Starting phenix.real_space_refine on Tue Mar 3 23:07:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2026/8d81_27242.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 56 5.16 5 C 5883 2.51 5 N 1563 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6290 Classifications: {'peptide': 817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 790} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2937 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 8, 'HIS:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' ZN': 1, 'Y70': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8449 SG CYS B 323 14.794 80.857 40.508 1.00 0.00 S ATOM 8465 SG CYS B 326 11.359 81.448 42.109 1.00 0.00 S ATOM 8965 SG CYS B 391 12.206 83.079 38.765 1.00 0.00 S ATOM 8984 SG CYS B 394 13.753 84.339 41.887 1.00 0.00 S Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9248 At special positions: 0 Unit cell: (98.28, 114.66, 99.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 56 16.00 O 1745 8.00 N 1563 7.00 C 5883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 426.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " Number of angles added : 6 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 22 sheets defined 15.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.195A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 removed outlier: 3.736A pdb=" N ASN A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A1059 " --> pdb=" O GLN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.547A pdb=" N LYS A1067 " --> pdb=" O SER A1064 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A1068 " --> pdb=" O VAL A1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1068' Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1100 Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 3.743A pdb=" N GLN A1106 " --> pdb=" O ARG A1102 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.661A pdb=" N ILE A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.701A pdb=" N GLN B 225 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 4.219A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.880A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 318 Processing helix chain 'B' and resid 329 through 333 removed outlier: 3.618A pdb=" N THR B 332 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.857A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A1038 " --> pdb=" O PHE A1030 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.633A pdb=" N GLY A 21 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 30 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 42 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 6.692A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 81 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 92 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 99 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.855A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 189 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.524A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.589A pdb=" N ILE A 248 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.505A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 262 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 272 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 289 through 290 removed outlier: 4.339A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 296 " --> pdb=" O GLU A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.687A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 348 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.641A pdb=" N ILE A 390 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.477A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 736 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 732 " --> pdb=" O GLN A 727 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.647A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.836A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 883 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 914 through 917 removed outlier: 3.575A pdb=" N LYS A 915 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 957 through 959 removed outlier: 3.501A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 66 removed outlier: 8.278A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 142 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.645A pdb=" N ILE B 81 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 142 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.613A pdb=" N LEU B 423 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 348 through 351 removed outlier: 4.318A pdb=" N ASN B 351 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.533A pdb=" N VAL B 362 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 368 through 370 removed outlier: 4.475A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1559 1.31 - 1.44: 2435 1.44 - 1.56: 5357 1.56 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 9433 Sorted by residual: bond pdb=" C15 Y70 B 502 " pdb=" N16 Y70 B 502 " ideal model delta sigma weight residual 1.372 1.483 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C6 Y70 B 502 " pdb=" N10 Y70 B 502 " ideal model delta sigma weight residual 1.343 1.453 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C17 Y70 B 502 " pdb=" N16 Y70 B 502 " ideal model delta sigma weight residual 1.383 1.489 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" N PRO A 825 " pdb=" CA PRO A 825 " ideal model delta sigma weight residual 1.469 1.530 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" C5 Y70 B 