Starting phenix.real_space_refine on Sat Aug 23 18:12:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bnz_16137/08_2025/8bnz_16137.map" } resolution = 3.5 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= 0.031 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 41 5.16 5 C 8855 2.51 5 N 2409 2.21 5 O 2768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 14073 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6209 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 6, 'TRANS': 50} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "P" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2333 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Time building chain proxies: 3.55, per 1000 atoms: 0.25 Number of scatterers: 14073 At special positions: 0 Unit cell: (127.41, 131.13, 139.5, 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 41 16.00 O 2768 8.00 N 2409 7.00 C 8855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS P1293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 687.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 21.1% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.641A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.371A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.618A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.873A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.624A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.715A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.880A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.626A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.102A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.955A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.739A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'P' and resid 1000 through 1036 removed outlier: 4.289A pdb=" N ASP P1014 " --> pdb=" O LEU P1010 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR P1015 " --> pdb=" O PHE P1011 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P1027 " --> pdb=" O ASN P1023 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG P1028 " --> pdb=" O ASN P1024 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET P1029 " --> pdb=" O LEU P1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 5.736A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 167 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 4.573A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 183 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 4.236A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 343 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 276 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.255A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.255A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.438A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL P1292 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P1202 " --> pdb=" O LEU P1233 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.438A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL P1292 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P1202 " --> pdb=" O LEU P1233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA P1117 " --> pdb=" O PHE P1113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P1097 " --> pdb=" O THR P1133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.152A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.154A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 389 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.548A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.501A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.693A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.543A pdb=" N ARG B 295 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 308 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.473A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.985A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.697A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 1181 through 1184 removed outlier: 4.688A pdb=" N LYS P1181 " --> pdb=" O ASP P1196 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP P1196 " --> pdb=" O LYS P1181 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2115 1.25 - 1.40: 3237 1.40 - 1.54: 7250 1.54 - 1.69: 1696 1.69 - 1.83: 80 Bond restraints: 14378 Sorted by residual: bond pdb=" CA VAL A 173 " pdb=" CB VAL A 173 " ideal model delta sigma weight residual 1.548 1.399 0.150 1.49e-02 4.50e+03 1.01e+02 bond pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta sigma weight residual 1.530 1.706 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" CA