc_final: 0.7971 (p) REVERT: R 212 TYR cc_start: 0.6952 (m-80) cc_final: 0.6285 (m-80) REVERT: A 197 LYS cc_start: 0.8515 (mttt) cc_final: 0.8071 (mmtm) REVERT: A 305 CYS cc_start: 0.8122 (t) cc_final: 0.7447 (t) REVERT: A 308 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: A 309 ASP cc_start: 0.7035 (m-30) cc_final: 0.6793 (m-30) REVERT: B 172 GLU cc_start: 0.7214 (tp30) cc_final: 0.6802 (tm-30) REVERT: C 18 GLN cc_start: 0.6979 (tp40) cc_final: 0.6385 (mm110) REVERT: E 55 SER cc_start: 0.7658 (m) cc_final: 0.7084 (p) REVERT: E 161 ARG cc_start: 0.6975 (mmm160) cc_final: 0.6485 (mpp80) REVERT: E 220 LEU cc_start: 0.8263 (tp) cc_final: 0.8001 (tt) outliers start: 17 outliers final: 12 residues processed: 242 average time/residue: 0.1248 time to fit residues: 42.1618 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 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 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: 0.9980 chunk 118 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 321 HIS M 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.190730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156272 restraints weight = 13511.372| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.98 r_work: 0.3722 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3200 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= 0.127 Angle : 0.512 6.162 16305 Z= 0.270 Chirality : 0.040 0.140 1903 Planarity : 0.004 0.046 1962 Dihedral : 5.032 32.065 2215 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.14 % Allowed : 8.72 % Favored : 89.14 % 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 aren not related in a simple way. whole: 1.34 (0.22), residues: 1421 helix: 2.31 (0.19), residues: 656 sheet: 0.26 (0.31), residues: 290 loop : -0.71 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.015 0.001 TYR E 191 PHE 0.021 0.001 PHE E 27 TRP 0.024 0.002 TRP Q 3 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00286 (11977) covalent geometry : angle 0.51208 (16299) SS BOND : bond 0.00379 ( 3) SS BOND : angle 0.65329 ( 6) hydrogen bonds : bond 0.03647 ( 653) hydrogen bonds : angle 4.58511 ( 1890) Misc. bond : bond 0.00022 ( 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 241 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 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: 0.8289 (tpp) cc_final: 0.7704 (tpt) REVERT: R 102 LYS cc_start: 0.7488 (ptpt) cc_final: 0.6752 (mmtm) REVERT: R 147 SER cc_start: 0.8070 (t) cc_final: 0.7845 (m) REVERT: R 195 ILE cc_start: 0.8746 (mt) cc_final: 0.8059 (mm) REVERT: R 198 SER cc_start: 0.8607 (t) cc_final: 0.8082 (p) REVERT: R 212 TYR cc_start: 0.6967 (m-80) cc_final: 0.6206 (m-80) REVERT: R 340 PHE cc_start: 0.7306 (m-10) cc_final: 0.6039 (t80) REVERT: A 197 LYS cc_start: 0.8686 (mttt) cc_final: 0.8236 (mmtt) REVERT: A 244 HIS cc_start: 0.8129 (m90) cc_final: 0.7636 (m-70) REVERT: A 298 GLU cc_start: 0.5858 (tt0) cc_final: 0.5208 (pt0) REVERT: A 305 CYS cc_start: 0.8215 (t) cc_final: 0.7897 (t) REVERT: A 308 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 172 GLU cc_start: 0.7548 (tp30) cc_final: 0.7142 (tm-30) REVERT: B 239 ASN cc_start: 0.7786 (m-40) cc_final: 0.7105 (p0) REVERT: E 55 SER cc_start: 0.7913 (m) cc_final: 0.7343 (p) REVERT: E 141 MET cc_start: 0.7479 (mmm) cc_final: 0.7152 (mmm) REVERT: E 161 ARG cc_start: 0.7029 (mmm160) cc_final: 0.6490 (mpp80) REVERT: E 220 LEU cc_start: 0.8242 (tp) cc_final: 0.7933 (tt) outliers start: 27 outliers final: 19 residues processed: 231 average time/residue: 0.1237 time to fit residues: 40.0441 Evaluate side-chains 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 307 PHE Chi-restraints excluded: chain A residue 308 GLU 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 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: 2.9990 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 230 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 299 HIS M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.188256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153889 restraints weight = 13395.331| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.36 r_work: 0.3681 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11982 Z= 0.121 Angle : 0.494 5.309 