Starting phenix.real_space_refine on Thu Feb 13 16:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_27242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_27242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_27242.map" model { file = "/net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_27242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d81_27242/02_2025/8d81_27242.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG: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: 5.35, per 1000 atoms: 0.58 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.29 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: 3.43 Time building geometry restraints manager: 2.72 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: 0.730 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- 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 9433 Z= 0.281 Angle : 0.654 10.247 12816 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 : 9.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP A 207 HIS 0.002 0.000 HIS B 73 PHE 0.010 0.001 PHE A1072 TYR 0.011 0.001 TYR A 828 ARG 0.003 0.000 ARG A 198 *********************** 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 : 1.111 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: 0.6307 (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: 0.1853 time to fit residues: 44.9359 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 : 0.986 ------------------------------------------------------------------------------- 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 100 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154035 restraints weight = 10536.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152642 restraints weight = 14196.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149838 restraints weight = 13965.080| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9433 Z= 0.273 Angle : 0.593 6.425 12816 Z= 0.308 Chirality : 0.045 0.247 1475 Planarity : 0.004 0.046 1648 Dihedral : 5.680 67.927 1302 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.55 % Favored : 93.03 % Rotamer: Outliers : 1.22 % Allowed : 9.75 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1190 helix: 0.05 (0.42), residues: 169 sheet: -1.29 (0.27), residues: 375 loop : -1.74 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.003 0.001 HIS A 805 PHE 0.029 0.002 PHE B 120 TYR 0.013 0.001 TYR A 91 ARG 0.003 0.000 ARG B 283 *********************** 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 132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.076 Fit side-chains REVERT: B 89 MET cc_start: 0.8001 (ptm) cc_final: 0.7515 (ptt) REVERT: B 357 HIS cc_start: 0.6994 (t-90) cc_final: 0.6782 (t-90) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.2049 time to fit residues: 38.9109 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 366 ASP Chi-restraints excluded: chain A residue 732 CYS 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 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 55 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 0.0020 overall best weight: 1.4194 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.190012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149376 restraints weight = 10687.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147671 restraints weight = 16786.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148192 restraints weight = 13780.446| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9433 Z= 0.235 Angle : 0.546 8.377 12816 Z= 0.284 Chirality : 0.044 0.187 1475 Planarity : 0.004 0.046 1648 Dihedral : 4.649 47.722 1300 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.47 % Favored : 93.19 % Rotamer: Outliers : 1.42 % Allowed : 13.20 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1190 helix: 0.17 (0.43), residues: 170 sheet: -1.24 (0.27), residues: 368 loop : -1.61 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.003 0.001 HIS A1070 PHE 0.028 0.002 PHE B 120 TYR 0.013 0.001 TYR A 91 ARG 0.005 0.000 ARG B 111 *********************** 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 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7769 (m-30) cc_final: 0.7564 (p0) REVERT: B 64 MET cc_start: 0.3687 (mmm) cc_final: 0.3290 (mmm) REVERT: B 89 MET cc_start: 0.8165 (ptm) cc_final: 0.7713 (ptt) REVERT: B 331 ILE cc_start: 0.7234 (pt) cc_final: 0.6971 (mm) outliers start: 14 outliers final: 11 residues processed: 142 average time/residue: 0.2314 time to fit residues: 46.4352 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 238 THR Chi-restraints excluded: chain B residue 358 GLU 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 61 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.0020 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 A 355 ASN A1070 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.195691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153977 restraints weight = 10624.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151403 restraints weight = 15745.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153338 restraints weight = 14886.013| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9433 Z= 0.152 Angle : 0.509 7.021 12816 Z= 0.266 Chirality : 0.043 0.193 1475 Planarity : 0.003 0.045 1648 Dihedral : 4.295 48.936 1300 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.13 % Favored : 93.53 % Rotamer: Outliers : 1.93 % Allowed : 14.01 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1190 helix: 0.28 (0.42), residues: 174 sheet: -1.10 (0.27), residues: 368 loop : -1.45 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.002 0.000 HIS A 261 PHE 0.030 0.001 PHE B 120 TYR 0.016 0.001 TYR B 363 ARG 0.003 0.000 ARG B 111 *********************** 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 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.995 Fit side-chains REVERT: A 207 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.6149 (p-90) REVERT: B 64 MET cc_start: 0.3616 (mmm) cc_final: 0.3149 (mmm) REVERT: B 89 MET cc_start: 0.8210 (ptm) cc_final: 0.7776 (ptt) outliers start: 19 outliers final: 8 residues processed: 141 average time/residue: 0.1963 time to fit residues: 40.3149 Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 355 ASN 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 255 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- 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 731 GLN A 796 GLN B 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.185425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148311 restraints weight = 10615.