LYS A 103 " pdb=" C LYS A 103 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.57e-02 4.06e+03 6.79e+01 bond pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 1.235 1.110 0.125 1.62e-02 3.81e+03 5.97e+01 bond pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " ideal model delta sigma weight residual 1.520 1.750 -0.230 3.00e-02 1.11e+03 5.88e+01 ... (remaining 14373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.27: 19393 6.27 - 12.54: 110 12.54 - 18.81: 7 18.81 - 25.07: 5 25.07 - 31.34: 1 Bond angle restraints: 19516 Sorted by residual: angle pdb=" O GLU B 27 " pdb=" C GLU B 27 " pdb=" N ASP B 28 " ideal model delta sigma weight residual 123.27 103.23 20.04 1.22e+00 6.72e-01 2.70e+02 angle pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 111.30 142.64 -31.34 2.30e+00 1.89e-01 1.86e+02 angle pdb=" CA LYS A 103 " pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 120.32 105.83 14.49 1.18e+00 7.18e-01 1.51e+02 angle pdb=" C GLU B 26 " pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta sigma weight residual 110.10 132.96 -22.86 1.90e+00 2.77e-01 1.45e+02 angle pdb=" C GLU B 26 " pdb=" N GLU B 27 " pdb=" CA GLU B 27 " ideal model delta sigma weight residual 122.73 142.21 -19.48 1.62e+00 3.81e-01 1.45e+02 ... (remaining 19511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7813 17.87 - 35.74: 498 35.74 - 53.60: 79 53.60 - 71.47: 49 71.47 - 89.34: 30 Dihedral angle restraints: 8469 sinusoidal: 3290 harmonic: 5179 Sorted by residual: dihedral pdb=" C SER A 104 " pdb=" N SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta harmonic sigma weight residual -122.60 -159.60 37.00 0 2.50e+00 1.60e-01 2.19e+02 dihedral pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta harmonic sigma weight residual 122.80 158.82 -36.02 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" N GLU B 26 " pdb=" C GLU B 26 " pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta harmonic sigma weight residual 122.80 104.54 18.26 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 2070 0.303 - 0.606: 41 0.606 - 0.908: 0 0.908 - 1.211: 0 1.211 - 1.514: 1 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA SER A 104 " pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CB SER A 104 " both_signs ideal model delta sigma weight residual False 2.51 1.00 1.51 2.00e-01 2.50e+01 5.73e+01 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA THR B 239 " pdb=" N THR B 239 " pdb=" C THR B 239 " pdb=" CB THR B 239 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.17e+00 ... (remaining 2109 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 184 " 0.167 2.00e-02 2.50e+03 9.35e-02 1.75e+02 pdb=" CG TYR D 184 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 184 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR D 184 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR D 184 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR D 184 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR D 184 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR D 184 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 229 " -0.078 2.00e-02 2.50e+03 8.10e-02 1.31e+02 pdb=" CG TYR A 229 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 229 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 229 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 229 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR A 229 " 0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 229 " 0.071 2.00e-02 2.50e+03 pdb=" OH TYR A 229 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 93 " 0.035 2.00e-02 2.50e+03 6.06e-02 9.19e+01 pdb=" CG TRP B 93 " -0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP B 93 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 93 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP B 93 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 TRP B 93 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 93 " 0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 93 " -0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 93 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP B 93 " -0.027 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 774 2.72 - 3.27: 12872 3.27 - 3.81: 22518 3.81 - 4.36: 29491 4.36 - 4.90: 49812 Nonbonded interactions: 115467 Sorted by model distance: nonbonded pdb=" O LYS A 103 " pdb=" CB LYS A 103 " model vdw 2.180 2.752 nonbonded pdb=" O GLU B 27 " pdb=" CA ASP B 28 " model vdw 2.292 2.776 nonbonded pdb=" O LYS A 103 " pdb=" CA GLU B 26 " model vdw 2.335 3.470 nonbonded pdb=" CB LYS A 103 " pdb=" O GLU B 27 " model vdw 2.346 3.440 nonbonded