502 " pdb=" C9 Y70 B 502 " ideal model delta sigma weight residual 1.459 1.542 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 9428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12542 2.05 - 4.10: 239 4.10 - 6.15: 26 6.15 - 8.20: 7 8.20 - 10.25: 2 Bond angle restraints: 12816 Sorted by residual: angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.25 111.06 -7.81 1.05e+00 9.07e-01 5.53e+01 angle pdb=" C ASP A 824 " pdb=" N PRO A 825 " pdb=" CA PRO A 825 " ideal model delta sigma weight residual 120.04 128.00 -7.96 1.08e+00 8.57e-01 5.43e+01 angle pdb=" C TRP A1073 " pdb=" N ARG A1074 " pdb=" CA ARG A1074 " ideal model delta sigma weight residual 122.29 114.11 8.18 1.56e+00 4.11e-01 2.75e+01 angle pdb=" C THR A1125 " pdb=" CA THR A1125 " pdb=" CB THR A1125 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N ASP A1116 " pdb=" CA ASP A1116 " pdb=" C ASP A1116 " ideal model delta sigma weight residual 112.93 107.41 5.52 1.33e+00 5.65e-01 1.72e+01 ... (remaining 12811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 5293 23.92 - 47.84: 316 47.84 - 71.77: 22 71.77 - 95.69: 15 95.69 - 119.61: 3 Dihedral angle restraints: 5649 sinusoidal: 2170 harmonic: 3479 Sorted by residual: dihedral pdb=" CA GLY B 69 " pdb=" C GLY B 69 " pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA VAL B 80 " pdb=" C VAL B 80 " pdb=" N ILE B 81 " pdb=" CA ILE B 81 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N GLU B 153 " pdb=" CA GLU B 153 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1249 0.064 - 0.127: 208 0.127 - 0.191: 9 0.191 - 0.254: 6 0.254 - 0.318: 3 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA VAL B 182 " pdb=" N VAL B 182 " pdb=" C VAL B 182 " pdb=" CB VAL B 182 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS A 725 " pdb=" N CYS A 725 " pdb=" C CYS A 725 " pdb=" CB CYS A 725 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL B 182 " pdb=" CA VAL B 182 " pdb=" CG1 VAL B 182 " pdb=" CG2 VAL B 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1472 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 724 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ILE A 724 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 724 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS A 725 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 180 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ALA B 180 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA B 180 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 181 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1022 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A1023 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1023 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1023 " 0.027 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2119 2.79 - 3.32: 8307 3.32 - 3.85: 14249 3.85 - 4.37: 16062 4.37 - 4.90: 28803 Nonbonded interactions: 69540 Sorted by model distance: nonbonded pdb=" ND2 ASN B 351 " pdb=" O TYR B 355 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLU A 213 " pdb=" OG SER A 236 " model vdw 2.267 3.040 nonbonded pdb=" N ASN A 826 " pdb=" OD1 ASN A 826 " model vdw 2.277 3.120 nonbonded pdb=" ND2 ASN A 36 " pdb=" OD1 ASN A1034 " model vdw 2.309 3.120 nonbonded pdb=" OE2 GLU A 72 " pdb=" NH2 ARG A 103 " model vdw 2.329 3.120 ... (remaining 69535 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: 1.000 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 9437 Z= 0.241 Angle : 0.656 10.247 12822 Z= 0.377 Chirality : 0.049 0.318 1475 Planarity : 0.004 0.048 1648 Dihedral : 14.939 119.609 3405 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % Rotamer: Outliers : 1.32 % Allowed : 1.02 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.24), residues: 1190 helix: -0.36 (0.42), residues: 164 sheet: -1.30 (0.29), residues: 352 loop : -1.89 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.011 0.001 TYR A 828 PHE 0.010 0.001 PHE A1072 TRP 0.013 0.001 TRP A 207 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9433) covalent geometry : angle 0.65428 (12816) hydrogen bonds : bond 0.26472 ( 253) hydrogen bonds : angle 9.71283 ( 699) metal coordination : bond 0.00399 ( 4) metal coordination : angle 2.35029 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.326 Fit side-chains REVERT: A 135 LEU cc_start: 0.8929 (mt) cc_final: 0.8694 (mp) REVERT: B 89 MET cc_start: 0.6768 (ptm) cc_final: 0.6308 (ptt) REVERT: B 313 ASP cc_start: 0.7336 (t70) cc_final: 0.6954 (t0) outliers start: 13 outliers final: 2 residues processed: 168 average time/residue: 0.0843 time to fit residues: 20.6913 Evaluate side-chains 121 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 ASN Chi-restraints excluded: chain B residue 73 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 163 HIS A 355 ASN B 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.194224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153285 restraints weight = 10734.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150828 restraints weight = 17079.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151611 restraints weight = 16006.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150469 restraints weight = 10980.