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145876 restraints weight = 18019.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145904 restraints weight = 16498.105| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9433 Z= 0.371 Angle : 0.613 12.409 12816 Z= 0.316 Chirality : 0.045 0.185 1475 Planarity : 0.004 0.050 1648 Dihedral : 4.687 51.915 1300 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.82 % Favored : 91.85 % Rotamer: Outliers : 2.94 % Allowed : 13.60 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.24), residues: 1190 helix: 0.21 (0.43), residues: 171 sheet: -1.22 (0.26), residues: 374 loop : -1.53 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.004 0.001 HIS A 805 PHE 0.032 0.002 PHE B 120 TYR 0.016 0.002 TYR A 91 ARG 0.006 0.000 ARG B 111 *********************** 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 156 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.6604 (p-90) REVERT: A 1128 ASP cc_start: 0.6905 (m-30) cc_final: 0.6604 (m-30) REVERT: B 89 MET cc_start: 0.8206 (ptm) cc_final: 0.7795 (ptt) REVERT: B 251 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8086 (tp30) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2116 time to fit residues: 45.7848 Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR 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 731 GLN 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 55 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 238 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 100 optimal weight: 0.0040 chunk 66 optimal weight: 0.0170 overall best weight: 1.5634 ------------------------------------------------------------------------------- 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 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145891 restraints weight = 10428.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144120 restraints weight = 17172.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144849 restraints weight = 15502.528| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9433 Z= 0.249 Angle : 0.573 11.681 12816 Z= 0.291 Chirality : 0.044 0.170 1475 Planarity : 0.004 0.048 1648 Dihedral : 4.576 52.051 1300 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.89 % Favored : 92.77 % Rotamer: Outliers : 2.44 % Allowed : 15.33 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1190 helix: 0.16 (0.42), residues: 173 sheet: -1.14 (0.27), residues: 373 loop : -1.50 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.003 0.001 HIS A 805 PHE 0.031 0.002 PHE B 120 TYR 0.013 0.001 TYR A 91 ARG 0.006 0.000 ARG B 111 *********************** 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 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8704 (mttt) cc_final: 0.8037 (mttp) REVERT: A 207 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.6472 (p-90) REVERT: A 731 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: A 1105 MET cc_start: 0.7581 (mtt) cc_final: 0.7331 (mtt) REVERT: A 1128 ASP cc_start: 0.6913 (m-30) cc_final: 0.6586 (m-30) REVERT: B 89 MET cc_start: 0.8213 (ptm) cc_final: 0.7792 (ptt) REVERT: B 251 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7997 (tp30) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.1920 time to fit residues: 40.4147 Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 731 GLN Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 817 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.184744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144504 restraints weight = 11020.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141641 restraints weight = 18684.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141916 restraints weight = 16351.250| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 9433 Z= 0.438 Angle : 0.662 9.874 12816 Z= 0.342 Chirality : 0.046 0.157 1475 Planarity : 0.004 0.054 1648 Dihedral : 5.015 53.648 1300 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.08 % Favored : 90.59 % Rotamer: Outliers : 2.74 % Allowed : 16.45 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.24), residues: 1190 helix: -0.07 (0.41), residues: 174 sheet: -1.28 (0.27), residues: 369 loop : -1.63 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.005 0.001 HIS A 805 PHE 0.032 0.002 PHE B 120 TYR 0.020 0.002 TYR B 363 ARG 0.005 0.000 ARG B 111 *********************** 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 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.6773 (p-90) REVERT: A 1105 MET cc_start: 0.7675 (mtt) cc_final: 0.7435 (mtt) REVERT: A 1128 ASP cc_start: 0.7017 (m-30) cc_final: 0.6710 (m-30) REVERT: B 301 ILE cc_start: 0.9141 (mm) cc_final: 0.8906 (mt) REVERT: B 357 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6308 (t-90) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.1928 time to fit residues: 38.4829 Evaluate side-chains 133 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 831 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 182 VAL 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 96 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.187629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151010 restraints weight = 10736.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149542 restraints weight = 16726.