pdb=" N VAL A 105 " pdb=" OE2 GLU B 26 " model vdw 2.353 3.120 ... (remaining 115462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 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 : 0.018 0.230 14380 Z= 1.091 Angle : 2.270 31.343 19520 Z= 1.605 Chirality : 0.122 1.514 2112 Planarity : 0.017 0.149 2571 Dihedral : 14.407 89.338 5177 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.67 % Allowed : 6.10 % Favored : 93.23 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.19), residues: 1795 helix: 1.93 (0.27), residues: 352 sheet: 0.37 (0.21), residues: 602 loop : -1.81 (0.18), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG A 212 TYR 0.167 0.022 TYR D 184 PHE 0.068 0.012 PHE B 356 TRP 0.123 0.018 TRP B 93 HIS 0.018 0.005 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.01752 (14378) covalent geometry : angle 2.26970 (19516) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.00743 ( 4) hydrogen bonds : bond 0.15430 ( 693) hydrogen bonds : angle 7.07216 ( 2553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 450 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 TYR cc_start: 0.5421 (m-80) cc_final: 0.5161 (m-10) REVERT: C 58 LEU cc_start: 0.8255 (mt) cc_final: 0.8052 (mp) REVERT: E 32 ILE cc_start: 0.8533 (mm) cc_final: 0.8268 (mt) REVERT: P 1285 LYS cc_start: 0.3243 (tttp) cc_final: 0.2608 (tmtt) outliers start: 10 outliers final: 3 residues processed: 460 average time/residue: 0.1344 time to fit residues: 88.3963 Evaluate side-chains 266 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain P residue 1053 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 215 GLN A 280 HIS A 448 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 563 ASN A 664 GLN A 731 ASN A 748 ASN B 70 ASN B 121 HIS B 170 GLN B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 359 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 104 ASN D 138 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN P1170 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.224120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.169787 restraints weight = 17360.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169714 restraints weight = 14255.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172592 restraints weight = 9539.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.171919 restraints weight = 6697.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172354 restraints weight = 6918.583| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14380 Z= 0.271 Angle : 0.729 14.385 19520 Z= 0.395 Chirality : 0.048 0.290 2112 Planarity : 0.005 0.080 2571 Dihedral : 5.969 67.767 1985 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.55 % Allowed : 12.00 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.19), residues: 1795 helix: 2.30 (0.27), residues: 356 sheet: 0.32 (0.21), residues: 619 loop : -1.43 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 338 TYR 0.024 0.002 TYR D 184 PHE 0.018 0.002 PHE A 804 TRP 0.030 0.003 TRP B 48 HIS 0.008 0.002 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00598 (14378) covalent geometry : angle 0.72923 (19516) SS BOND : bond 0.00373 ( 2) SS BOND : angle 0.82182 ( 4) hydrogen bonds : bond 0.04415 ( 693) hydrogen bonds : angle 5.34478 ( 2553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8045 (t80) cc_final: 0.7517 (t80) REVERT: A 340 ASN cc_start: 0.7959 (t0) cc_final: 0.7328 (p0) REVERT: A 391 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6861 (ttp80) REVERT: B 69 ASP cc_start: 0.7085 (t0) cc_final: 0.6831 (t0) REVERT: B 359 GLN cc_start: 0.5873 (OUTLIER) cc_final: 0.5468 (tt0) REVERT: B 368 GLN cc_start: 0.7791 (pp30) cc_final: 0.7589 (pp30) REVERT: C 58 LEU cc_start: 0.8912 (mt) cc_final: 0.8545 (mp) REVERT: D 99 ASN cc_start: 0.7545 (t0) cc_final: 0.7190 (t0) REVERT: D 146 ASP cc_start: 0.7777 (m-30) cc_final: 0.7478 (m-30) REVERT: P 1170 GLN cc_start: 0.4182 (pt0) cc_final: 0.3955 (pt0) outliers start: 53 outliers final: 30 residues processed: 291 average time/residue: 0.1271 time to fit residues: 55.4448 Evaluate side-chains 243 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 108 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 403 GLN A 441 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN P1160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.224052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160657 restraints weight = 17429.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164605 restraints weight = 10836.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165471 restraints weight = 7413.