16305 Z= 0.259 Chirality : 0.039 0.136 1903 Planarity : 0.003 0.045 1962 Dihedral : 4.849 32.222 2215 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.14 % Allowed : 11.42 % Favored : 86.44 % 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 aren not related in a simple way. whole: 1.60 (0.22), residues: 1421 helix: 2.52 (0.19), residues: 659 sheet: 0.30 (0.31), residues: 297 loop : -0.56 (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 M 125 TRP 0.015 0.002 TRP M 320 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00274 (11977) covalent geometry : angle 0.49376 (16299) SS BOND : bond 0.00321 ( 3) SS BOND : angle 0.74458 ( 6) hydrogen bonds : bond 0.03453 ( 653) hydrogen bonds : angle 4.40794 ( 1890) Misc. bond : bond 0.00002 ( 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 228 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8212 (tpp) cc_final: 0.7821 (tpt) REVERT: R 147 SER cc_start: 0.8016 (t) cc_final: 0.7781 (m) REVERT: R 195 ILE cc_start: 0.8729 (mt) cc_final: 0.8018 (mm) REVERT: R 198 SER cc_start: 0.8627 (t) cc_final: 0.8082 (p) REVERT: R 212 TYR cc_start: 0.6856 (m-80) cc_final: 0.6094 (m-80) REVERT: R 340 PHE cc_start: 0.7308 (m-10) cc_final: 0.6052 (t80) REVERT: A 197 LYS cc_start: 0.8565 (mttt) cc_final: 0.8254 (mttm) REVERT: A 244 HIS cc_start: 0.7997 (m90) cc_final: 0.7416 (m90) REVERT: A 298 GLU cc_start: 0.5761 (tt0) cc_final: 0.5175 (pt0) REVERT: A 305 CYS cc_start: 0.7961 (t) cc_final: 0.7711 (t) REVERT: A 306 GLN cc_start: 0.7168 (tp40) cc_final: 0.6868 (mm110) REVERT: B 82 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: B 172 GLU cc_start: 0.7354 (tp30) cc_final: 0.6997 (tm-30) REVERT: B 214 ARG cc_start: 0.7354 (mpp80) cc_final: 0.7079 (mmm-85) REVERT: E 55 SER cc_start: 0.7788 (m) cc_final: 0.7222 (p) REVERT: E 141 MET cc_start: 0.7442 (mmm) cc_final: 0.7006 (mmm) REVERT: E 161 ARG cc_start: 0.6989 (mmm160) cc_final: 0.6540 (mpp80) REVERT: E 181 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8252 (mtm-85) REVERT: E 221 GLU cc_start: 0.7557 (tt0) cc_final: 0.7286 (tt0) REVERT: E 231 MET cc_start: 0.7299 (ttt) cc_final: 0.6989 (ttm) REVERT: M 234 LEU cc_start: 0.8479 (tp) cc_final: 0.8088 (tp) outliers start: 27 outliers final: 17 residues processed: 222 average time/residue: 0.1264 time to fit residues: 38.9535 Evaluate side-chains 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS 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: 2.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.0000 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.189100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155710 restraints weight = 13265.686| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.88 r_work: 0.3705 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11982 Z= 0.104 Angle : 0.476 5.509 16305 Z= 0.246 Chirality : 0.038 0.129 1903 Planarity : 0.003 0.044 1962 Dihedral : 4.741 32.238 2215 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.38 % Allowed : 11.74 % Favored : 85.88 % 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 aren not related in a simple way. whole: 1.74 (0.22), residues: 1421 helix: 2.62 (0.20), residues: 659 sheet: 0.42 (0.31), residues: 295 loop : -0.49 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.014 0.001 TYR E 191 PHE 0.016 0.001 PHE E 27 TRP 0.017 0.002 TRP Q 3 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00229 (11977) covalent geometry : angle 0.47550 (16299) SS BOND : bond 0.00266 ( 3) SS BOND : angle 0.57110 ( 6) hydrogen bonds : bond 0.03258 ( 653) hydrogen bonds : angle 4.28671 ( 1890) Misc. bond : bond 0.00010 ( 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 228 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8292 (tpp) cc_final: 0.7731 (tpt) REVERT: R 147 SER cc_start: 0.8072 (t) cc_final: 0.7861 (m) REVERT: R 195 ILE cc_start: 0.8743 (mt) cc_final: 0.8019 (mm) REVERT: R 198 SER cc_start: 0.8707 (t) cc_final: 0.8154 (p) REVERT: R 212 TYR cc_start: 0.6802 (m-80) cc_final: 0.6088 (m-80) REVERT: R 340 PHE cc_start: 0.7302 (m-10) cc_final: 0.6000 (t80) REVERT: A 197 LYS cc_start: 0.8678 (mttt) cc_final: 0.8352 (mttm) REVERT: A 298 GLU cc_start: 0.5845 (tt0) cc_final: 0.5238 (pt0) REVERT: A 302 TYR cc_start: 0.8304 (t80) cc_final: 0.8090 (t80) REVERT: A 305 CYS cc_start: 0.8150 (t) cc_final: 0.7885 (t) REVERT: A 306 GLN cc_start: 0.7141 (tp40) cc_final: 0.6871 (mm110) REVERT: A 308 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 82 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: B 172 GLU cc_start: 0.7488 (tp30) cc_final: 0.7180 (tm-30) REVERT: B 214 ARG cc_start: 0.7341 (mpp80) cc_final: 0.7077 (mmm-85) REVERT: E 55 SER cc_start: 0.7825 (m) cc_final: 0.7257 (p) REVERT: E 141 MET cc_start: 0.7552 (mmm) cc_final: 0.7062 (mmm) REVERT: E 161 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6474 (mpp80) REVERT: E 231 MET cc_start: 0.7406 (ttt) cc_final: 0.7120 (ttm) REVERT: M 231 GLU cc_start: 0.7631 (tt0) cc_final: 0.7366 (tp30) outliers start: 30 outliers final: 20 residues processed: 221 average time/residue: 0.1170 time to fit residues: 36.7017 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 ASP 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 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR 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 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: 0.4980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 30 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 69 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 110 ASN ** 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 = 0.4223 r_free = 0.4223 target = 0.191546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159047 restraints weight = 13293.878| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.85 r_work: 0.3743 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11982 Z= 0.098 Angle : 0.475 7.599 16305 Z= 0.246 Chirality : 0.038 0.133 1903 Planarity : 0.003 0.044 1962 Dihedral : 4.609 30.076 2215 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.38 % Allowed : 11.74 % Favored : 85.88 % 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 aren not related in a simple way. whole: 1.87 (0.22), residues: 1421 helix: 2.71 (0.20), residues: 660 sheet: 0.52 (0.31), residues: 295 loop : -0.44 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.013 0.001 TYR E 191 PHE 0.015 0.001 PHE E 27 TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00209 (11977) covalent geometry : angle 0.47459 (16299) SS BOND : bond 0.00301 ( 3) SS BOND : angle 0.58943 ( 6) hydrogen bonds : bond 0.03140 ( 653) hydrogen bonds : angle 4.16770 ( 1890) Misc. bond : bond 0.00003 ( 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: 30 poor density : 182 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8254 (tpp) cc_final: 0.7700 (tpt) REVERT: R 195 ILE cc_start: 0.8705 (mt) cc_final: 0.8000 (mm) REVERT: R 198 SER cc_start: 0.8661 (t) cc_final: 0.8094 (p) REVERT: R 283 MET cc_start: 0.7461 (tpp) cc_final: 0.6754 (mtt) REVERT: R 340 PHE cc_start: 0.7224 (m-10) cc_final: 0.5982 (t80) REVERT: A 197 LYS cc_start: 0.8683 (mttt) cc_final: 0.8381 (mttm) REVERT: A 298 GLU cc_start: 0.5890 (tt0) cc_final: 0.5295 (pt0) REVERT: A 305 CYS cc_start: 0.8116 (t) cc_final: 0.7866 (t) REVERT: A 308 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: B 82 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: B 172 GLU cc_start: 0.7493 (tp30) cc_final: 0.7255 (tm-30) REVERT: B 214 ARG cc_start: 0.7318 (mpp80) cc_final: 0.7015 (mmm-85) REVERT: B 292 PHE cc_start: 0.6662 (m-80) cc_final: 0.6221 (m-10) REVERT: E 55 SER cc_start: 0.7779 (m) cc_final: 0.7197 (p) REVERT: E 73 ASP cc_start: 0.5693 (OUTLIER) cc_final: 0.5381 (t70) REVERT: E 141 MET cc_start: 0.7490 (mmm) cc_final: 0.7002 (mmm) REVERT: E 181 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8204 (mtm-85) REVERT: E 231 MET cc_start: 0.7390 (ttt) cc_final: 0.7096 (ttm) REVERT: M 231 GLU cc_start: 0.7624 (tt0) cc_final: 0.7348 (tp30) outliers start: 30 outliers final: 19 residues processed: 204 average time/residue: 0.1175 time to fit residues: 34.0162 Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU 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 73 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 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 164 SER Chi-restraints excluded: chain M residue 179 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 176 GLN B 230 ASN E 77 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153627 