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151594 restraints weight = 9979.109| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9437 Z= 0.147 Angle : 0.587 6.896 12822 Z= 0.302 Chirality : 0.045 0.263 1475 Planarity : 0.004 0.045 1648 Dihedral : 5.592 67.360 1302 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.22 % Favored : 93.36 % Rotamer: Outliers : 1.02 % Allowed : 9.85 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.24), residues: 1190 helix: 0.08 (0.42), residues: 169 sheet: -1.27 (0.27), residues: 375 loop : -1.71 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.011 0.001 TYR A 91 PHE 0.028 0.001 PHE B 120 TRP 0.013 0.001 TRP A 207 HIS 0.005 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9433) covalent geometry : angle 0.58144 (12816) hydrogen bonds : bond 0.03764 ( 253) hydrogen bonds : angle 6.05453 ( 699) metal coordination : bond 0.00733 ( 4) metal coordination : angle 3.84736 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.357 Fit side-chains REVERT: A 135 LEU cc_start: 0.9144 (mt) cc_final: 0.8938 (mp) REVERT: B 89 MET cc_start: 0.8167 (ptm) cc_final: 0.7694 (ptt) REVERT: B 357 HIS cc_start: 0.6947 (t-90) cc_final: 0.6747 (t-90) outliers start: 10 outliers final: 9 residues processed: 133 average time/residue: 0.0796 time to fit residues: 15.6246 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.193369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152310 restraints weight = 10793.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150228 restraints weight = 16940.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151217 restraints weight = 13698.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149455 restraints weight = 10175.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150810 restraints weight = 9083.422| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9437 Z= 0.139 Angle : 0.549 8.570 12822 Z= 0.283 Chirality : 0.044 0.200 1475 Planarity : 0.004 0.046 1648 Dihedral : 4.634 49.653 1300 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.11 % Rotamer: Outliers : 1.52 % Allowed : 12.49 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.24), residues: 1190 helix: 0.22 (0.43), residues: 170 sheet: -1.22 (0.27), residues: 370 loop : -1.58 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.012 0.001 TYR A 91 PHE 0.029 0.001 PHE B 120 TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A1070 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9433) covalent geometry : angle 0.54317 (12816) hydrogen bonds : bond 0.03429 ( 253) hydrogen bonds : angle 5.53816 ( 699) metal coordination : bond 0.00627 ( 4) metal coordination : angle 3.66349 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.375 Fit side-chains REVERT: B 64 MET cc_start: 0.3561 (mmm) cc_final: 0.3182 (mmm) REVERT: B 89 MET cc_start: 0.8111 (ptm) cc_final: 0.7684 (ptt) REVERT: B 331 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6867 (mm) outliers start: 15 outliers final: 9 residues processed: 136 average time/residue: 0.0802 time to fit residues: 16.3740 Evaluate side-chains 127 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 331 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.193299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154838 restraints weight = 10531.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152865 restraints weight = 16265.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153736 restraints weight = 15314.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151564 restraints weight = 10820.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153676 restraints weight = 9520.645| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9437 Z= 0.097 Angle : 0.518 7.249 12822 Z= 0.268 Chirality : 0.043 0.203 1475 Planarity : 0.003 0.045 1648 Dihedral : 4.340 50.229 1300 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.88 % Favored : 93.78 % Rotamer: Outliers : 1.93 % Allowed : 13.71 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.24), residues: 1190 helix: 0.26 (0.42), residues: 174 sheet: -1.08 (0.27), residues: 375 loop : -1.46 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.009 0.001 TYR A 91 PHE 0.031 0.001 PHE B 120 TRP 0.011 0.001 TRP A 207 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9433) covalent geometry : angle 0.51357 (12816) hydrogen bonds : bond 0.02861 ( 253) hydrogen bonds : angle 5.07319 ( 699) metal coordination : bond 0.00540 ( 4) metal coordination : angle 3.22356 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.343 Fit side-chains REVERT: A 35 LYS cc_start: 0.8661 (mttt) cc_final: 0.8057 (mttp) REVERT: A 207 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.6197 (p-90) REVERT: B 64 MET cc_start: 0.3552 (mmm) cc_final: 0.3096 (mmm) REVERT: B 89 MET cc_start: 0.8100 (ptm) cc_final: 0.7672 (ptt) REVERT: B 111 ARG cc_start: 0.7337 (ptp90) cc_final: 0.7109 (ptt-90) outliers start: 19 outliers final: 9 residues processed: 139 average time/residue: 0.0838 time to fit residues: 16.9624 Evaluate side-chains 127 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152502 restraints weight = 10513.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151743 restraints weight = 17506.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151671 restraints weight = 15912.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149412 restraints weight = 12843.