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165981 restraints weight = 7248.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166196 restraints weight = 7069.726| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14380 Z= 0.194 Angle : 0.628 10.330 19520 Z= 0.339 Chirality : 0.044 0.172 2112 Planarity : 0.004 0.060 2571 Dihedral : 5.545 61.913 1981 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.49 % Allowed : 13.47 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1795 helix: 2.12 (0.27), residues: 355 sheet: 0.28 (0.20), residues: 632 loop : -1.28 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 112 TYR 0.024 0.002 TYR D 184 PHE 0.021 0.002 PHE A 804 TRP 0.036 0.002 TRP B 48 HIS 0.009 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00417 (14378) covalent geometry : angle 0.62809 (19516) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.64155 ( 4) hydrogen bonds : bond 0.03896 ( 693) hydrogen bonds : angle 4.90700 ( 2553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7583 (m-30) cc_final: 0.7355 (t0) REVERT: A 229 TYR cc_start: 0.8395 (t80) cc_final: 0.7862 (t80) REVERT: A 339 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 340 ASN cc_start: 0.8007 (t0) cc_final: 0.7268 (p0) REVERT: A 391 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6755 (ttp80) REVERT: B 69 ASP cc_start: 0.7144 (t0) cc_final: 0.6868 (t0) REVERT: B 228 TRP cc_start: 0.8061 (p-90) cc_final: 0.7851 (p90) REVERT: B 246 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5910 (m-30) REVERT: C 58 LEU cc_start: 0.8934 (mt) cc_final: 0.8525 (mp) REVERT: D 99 ASN cc_start: 0.7642 (t0) cc_final: 0.7431 (t0) REVERT: P 1060 TYR cc_start: 0.6185 (p90) cc_final: 0.5959 (p90) REVERT: P 1144 TYR cc_start: 0.6211 (t80) cc_final: 0.5874 (t80) outliers start: 52 outliers final: 33 residues processed: 273 average time/residue: 0.1151 time to fit residues: 48.0053 Evaluate side-chains 249 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 50.0000 chunk 86 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.223467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163157 restraints weight = 17392.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163395 restraints weight = 11091.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162804 restraints weight = 8964.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163915 restraints weight = 8641.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164131 restraints weight = 7632.515| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14380 Z= 0.140 Angle : 0.586 8.160 19520 Z= 0.313 Chirality : 0.043 0.154 2112 Planarity : 0.004 0.053 2571 Dihedral : 5.257 59.991 1981 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.75 % Allowed : 14.81 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1795 helix: 2.26 (0.27), residues: 348 sheet: 0.29 (0.20), residues: 635 loop : -1.19 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 61 TYR 0.023 0.001 TYR D 184 PHE 0.024 0.001 PHE A 804 TRP 0.033 0.002 TRP B 48 HIS 0.009 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00295 (14378) covalent geometry : angle 0.58598 (19516) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.46922 ( 4) hydrogen bonds : bond 0.03547 ( 693) hydrogen bonds : angle 4.65961 ( 2553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8455 (t80) cc_final: 0.7929 (t80) REVERT: A 306 ASP cc_start: 0.7439 (m-30) cc_final: 0.7180 (m-30) REVERT: A 340 ASN cc_start: 0.8006 (t0) cc_final: 0.7263 (p0) REVERT: A 353 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7706 (mtp-110) REVERT: B 69 ASP cc_start: 0.7262 (t0) cc_final: 0.6961 (t0) REVERT: B 246 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5666 (m-30) REVERT: C 58 LEU cc_start: 0.8933 (mt) cc_final: 0.8501 (mp) REVERT: P 1112 MET cc_start: 0.6185 (mmm) cc_final: 0.5884 (ppp) outliers start: 41 outliers final: 27 residues processed: 263 average time/residue: 0.1170 time to fit residues: 46.2744 Evaluate side-chains 235 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 176 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 448 ASN B 168 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN P1020 ASN P1023 ASN P1024 ASN ** P1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.219734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164810 restraints weight = 17486.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164836 restraints weight = 15359.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167367 restraints weight = 9828.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.166000 restraints weight = 7601.