restraints weight = 13337.757| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.85 r_work: 0.3674 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11982 Z= 0.130 Angle : 0.498 6.182 16305 Z= 0.257 Chirality : 0.039 0.139 1903 Planarity : 0.003 0.045 1962 Dihedral : 4.687 30.356 2215 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.38 % Allowed : 12.05 % Favored : 85.57 % 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 aren not related in a simple way. whole: 1.80 (0.22), residues: 1421 helix: 2.65 (0.20), residues: 660 sheet: 0.49 (0.31), residues: 294 loop : -0.48 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.013 0.001 TYR E 191 PHE 0.014 0.001 PHE B 278 TRP 0.014 0.002 TRP E 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (11977) covalent geometry : angle 0.49752 (16299) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.65163 ( 6) hydrogen bonds : bond 0.03302 ( 653) hydrogen bonds : angle 4.21459 ( 1890) Misc. bond : bond 0.00002 ( 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 209 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8232 (tpp) cc_final: 0.7698 (tpt) REVERT: R 195 ILE cc_start: 0.8764 (mt) cc_final: 0.8067 (mm) REVERT: R 198 SER cc_start: 0.8725 (t) cc_final: 0.8185 (p) REVERT: R 212 TYR cc_start: 0.6679 (m-80) cc_final: 0.6017 (m-80) REVERT: R 340 PHE cc_start: 0.7347 (m-10) cc_final: 0.6035 (t80) REVERT: A 21 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7598 (ttm110) REVERT: A 197 LYS cc_start: 0.8678 (mttt) cc_final: 0.8362 (mttm) REVERT: A 298 GLU cc_start: 0.5836 (tt0) cc_final: 0.5237 (pt0) REVERT: A 305 CYS cc_start: 0.8057 (t) cc_final: 0.7824 (t) REVERT: A 308 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: B 82 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: B 172 GLU cc_start: 0.7584 (tp30) cc_final: 0.7334 (tm-30) REVERT: B 292 PHE cc_start: 0.7103 (m-80) cc_final: 0.6687 (m-10) REVERT: C 62 ARG cc_start: 0.6048 (mtm-85) cc_final: 0.5473 (mtt180) REVERT: E 55 SER cc_start: 0.7781 (m) cc_final: 0.7237 (p) REVERT: E 141 MET cc_start: 0.7593 (mmm) cc_final: 0.7076 (mmm) REVERT: E 161 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6522 (mpp80) REVERT: E 181 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: E 231 MET cc_start: 0.7479 (ttt) cc_final: 0.7165 (ttm) REVERT: M 92 MET cc_start: 0.6158 (mmt) cc_final: 0.5508 (mmt) REVERT: M 231 GLU cc_start: 0.7631 (tt0) cc_final: 0.7343 (tp30) REVERT: M 234 LEU cc_start: 0.8519 (tp) cc_final: 0.8158 (tp) outliers start: 30 outliers final: 24 residues processed: 201 average time/residue: 0.1245 time to fit residues: 35.0371 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 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 210 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN 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 142 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=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: 7.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 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 = 0.4119 r_free = 0.4119 target = 0.180681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146799 restraints weight = 13514.478| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.00 r_work: 0.3583 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11982 Z= 0.163 Angle : 0.547 5.885 16305 Z= 0.283 Chirality : 0.041 0.140 1903 Planarity : 0.004 0.045 1962 Dihedral : 5.040 32.270 2215 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 11.74 % Favored : 85.65 % 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 aren not related in a simple way. whole: 1.66 (0.22), residues: 1421 helix: 2.49 (0.20), residues: 660 sheet: 0.51 (0.31), residues: 292 loop : -0.53 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.014 0.002 TYR R 301 PHE 0.017 0.002 PHE E 80 TRP 0.021 0.002 TRP B 99 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00380 (11977) covalent geometry : angle 0.54719 (16299) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.73847 ( 6) hydrogen bonds : bond 0.03611 ( 653) hydrogen bonds : angle 4.41528 ( 1890) Misc. bond : bond 0.00010 ( 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 222 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8304 (tpp) cc_final: 0.7980 (tpt) REVERT: R 195 ILE cc_start: 0.8748 (mt) cc_final: 0.8048 (mm) REVERT: R 198 SER cc_start: 0.8793 (t) cc_final: 0.8274 (p) REVERT: R 212 TYR cc_start: 0.6534 (m-80) cc_final: 0.5988 (m-80) REVERT: R 283 MET cc_start: 0.7641 (tpp) cc_final: 0.6964 (mtt) REVERT: R 340 PHE cc_start: 0.7712 (m-10) cc_final: 0.6191 (t80) REVERT: A 197 LYS cc_start: 0.8706 (mttt) cc_final: 0.8402 (mttm) REVERT: A 298 GLU cc_start: 0.5618 (tt0) cc_final: 0.5106 (pt0) REVERT: A 305 CYS cc_start: 0.8119 (t) cc_final: 0.7883 (t) REVERT: A 308 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 82 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: B 134 ARG cc_start: 0.7193 (ptt-90) cc_final: 0.6504 (ttt180) REVERT: B 172 GLU cc_start: 0.7556 (tp30) cc_final: 0.7346 (tm-30) REVERT: B 292 PHE cc_start: 0.7596 (m-80) cc_final: 0.7307 (m-10) REVERT: E 141 MET cc_start: 0.7622 (mmm) cc_final: 0.7065 (mmm) REVERT: E 161 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6563 (mpp80) REVERT: E 193 MET cc_start: 0.6460 (mmm) cc_final: 0.5933 (ttp) REVERT: M 92 MET cc_start: 0.6120 (mmt) cc_final: 0.5425 (mmt) REVERT: M 231 GLU cc_start: 0.7583 (tt0) cc_final: 0.7321 (tp30) outliers start: 33 outliers final: 23 residues processed: 213 average time/residue: 0.1300 time to fit residues: 38.7813 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain A residue 48 THR 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 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: 2.9990 chunk 13 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 214 GLN R 330 ASN A 306 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148954 restraints weight = 13322.888| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.84 r_work: 0.3631 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11982 Z= 0.126 Angle : 0.515 7.445 16305 Z= 0.264 Chirality : 0.039 0.138 1903 Planarity : 0.003 0.043 1962 Dihedral : 4.874 31.631 2215 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.06 % Allowed : 12.85 % Favored : 85.09 % 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 aren not related in a simple way. whole: 1.69 (0.22), residues: 1421 helix: 2.48 (0.20), residues: 662 sheet: 0.45 (0.31), residues: 295 loop : -0.42 (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 95 PHE 0.022 0.001 PHE A 334 TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00292 (11977) covalent geometry : angle 0.51477 (16299) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.74800 ( 6) hydrogen bonds : bond 0.03405 ( 653) hydrogen bonds : angle 4.31827 ( 1890) Misc. bond : bond 0.00011 ( 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 207 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8213 (tpp) cc_final: 0.7848 (tpt) REVERT: R 195 ILE cc_start: 0.8713 (mt) cc_final: 0.7993 (mm) REVERT: R 198 SER cc_start: 0.8761 (t) cc_final: 0.8219 (p) REVERT: R 212 TYR cc_start: 0.6515 (m-80) cc_final: 0.5971 (m-80) REVERT: R 283 MET cc_start: 0.7456 (tpp) cc_final: 0.6901 (mtt) REVERT: R 340 PHE cc_start: 0.7685 (m-10) cc_final: 0.7279 (m-10) REVERT: A 197 LYS cc_start: 0.8609 (mttt) cc_final: 0.8348 (mttm) REVERT: A 298 GLU cc_start: 0.5522 (tt0) cc_final: 0.5018 (pt0) REVERT: A 305 CYS cc_start: 0.8064 (t) cc_final: 0.7820 (t) REVERT: A 308 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: B 52 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7756 (mmt180) REVERT: B 82 TRP cc_start: 0.7549 (OUTLIER) cc_final: 0.6938 (m-10) REVERT: B 134 ARG cc_start: 0.7042 (ptt-90) cc_final: 0.6350 (ttt180) REVERT: B 292 PHE cc_start: 0.7508 (m-80) cc_final: 0.7106 (m-10) REVERT: C 62 ARG cc_start: 0.5969 (mtm-85) cc_final: 0.5454 (mtt180) REVERT: E 141 MET cc_start: 0.7598 (mmm) cc_final: 0.7029 (mmm) REVERT: E 161 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6532 (mpp80) REVERT: E 193 MET cc_start: 0.6459 (mmm) cc_final: 0.5951 (ttp) REVERT: M 92 MET cc_start: 0.6042 (mmt) cc_final: 0.5482 (mmt) REVERT: M 231 GLU cc_start: 0.7515 (tt0) cc_final: 0.7271 (tp30) REVERT: Q 3 TRP cc_start: 0.7407 (t-100) cc_final: 0.7099 (t-100) outliers start: 26 outliers final: 23 residues processed: 201 average time/residue: 0.1290 time to fit residues: 36.0724 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU 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 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 140 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: 0.9990 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4102 r_free = 0.4102 target = 0.179302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145746 restraints weight = 13586.772| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.79 r_work: 0.3595 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11982 Z= 0.158 Angle : 0.552 8.786 16305 Z= 0.285 Chirality : 0.040 0.134 1903 Planarity : 0.004 0.044 1962 Dihedral : 5.059 35.385 2215 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.46 % Allowed : 13.01 % Favored : 84.54 % 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 aren not related in a simple way. whole: 1.56 (0.22), residues: 1421 helix: 2.38 (0.20), residues: 662 sheet: 0.41 (0.31), residues: 293 loop : -0.51 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.013 0.001 TYR R 301 PHE 0.021 0.002 PHE A 334 TRP 0.021 0.002 TRP B 99 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00373 (11977) covalent geometry : angle 0.55230 (16299) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.95046 ( 6) hydrogen bonds : bond 0.03576 ( 653) hydrogen bonds : angle 4.42068 ( 1890) Misc. bond : bond 0.00007 ( 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 214 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8273 (tpp) cc_final: 0.7939 (tpt) REVERT: R 195 ILE cc_start: 0.8744 (mt) cc_final: 0.8034 (mm) REVERT: R 198 SER cc_start: 0.8778 (t) cc_final: 0.8246 (p) REVERT: R 212 TYR cc_start: 0.6500 (m-80) cc_final: 0.5941 (m-80) REVERT: R 283 MET cc_start: 0.7549 (tpp) cc_final: 0.6979 (mtt) REVERT: A 197 LYS cc_start: 0.8616 (mttt) cc_final: 0.8391 (mttm) REVERT: A 298 GLU cc_start: 0.5369 (tt0) cc_final: 0.4909 (pt0) REVERT: A 305 CYS cc_start: 0.8083 (t) cc_final: 0.7813 (t) REVERT: A 308 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 52 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7920 (mmt180) REVERT: B 82 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.7022 (m-10) REVERT: B 134 ARG cc_start: 0.6990 (ptt-90) cc_final: 0.6346 (ttt180) REVERT: B 239 ASN cc_start: 0.7863 (m-40) cc_final: 0.7300 (p0) REVERT: B 292 PHE cc_start: 0.7612 (m-80) cc_final: 0.7192 (m-10) REVERT: E 141 MET cc_start: 0.7599 (mmm) cc_final: 0.7064 (mmm) REVERT: E 161 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6496 (mpp80) REVERT: E 193 MET cc_start: 0.6453 (mmm) cc_final: 0.5943 (ttp) REVERT: M 92 MET cc_start: 0.6047 (mmt) cc_final: 0.5325 (mmt) REVERT: M 163 MET cc_start: 0.8039 (ttm) cc_final: 0.7717 (mtm) REVERT: M 231 GLU cc_start: 0.7533 (tt0) cc_final: 0.7276 (tp30) outliers start: 31 outliers final: 25 residues processed: 205 average time/residue: 0.1204 time to fit residues: 34.8766 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 110 ASN Chi-restraints excluded: chain B residue 146 LEU 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 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 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 24 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145593 restraints weight = 13435.868| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.01 r_work: 0.3601 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11982 Z= 0.140 Angle : 0.539 9.162 16305 Z= 0.278 Chirality : 0.040 0.129 1903 Planarity : 0.004 0.043 1962 Dihedral : 4.980 35.826 2215 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.22 % Allowed : 13.80 % Favored : 83.98 % 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 aren not related in a simple way. whole: 1.56 (0.22), residues: 1421 helix: 2.37 (0.20), residues: 662 sheet: 0.48 (0.31), residues: 283 loop : -0.54 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.012 0.001 TYR E 95 PHE 0.022 0.001 PHE A 334 TRP 0.023 0.002 TRP E 47 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00330 (11977) covalent geometry : angle 0.53903 (16299) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.78255 ( 6) hydrogen bonds : bond 0.03500 ( 653) hydrogen bonds : angle 4.43380 ( 1890) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.91 seconds wall clock time: 57 minutes 55.02 seconds (3475.02 seconds total)