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151083 restraints weight = 10332.400| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9437 Z= 0.119 Angle : 0.527 12.421 12822 Z= 0.268 Chirality : 0.043 0.176 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.290 51.516 1300 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.47 % Favored : 93.19 % Rotamer: Outliers : 2.13 % Allowed : 13.20 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1190 helix: 0.36 (0.43), residues: 172 sheet: -1.09 (0.26), residues: 383 loop : -1.42 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.010 0.001 TYR A 91 PHE 0.031 0.001 PHE B 120 TRP 0.011 0.001 TRP A 207 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9433) covalent geometry : angle 0.52237 (12816) hydrogen bonds : bond 0.02869 ( 253) hydrogen bonds : angle 4.94081 ( 699) metal coordination : bond 0.00522 ( 4) metal coordination : angle 3.09866 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.348 Fit side-chains REVERT: A 35 LYS cc_start: 0.8696 (mttt) cc_final: 0.8069 (mttp) REVERT: A 207 TRP cc_start: 0.8557 (OUTLIER) cc_final: 0.6267 (p-90) REVERT: B 64 MET cc_start: 0.3596 (mmm) cc_final: 0.3057 (mmm) REVERT: B 89 MET cc_start: 0.8110 (ptm) cc_final: 0.7715 (ptt) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.0796 time to fit residues: 15.6237 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.188913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150622 restraints weight = 10622.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149069 restraints weight = 16800.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148868 restraints weight = 15060.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146477 restraints weight = 13457.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148161 restraints weight = 10481.984| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9437 Z= 0.146 Angle : 0.555 11.360 12822 Z= 0.280 Chirality : 0.044 0.159 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.397 53.034 1300 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.28 % Rotamer: Outliers : 2.44 % Allowed : 14.01 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1190 helix: 0.23 (0.42), residues: 173 sheet: -1.06 (0.27), residues: 383 loop : -1.40 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1138 TYR 0.012 0.001 TYR A 91 PHE 0.033 0.001 PHE B 120 TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9433) covalent geometry : angle 0.55152 (12816) hydrogen bonds : bond 0.02936 ( 253) hydrogen bonds : angle 4.96309 ( 699) metal coordination : bond 0.00520 ( 4) metal coordination : angle 3.07374 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8709 (mttt) cc_final: 0.8003 (mttp) REVERT: A 207 TRP cc_start: 0.8638 (OUTLIER) cc_final: 0.6378 (p-90) REVERT: A 1105 MET cc_start: 0.7598 (mtt) cc_final: 0.7323 (mtt) REVERT: B 89 MET cc_start: 0.8212 (ptm) cc_final: 0.7829 (ptt) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.0783 time to fit residues: 15.6100 Evaluate side-chains 134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149840 restraints weight = 10882.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148343 restraints weight = 15533.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147332 restraints weight = 15771.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146081 restraints weight = 11314.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148006 restraints weight = 9678.731| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9437 Z= 0.178 Angle : 0.576 10.304 12822 Z= 0.291 Chirality : 0.044 0.149 1475 Planarity : 0.004 0.048 1648 Dihedral : 4.555 54.337 1300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.11 % Rotamer: Outliers : 2.23 % Allowed : 15.33 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1190 helix: 0.19 (0.42), residues: 173 sheet: -1.01 (0.27), residues: 373 loop : -1.46 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1138 TYR 0.014 0.001 TYR A 91 PHE 0.033 0.002 PHE B 120 TRP 0.012 0.001 TRP A 207 HIS 0.014 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9433) covalent geometry : angle 0.57168 (12816) hydrogen bonds : bond 0.03073 ( 253) hydrogen bonds : angle 5.05464 ( 699) metal coordination : bond 0.00554 ( 4) metal coordination : angle 3.16655 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.343 Fit side-chains REVERT: A 207 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.6533 (p-90) REVERT: A 1128 ASP cc_start: 0.6815 (m-30) cc_final: 0.6541 (m-30) REVERT: B 89 MET cc_start: 0.8211 (ptm) cc_final: 0.7800 (ptt) outliers start: 22 outliers final: 17 residues processed: 134 average time/residue: 0.0826 time to fit residues: 16.3481 Evaluate side-chains 134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 0.0010 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.193346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152634 restraints weight = 10752.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151405 restraints weight = 14649.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152235 restraints weight = 13849.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150952 restraints weight = 9677.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152215 restraints weight = 8900.240| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9437 Z= 0.105 Angle : 0.537 9.972 12822 Z= 0.269 Chirality : 0.043 0.142 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.349 54.352 1300 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.05 % Favored : 93.61 % Rotamer: Outliers : 1.93 % Allowed : 16.35 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1190 helix: 0.22 (0.42), residues: 174 sheet: -0.92 (0.27), residues: 372 loop : -1.38 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.010 0.001 TYR A 91 PHE 0.032 0.001 PHE B 120 TRP 0.011 0.001 TRP A 207 HIS 0.007 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9433) covalent geometry : angle 0.53330 (12816) hydrogen bonds : bond 0.02630 ( 253) hydrogen bonds : angle 4.84396 ( 699) metal coordination : bond 0.00477 ( 4) metal coordination : angle 2.92723 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5815 (mmm) cc_final: 0.5407 (mmm) REVERT: A 207 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.6264 (p-90) REVERT: B 89 MET cc_start: 0.8210 (ptm) cc_final: 0.7834 (ptt) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.0754 time to fit residues: 14.9151 Evaluate side-chains 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 111 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152913 restraints weight = 10501.