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.166211 restraints weight = 8175.960| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14380 Z= 0.259 Angle : 0.663 12.693 19520 Z= 0.354 Chirality : 0.046 0.224 2112 Planarity : 0.005 0.059 2571 Dihedral : 5.492 63.218 1981 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.55 % Allowed : 15.88 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1795 helix: 1.69 (0.27), residues: 348 sheet: 0.05 (0.20), residues: 635 loop : -1.23 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 325 TYR 0.023 0.002 TYR A 550 PHE 0.025 0.002 PHE A 804 TRP 0.038 0.002 TRP B 93 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00566 (14378) covalent geometry : angle 0.66342 (19516) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.77957 ( 4) hydrogen bonds : bond 0.03987 ( 693) hydrogen bonds : angle 4.96965 ( 2553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8157 (t80) cc_final: 0.7689 (t80) REVERT: A 340 ASN cc_start: 0.8061 (t0) cc_final: 0.7417 (p0) REVERT: A 777 MET cc_start: 0.7008 (mmp) cc_final: 0.6622 (mmt) REVERT: B 69 ASP cc_start: 0.7065 (t0) cc_final: 0.6824 (t0) REVERT: B 246 ASP cc_start: 0.5793 (OUTLIER) cc_final: 0.5554 (m-30) REVERT: E 51 THR cc_start: 0.8065 (m) cc_final: 0.7526 (m) REVERT: E 54 GLN cc_start: 0.8359 (mt0) cc_final: 0.8084 (mt0) REVERT: E 70 THR cc_start: 0.7940 (p) cc_final: 0.7738 (p) outliers start: 53 outliers final: 37 residues processed: 253 average time/residue: 0.1044 time to fit residues: 40.3785 Evaluate side-chains 234 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1285 LYS Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 561 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1062 HIS P1064 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.219182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156542 restraints weight = 17444.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156772 restraints weight = 10344.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158495 restraints weight = 9301.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159047 restraints weight = 7742.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159431 restraints weight = 7617.263| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14380 Z= 0.248 Angle : 0.650 11.426 19520 Z= 0.348 Chirality : 0.045 0.206 2112 Planarity : 0.004 0.059 2571 Dihedral : 5.465 63.300 1981 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.69 % Allowed : 16.15 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.19), residues: 1795 helix: 1.48 (0.27), residues: 350 sheet: -0.10 (0.20), residues: 621 loop : -1.31 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 325 TYR 0.023 0.002 TYR P1150 PHE 0.017 0.002 PHE A 804 TRP 0.017 0.002 TRP A 776 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00541 (14378) covalent geometry : angle 0.64952 (19516) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.69401 ( 4) hydrogen bonds : bond 0.03893 ( 693) hydrogen bonds : angle 4.93841 ( 2553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8539 (t80) cc_final: 0.7927 (t80) REVERT: A 340 ASN cc_start: 0.8129 (t0) cc_final: 0.7300 (p0) REVERT: A 777 MET cc_start: 0.7603 (mmp) cc_final: 0.7266 (mmt) REVERT: B 69 ASP cc_start: 0.7313 (t0) cc_final: 0.7039 (t0) REVERT: B 246 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5711 (m-30) REVERT: C 80 LEU cc_start: 0.7068 (tp) cc_final: 0.6708 (tp) REVERT: D 114 LEU cc_start: 0.9188 (tp) cc_final: 0.8962 (tp) REVERT: D 146 ASP cc_start: 0.7600 (m-30) cc_final: 0.7331 (m-30) REVERT: E 51 THR cc_start: 0.8163 (m) cc_final: 0.7513 (m) REVERT: E 54 GLN cc_start: 0.8375 (mt0) cc_final: 0.8002 (mt0) REVERT: P 1062 HIS cc_start: 0.6777 (t70) cc_final: 0.5913 (t-90) REVERT: P 1064 GLN cc_start: 0.7709 (mt0) cc_final: 0.7481 (mp10) REVERT: P 1112 MET cc_start: 0.6179 (mmm) cc_final: 0.5900 (ppp) outliers start: 55 outliers final: 40 residues processed: 258 average time/residue: 0.1048 time to fit residues: 41.5344 Evaluate side-chains 247 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 803 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS P1200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.218106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152571 restraints weight = 17404.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156045 restraints weight = 10802.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156358 restraints weight = 8702.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157174 restraints weight = 7456.