Starting phenix.real_space_refine on Sun Jul 27 07:21:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d81_27242/07_2025/8d81_27242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d81_27242/07_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_27242/07_2025/8d81_27242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d81_27242/07_2025/8d81_27242.map" model { file = "/net/cci-nas-00/data/ceres_data/8d81_27242/07_2025/8d81_27242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d81_27242/07_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.15, per 1000 atoms: 0.67 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 3.38 Time building geometry restraints manager: 3.00 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: 0.560 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.210 Find NCS groups from input model: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- 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 : 9.87 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 Details of bonding type rmsd hydrogen bonds : bond 0.26472 ( 253) hydrogen bonds : angle 9.71283 ( 699) metal coordination : bond 0.00399 ( 4) metal coordination : angle 2.35029 ( 6) covalent geometry : bond 0.00412 ( 9433) covalent geometry : angle 0.65428 (12816) *********************** 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 : 1.020 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: 0.2128 time to fit residues: 51.7955 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 : 1.048 ------------------------------------------------------------------------------- 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 = 0.154034 restraints weight = 10536.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152632 restraints weight = 14196.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149832 restraints weight = 13991.607| |-----------------------------------------------------------------------------| 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 9437 Z= 0.168 Angle : 0.599 6.425 12822 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 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 253) hydrogen bonds : angle 6.14837 ( 699) metal coordination : bond 0.00724 ( 4) metal coordination : angle 3.81974 ( 6) covalent geometry : bond 0.00401 ( 9433) covalent geometry : angle 0.59312 (12816) *********************** 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 : 1.099 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: 0.1914 time to fit residues: 36.3112 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.3980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0000 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 0.0470 overall best weight: 0.8484 ------------------------------------------------------------------------------- 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 A 789 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152956 restraints weight = 10765.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150505 restraints weight = 17539.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151560 restraints weight = 14905.461| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9437 Z= 0.112 Angle : 0.532 8.457 12822 Z= 0.273 Chirality : 0.044 0.179 1475 Planarity : 0.004 0.045 1648 Dihedral : 4.530 47.360 1300 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.05 % Favored : 93.61 % Rotamer: Outliers : 1.32 % Allowed : 12.79 % Favored : 85.89 % 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: -1.82 (0.24), residues: 1190 helix: 0.16 (0.42), residues: 172 sheet: -1.21 (0.27), residues: 370 loop : -1.58 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS B 73 PHE 0.028 0.001 PHE B 120 TYR 0.011 0.001 TYR A 91 ARG 0.006 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 253) hydrogen bonds : angle 5.45698 ( 699) metal coordination : bond 0.00638 ( 4) metal coordination : angle 3.63910 ( 6) covalent geometry : bond 0.00264 ( 9433) covalent geometry : angle 0.52626 (12816) *********************** 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: 13 poor density : 136 time to evaluate : 1.126 Fit side-chains REVERT: A 137 ASP cc_start: 0.7727 (m-30) cc_final: 0.7523 (p0) REVERT: B 64 MET cc_start: 0.3634 (mmm) cc_final: 0.3240 (mmm) REVERT: B 89 MET cc_start: 0.8152 (ptm) cc_final: 0.7729 (ptt) REVERT: B 331 ILE cc_start: 0.7232 (pt) cc_final: 0.6935 (mm) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 0.2070 time to fit residues: 43.2032 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.1350 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150411 restraints weight = 10671.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148343 restraints weight = 18097.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149163 restraints weight = 13567.543| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9437 Z= 0.126 Angle : 0.534 7.172 12822 Z= 0.276 Chirality : 0.044 0.210 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.425 48.683 1300 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Rotamer: Outliers : 2.03 % Allowed : 13.71 % Favored : 84.26 % 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: -1.70 (0.24), residues: 1190 helix: 0.29 (0.43), residues: 172 sheet: -1.08 (0.27), residues: 362 loop : -1.55 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.002 0.001 HIS A 789 PHE 0.031 0.001 PHE B 120 TYR 0.011 0.001 TYR A 91 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 253) hydrogen bonds : angle 5.19628 ( 699) metal coordination : bond 0.00569 ( 4) metal coordination : angle 3.31805 ( 6) covalent geometry : bond 0.00300 ( 9433) covalent geometry : angle 0.52951 (12816) *********************** 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 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.756 Fit side-chains REVERT: A 35 LYS cc_start: 0.8704 (mttt) cc_final: 0.8054 (mttp) REVERT: A 207 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.6287 (p-90) REVERT: B 64 MET cc_start: 0.3635 (mmm) cc_final: 0.3152 (mmm) REVERT: B 89 MET cc_start: 0.8218 (ptm) cc_final: 0.7812 (ptt) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.2091 time to fit residues: 43.9916 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 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 255 ASP 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 22 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 109 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- 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 796 GLN B 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147054 restraints weight = 10654.