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151426 restraints weight = 17441.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151683 restraints weight = 15458.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149085 restraints weight = 12670.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150760 restraints weight = 10010.448| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9437 Z= 0.112 Angle : 0.548 9.346 12822 Z= 0.275 Chirality : 0.043 0.162 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.336 55.037 1300 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Rotamer: Outliers : 1.73 % Allowed : 17.06 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1190 helix: 0.19 (0.41), residues: 173 sheet: -0.88 (0.27), residues: 372 loop : -1.40 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1138 TYR 0.015 0.001 TYR B 363 PHE 0.033 0.001 PHE B 120 TRP 0.011 0.001 TRP A 207 HIS 0.002 0.000 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9433) covalent geometry : angle 0.54497 (12816) hydrogen bonds : bond 0.02685 ( 253) hydrogen bonds : angle 4.80000 ( 699) metal coordination : bond 0.00474 ( 4) metal coordination : angle 2.85535 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5910 (mmm) cc_final: 0.5511 (mmm) REVERT: A 35 LYS cc_start: 0.8778 (mttt) cc_final: 0.8118 (mttp) REVERT: A 207 TRP cc_start: 0.8545 (OUTLIER) cc_final: 0.6320 (p-90) REVERT: A 1024 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8910 (t) REVERT: B 89 MET cc_start: 0.8174 (ptm) cc_final: 0.7783 (ptt) REVERT: B 251 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8013 (tp30) REVERT: B 409 MET cc_start: 0.5710 (mmm) cc_final: 0.5486 (ppp) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.0799 time to fit residues: 15.7676 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.194662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152646 restraints weight = 10718.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150677 restraints weight = 16698.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151182 restraints weight = 15579.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148283 restraints weight = 10129.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149886 restraints weight = 8609.904| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9437 Z= 0.102 Angle : 0.545 9.906 12822 Z= 0.275 Chirality : 0.043 0.155 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.250 55.366 1300 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.71 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 16.65 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.24), residues: 1190 helix: 0.12 (0.41), residues: 173 sheet: -0.81 (0.28), residues: 357 loop : -1.36 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1138 TYR 0.012 0.001 TYR B 363 PHE 0.032 0.001 PHE B 120 TRP 0.010 0.001 TRP A 207 HIS 0.004 0.000 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9433) covalent geometry : angle 0.54214 (12816) hydrogen bonds : bond 0.02625 ( 253) hydrogen bonds : angle 4.69808 ( 699) metal coordination : bond 0.00446 ( 4) metal coordination : angle 2.75722 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5900 (mmm) cc_final: 0.5539 (mmm) REVERT: A 207 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.6187 (p-90) REVERT: A 1024 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8870 (t) REVERT: A 1128 ASP cc_start: 0.6776 (m-30) cc_final: 0.6418 (m-30) REVERT: B 89 MET cc_start: 0.8279 (ptm) cc_final: 0.7896 (ptt) REVERT: B 187 GLU cc_start: 0.7579 (pp20) cc_final: 0.6981 (mm-30) REVERT: B 251 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7978 (tp30) REVERT: B 409 MET cc_start: 0.5818 (mmm) cc_final: 0.5408 (ppp) outliers start: 19 outliers final: 16 residues processed: 133 average time/residue: 0.0816 time to fit residues: 16.1344 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153351 restraints weight = 10454.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152288 restraints weight = 15228.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147489 restraints weight = 15681.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145517 restraints weight = 10472.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144628 restraints weight = 9366.717| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9437 Z= 0.126 Angle : 0.559 9.749 12822 Z= 0.283 Chirality : 0.043 0.157 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.335 56.260 1300 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.11 % Rotamer: Outliers : 2.34 % Allowed : 16.95 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1190 helix: 0.09 (0.41), residues: 170 sheet: -0.87 (0.27), residues: 372 loop : -1.36 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1074 TYR 0.019 0.001 TYR B 363 PHE 0.032 0.001 PHE B 120 TRP 0.011 0.001 TRP A 207 HIS 0.003 0.000 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9433) covalent geometry : angle 0.55596 (12816) hydrogen bonds : bond 0.02739 ( 253) hydrogen bonds : angle 4.77924 ( 699) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.74378 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.71 seconds wall clock time: 23 minutes 43.01 seconds (1423.01 seconds total)