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157746 restraints weight = 7357.173| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14380 Z= 0.198 Angle : 0.627 11.033 19520 Z= 0.336 Chirality : 0.045 0.208 2112 Planarity : 0.004 0.056 2571 Dihedral : 5.328 61.478 1981 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.88 % Allowed : 18.16 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.19), residues: 1795 helix: 1.56 (0.27), residues: 350 sheet: -0.17 (0.20), residues: 626 loop : -1.29 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.023 0.002 TYR D 184 PHE 0.012 0.001 PHE A 804 TRP 0.017 0.002 TRP A 776 HIS 0.013 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00433 (14378) covalent geometry : angle 0.62712 (19516) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.51164 ( 4) hydrogen bonds : bond 0.03727 ( 693) hydrogen bonds : angle 4.80571 ( 2553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8522 (t80) cc_final: 0.7941 (t80) REVERT: A 340 ASN cc_start: 0.8122 (t0) cc_final: 0.7303 (p0) REVERT: A 430 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 69 ASP cc_start: 0.7356 (t0) cc_final: 0.7087 (t0) REVERT: D 87 LEU cc_start: 0.9114 (mt) cc_final: 0.8822 (mt) REVERT: E 51 THR cc_start: 0.8041 (m) cc_final: 0.6957 (m) REVERT: E 54 GLN cc_start: 0.8331 (mt0) cc_final: 0.8091 (mt0) REVERT: P 1112 MET cc_start: 0.6315 (mmm) cc_final: 0.5895 (ppp) outliers start: 43 outliers final: 36 residues processed: 239 average time/residue: 0.1043 time to fit residues: 38.2229 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 125 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN P1020 ASN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.217860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.162892 restraints weight = 17140.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163079 restraints weight = 14198.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165377 restraints weight = 10568.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165136 restraints weight = 8922.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165595 restraints weight = 8658.531| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14380 Z= 0.263 Angle : 0.663 10.558 19520 Z= 0.355 Chirality : 0.046 0.224 2112 Planarity : 0.004 0.060 2571 Dihedral : 5.467 62.643 1981 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.69 % Allowed : 17.56 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1795 helix: 1.34 (0.27), residues: 353 sheet: -0.30 (0.20), residues: 626 loop : -1.34 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 281 TYR 0.023 0.002 TYR D 184 PHE 0.024 0.002 PHE A 804 TRP 0.018 0.002 TRP A 776 HIS 0.011 0.002 HIS P1128 Details of bonding type rmsd covalent geometry : bond 0.00580 (14378) covalent geometry : angle 0.66295 (19516) SS BOND : bond 0.00389 ( 2) SS BOND : angle 0.61287 ( 4) hydrogen bonds : bond 0.03980 ( 693) hydrogen bonds : angle 4.95685 ( 2553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8088 (t80) cc_final: 0.7661 (t80) REVERT: A 340 ASN cc_start: 0.8100 (t0) cc_final: 0.7352 (p0) REVERT: A 777 MET cc_start: 0.6971 (mmp) cc_final: 0.6585 (mmt) REVERT: B 69 ASP cc_start: 0.7037 (t0) cc_final: 0.6820 (t0) REVERT: C 41 TYR cc_start: 0.2321 (p90) cc_final: 0.1539 (p90) REVERT: D 34 GLU cc_start: 0.6881 (mp0) cc_final: 0.6493 (mp0) REVERT: D 87 LEU cc_start: 0.9076 (mt) cc_final: 0.8801 (mt) outliers start: 55 outliers final: 46 residues processed: 246 average time/residue: 0.1009 time to fit residues: 38.4464 Evaluate side-chains 246 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 chunk 99 optimal weight: 0.3980 chunk 168 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 448 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 225 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.223521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175645 restraints weight = 17390.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173901 restraints weight = 17320.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165753 restraints weight = 9564.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166615 restraints weight = 9064.