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148680 restraints weight = 16342.412| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9433 Z= 0.199 Angle : 0.555 10.159 12816 Z= 0.284 Chirality : 0.043 0.147 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.590 53.145 1300 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.88 % Favored : 93.78 % Rotamer: Outliers : 1.83 % Allowed : 17.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1190 helix: 0.09 (0.42), residues: 173 sheet: -1.17 (0.27), residues: 378 loop : -1.54 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 207 HIS 0.002 0.000 HIS B 73 PHE 0.032 0.001 PHE B 120 TYR 0.013 0.001 TYR B 144 ARG 0.004 0.000 ARG B 111 *********************** 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 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8638 (OUTLIER) cc_final: 0.6603 (p-90) REVERT: A 1128 ASP cc_start: 0.6774 (m-30) cc_final: 0.6550 (m-30) REVERT: B 89 MET cc_start: 0.8089 (ptm) cc_final: 0.7675 (ptt) REVERT: B 357 HIS cc_start: 0.6573 (OUTLIER) cc_final: 0.6174 (t-90) outliers start: 18 outliers final: 15 residues processed: 131 average time/residue: 0.1966 time to fit residues: 37.9510 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR 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 255 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 357 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** A1005 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150744 restraints weight = 10793.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150122 restraints weight = 16276.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.150300 restraints weight = 15036.830| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9433 Z= 0.225 Angle : 0.562 9.447 12816 Z= 0.288 Chirality : 0.043 0.145 1475 Planarity : 0.003 0.048 1648 Dihedral : 4.539 54.366 1300 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.56 % Favored : 92.10 % Rotamer: Outliers : 1.93 % Allowed : 18.07 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1190 helix: 0.13 (0.42), residues: 173 sheet: -1.11 (0.27), residues: 372 loop : -1.55 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.002 0.000 HIS A 805 PHE 0.032 0.002 PHE B 120 TYR 0.018 0.001 TYR B 363 ARG 0.004 0.000 ARG B 111 *********************** 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 137 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8710 (OUTLIER) cc_final: 0.6676 (p-90) REVERT: A 1128 ASP cc_start: 0.6950 (m-30) cc_final: 0.6622 (m-30) REVERT: B 89 MET cc_start: 0.8187 (ptm) cc_final: 0.7789 (ptt) REVERT: B 141 ILE cc_start: 0.7125 (mm) cc_final: 0.6851 (mm) REVERT: B 251 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8002 (tp30) REVERT: B 409 MET cc_start: 0.5789 (mmm) cc_final: 0.5509 (ppp) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 0.1892 time to fit residues: 36.9667 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR 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 817 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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 = 0.192581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153628 restraints weight = 10873.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151912 restraints weight = 14189.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148210 restraints weight = 14993.894| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9433 Z= 0.179 Angle : 0.556 9.746 12816 Z= 0.282 Chirality : 0.043 0.149 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.399 54.070 1300 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.13 % Favored : 93.53 % Rotamer: Outliers : 1.73 % Allowed : 18.17 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1190 helix: 0.23 (0.42), residues: 173 sheet: -1.00 (0.27), residues: 370 loop : -1.51 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.009 0.001 HIS A 789 PHE 0.033 0.001 PHE B 120 TYR 0.016 0.001 TYR B 363 ARG 0.004 0.000 ARG B 111 ********************** 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 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5972 (mmm) cc_final: 0.5578 (mmm) REVERT: A 207 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.6517 (p-90) REVERT: A 1128 ASP cc_start: 0.7045 (m-30) cc_final: 0.6656 (m-30) REVERT: B 89 MET cc_start: 0.8323 (ptm) cc_final: 0.7918 (ptt) REVERT: B 141 ILE cc_start: 0.7035 (mm) cc_final: 0.6771 (mm) REVERT: B 338 PHE cc_start: 0.4617 (m-80) cc_final: 0.4413 (m-80) REVERT: B 409 MET cc_start: 0.5932 (mmm) cc_final: 0.5494 (ppp) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.1891 time to fit residues: 36.1520 Evaluate side-chains 134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 178 ILE 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 817 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 331 ILE Chi-restraints excluded: chain B residue 357 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 45 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.186496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148256 restraints weight = 10680.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145311 restraints weight = 19574.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146014 restraints weight = 16389.073| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9433 Z= 0.266 Angle : 0.586 9.182 12816 Z= 0.300 Chirality : 0.044 0.219 1475 Planarity : 0.003 0.048 1648 Dihedral : 4.591 55.564 1300 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.39 % Favored : 92.27 % Rotamer: Outliers : 1.73 % Allowed : 18.07 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.24), residues: 1190 helix: 0.15 (0.41), residues: 173 sheet: -1.11 (0.27), residues: 372 loop : -1.53 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.032 0.002 PHE B 120 TYR 0.017 0.001 TYR B 363 ARG 0.003 0.000 ARG B 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.31 seconds wall clock time: 46 minutes 48.14 seconds (2808.14 seconds total)