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145315 restraints weight = 18104.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144215 restraints weight = 16200.591| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9437 Z= 0.226 Angle : 0.626 11.487 12822 Z= 0.322 Chirality : 0.045 0.190 1475 Planarity : 0.004 0.048 1648 Dihedral : 4.838 52.228 1300 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.90 % Favored : 91.76 % Rotamer: Outliers : 3.05 % Allowed : 14.01 % Favored : 82.94 % 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: -1.83 (0.24), residues: 1190 helix: 0.15 (0.42), residues: 171 sheet: -1.22 (0.27), residues: 369 loop : -1.58 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.004 0.001 HIS A1070 PHE 0.032 0.002 PHE B 120 TYR 0.017 0.002 TYR A 91 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 253) hydrogen bonds : angle 5.46691 ( 699) metal coordination : bond 0.00608 ( 4) metal coordination : angle 3.41226 ( 6) covalent geometry : bond 0.00547 ( 9433) covalent geometry : angle 0.62130 (12816) *********************** 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 153 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.6762 (p-90) REVERT: A 1128 ASP cc_start: 0.6928 (m-30) cc_final: 0.6663 (m-30) REVERT: B 89 MET cc_start: 0.8259 (ptm) cc_final: 0.7849 (ptt) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.1907 time to fit residues: 40.5391 Evaluate side-chains 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 114 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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** A1070 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152234 restraints weight = 10414.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150458 restraints weight = 17922.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151049 restraints weight = 15918.084| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2375 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= 0.103 Angle : 0.554 12.088 12822 Z= 0.278 Chirality : 0.043 0.159 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.433 51.421 1300 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.38 % Favored : 94.29 % Rotamer: Outliers : 2.03 % Allowed : 15.94 % Favored : 82.03 % 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: 0.30 (0.43), residues: 168 sheet: -1.15 (0.27), residues: 381 loop : -1.42 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.003 0.000 HIS A 261 PHE 0.032 0.001 PHE B 120 TYR 0.010 0.001 TYR A 91 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 253) hydrogen bonds : angle 5.05279 ( 699) metal coordination : bond 0.00493 ( 4) metal coordination : angle 3.01603 ( 6) covalent geometry : bond 0.00241 ( 9433) covalent geometry : angle 0.54996 (12816) *********************** 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 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.6215 (p-90) REVERT: A 1105 MET cc_start: 0.7549 (mtt) cc_final: 0.7289 (mtt) REVERT: B 89 MET cc_start: 0.8222 (ptm) cc_final: 0.7791 (ptt) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.2004 time to fit residues: 39.2876 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 10.0000 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 0.0010 chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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 789 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146254 restraints weight = 10685.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144409 restraints weight = 18870.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143186 restraints weight = 16643.283| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9437 Z= 0.247 Angle : 0.638 10.169 12822 Z= 0.327 Chirality : 0.046 0.153 1475 Planarity : 0.004 0.050 1648 Dihedral : 4.845 53.655 1300 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.40 % Favored : 91.26 % Rotamer: Outliers : 2.44 % Allowed : 16.04 % Favored : 81.52 % 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: -1.81 (0.24), residues: 1190 helix: 0.10 (0.42), residues: 171 sheet: -1.20 (0.27), residues: 374 loop : -1.54 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.005 0.001 HIS A 805 PHE 0.032 0.002 PHE B 120 TYR 0.018 0.002 TYR A 91 ARG 0.006 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 253) hydrogen bonds : angle 5.38607 ( 699) metal coordination : bond 0.00597 ( 4) metal coordination : angle 3.30161 ( 6) covalent geometry : bond 0.00595 ( 9433) covalent geometry : angle 0.63459 (12816) *********************** 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 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8780 (OUTLIER) cc_final: 0.6668 (p-90) REVERT: A 1105 MET cc_start: 0.7604 (mtt) cc_final: 0.7391 (mtt) REVERT: A 1128 ASP cc_start: 0.6891 (m-30) cc_final: 0.6623 (m-30) REVERT: B 89 MET cc_start: 0.8250 (ptm) cc_final: 0.7801 (ptt) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.1867 time to fit residues: 36.9190 Evaluate side-chains 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 218 MET 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 1004 VAL Chi-restraints excluded: chain B residue 73 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 358 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.189212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151991 restraints weight = 10712.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149187 restraints weight = 19100.