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166745 restraints weight = 7980.505| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14380 Z= 0.171 Angle : 0.637 11.550 19520 Z= 0.334 Chirality : 0.045 0.371 2112 Planarity : 0.004 0.057 2571 Dihedral : 5.298 59.664 1981 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.08 % Allowed : 18.10 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.19), residues: 1795 helix: 1.54 (0.27), residues: 353 sheet: -0.23 (0.21), residues: 608 loop : -1.28 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.033 0.001 TYR A 550 PHE 0.016 0.001 PHE P1283 TRP 0.022 0.002 TRP P1219 HIS 0.007 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00370 (14378) covalent geometry : angle 0.63699 (19516) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.48227 ( 4) hydrogen bonds : bond 0.03663 ( 693) hydrogen bonds : angle 4.73899 ( 2553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8372 (t80) cc_final: 0.7876 (t80) REVERT: A 340 ASN cc_start: 0.8105 (t0) cc_final: 0.7325 (p0) REVERT: A 430 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7724 (tt) REVERT: A 551 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (p) REVERT: A 777 MET cc_start: 0.7294 (mmp) cc_final: 0.6906 (mmt) REVERT: B 32 MET cc_start: 0.7342 (tpp) cc_final: 0.7100 (tpp) REVERT: B 69 ASP cc_start: 0.7163 (t0) cc_final: 0.6957 (t0) outliers start: 46 outliers final: 41 residues processed: 238 average time/residue: 0.0884 time to fit residues: 32.4389 Evaluate side-chains 242 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 0.0010 chunk 138 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 448 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 225 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN P1128 HIS P1200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.220404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.172384 restraints weight = 17423.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172708 restraints weight = 17670.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166967 restraints weight = 9365.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165591 restraints weight = 10149.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167432 restraints weight = 10260.401| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14380 Z= 0.309 Angle : 0.721 16.263 19520 Z= 0.382 Chirality : 0.048 0.308 2112 Planarity : 0.005 0.058 2571 Dihedral : 5.606 63.214 1981 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.35 % Allowed : 17.96 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.19), residues: 1795 helix: 1.15 (0.27), residues: 353 sheet: -0.42 (0.20), residues: 615 loop : -1.36 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 355 TYR 0.032 0.002 TYR A 608 PHE 0.021 0.002 PHE A 804 TRP 0.022 0.003 TRP P1219 HIS 0.016 0.002 HIS P1128 Details of bonding type rmsd covalent geometry : bond 0.00681 (14378) covalent geometry : angle 0.72149 (19516) SS BOND : bond 0.00468 ( 2) SS BOND : angle 0.72394 ( 4) hydrogen bonds : bond 0.04150 ( 693) hydrogen bonds : angle 5.12175 ( 2553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8281 (t80) cc_final: 0.7887 (t80) REVERT: A 340 ASN cc_start: 0.8146 (t0) cc_final: 0.7328 (p0) REVERT: A 777 MET cc_start: 0.7154 (mmp) cc_final: 0.6775 (mmt) REVERT: B 69 ASP cc_start: 0.7089 (t0) cc_final: 0.6874 (t0) REVERT: C 41 TYR cc_start: 0.2256 (p90) cc_final: 0.1577 (p90) REVERT: P 1257 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6696 (mtm-85) outliers start: 50 outliers final: 45 residues processed: 239 average time/residue: 0.0960 time to fit residues: 34.9190 Evaluate side-chains 245 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1099 LYS Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.220644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.173174 restraints weight = 17315.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169245 restraints weight = 17425.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165112 restraints weight = 11202.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164965 restraints weight = 10841.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165631 restraints weight = 9380.234| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14380 Z= 0.261 Angle : 0.677 13.285 19520 Z= 0.361 Chirality : 0.047 0.270 2112 Planarity : 0.005 0.060 2571 Dihedral : 5.653 64.181 1981 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.15 % Allowed : 18.50 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 1795 helix: 1.12 (0.27), residues: 355 sheet: -0.47 (0.20), residues: 615 loop : -1.39 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 321 TYR 0.032 0.002 TYR A 550 PHE 0.019 0.002 PHE A 804 TRP 0.023 0.002 TRP B 48 HIS 0.007 0.001 HIS P1128 Details of bonding type rmsd covalent geometry : bond 0.00572 (14378) covalent geometry : angle 0.67744 (19516) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.63129 ( 4) hydrogen bonds : bond 0.03934 ( 693) hydrogen bonds : angle 5.01762 ( 2553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.84 seconds wall clock time: 49 minutes 57.16 seconds (2997.16 seconds total)