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149347 restraints weight = 17007.487| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9437 Z= 0.115 Angle : 0.558 10.383 12822 Z= 0.283 Chirality : 0.043 0.142 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.510 53.338 1300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.80 % Favored : 93.87 % Rotamer: Outliers : 1.52 % Allowed : 18.17 % Favored : 80.30 % 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: -0.02 (0.41), residues: 177 sheet: -1.11 (0.27), residues: 373 loop : -1.48 (0.24), residues: 640 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 0.033 0.001 PHE B 120 TYR 0.018 0.001 TYR B 144 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 253) hydrogen bonds : angle 5.01294 ( 699) metal coordination : bond 0.00500 ( 4) metal coordination : angle 3.06072 ( 6) covalent geometry : bond 0.00271 ( 9433) covalent geometry : angle 0.55460 (12816) *********************** 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 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.6573 (p-90) REVERT: B 89 MET cc_start: 0.8202 (ptm) cc_final: 0.7789 (ptt) REVERT: B 338 PHE cc_start: 0.4758 (m-80) cc_final: 0.3687 (m-80) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.2283 time to fit residues: 43.8446 Evaluate side-chains 125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 366 ASP 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 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 19 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 0.0370 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 overall best weight: 0.5874 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.193938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152183 restraints weight = 10692.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150567 restraints weight = 16001.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151192 restraints weight = 15326.156| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2711 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= 0.100 Angle : 0.547 9.739 12822 Z= 0.277 Chirality : 0.043 0.135 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.290 53.749 1300 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.47 % Favored : 93.19 % Rotamer: Outliers : 1.52 % Allowed : 18.58 % Favored : 79.90 % 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: -1.57 (0.24), residues: 1190 helix: 0.33 (0.42), residues: 168 sheet: -0.93 (0.28), residues: 357 loop : -1.47 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.007 0.000 HIS A 789 PHE 0.032 0.001 PHE B 120 TYR 0.009 0.001 TYR B 144 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 253) hydrogen bonds : angle 4.78260 ( 699) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.84397 ( 6) covalent geometry : bond 0.00232 ( 9433) covalent geometry : angle 0.54385 (12816) *********************** 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 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5949 (mmm) cc_final: 0.5581 (mmm) REVERT: A 207 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.6392 (p-90) REVERT: B 89 MET cc_start: 0.8325 (ptm) cc_final: 0.7964 (ptt) REVERT: B 338 PHE cc_start: 0.4662 (m-80) cc_final: 0.3537 (m-80) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.2483 time to fit residues: 47.8624 Evaluate side-chains 126 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 THR Chi-restraints excluded: chain B residue 329 THR 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 22 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 104 optimal weight: 0.0770 chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.191625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154263 restraints weight = 10731.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152163 restraints weight = 17236.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150928 restraints weight = 16611.129| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9437 Z= 0.113 Angle : 0.567 9.662 12822 Z= 0.285 Chirality : 0.043 0.153 1475 Planarity : 0.003 0.047 1648 Dihedral : 4.342 54.328 1300 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Rotamer: Outliers : 1.42 % Allowed : 19.09 % Favored : 79.49 % 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: -1.55 (0.24), residues: 1190 helix: 0.20 (0.42), residues: 174 sheet: -0.95 (0.27), residues: 372 loop : -1.40 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.007 0.001 HIS A 789 PHE 0.033 0.001 PHE B 120 TYR 0.018 0.001 TYR B 363 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 253) hydrogen bonds : angle 4.77186 ( 699) metal coordination : bond 0.00461 ( 4) metal coordination : angle 2.84366 ( 6) covalent geometry : bond 0.00269 ( 9433) covalent geometry : angle 0.56344 (12816) ********************** 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 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5975 (mmm) cc_final: 0.5597 (mmm) REVERT: A 207 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.6533 (p-90) REVERT: A 1128 ASP cc_start: 0.6805 (m-30) cc_final: 0.6507 (m-30) REVERT: B 89 MET cc_start: 0.8228 (ptm) cc_final: 0.7856 (ptt) REVERT: B 251 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8015 (tp30) outliers start: 14 outliers final: 11 residues processed: 126 average time/residue: 0.2053 time to fit residues: 38.6312 Evaluate side-chains 124 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 119 THR Chi-restraints excluded: chain B residue 329 THR 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: 9.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 91 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 overall best weight: 2.2524 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.185788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150042 restraints weight = 10724.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148386 restraints weight = 17094.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146086 restraints weight = 16873.343| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9437 Z= 0.202 Angle : 0.632 9.355 12822 Z= 0.321 Chirality : 0.045 0.145 1475 Planarity : 0.004 0.049 1648 Dihedral : 4.713 56.161 1300 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.82 % Favored : 91.85 % Rotamer: Outliers : 1.52 % Allowed : 19.19 % Favored : 79.29 % 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: 0.04 (0.41), residues: 174 sheet: -1.06 (0.27), residues: 372 loop : -1.53 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.007 0.001 HIS A 789 PHE 0.031 0.002 PHE B 120 TYR 0.016 0.001 TYR B 363 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 253) hydrogen bonds : angle 5.14634 ( 699) metal coordination : bond 0.00581 ( 4) metal coordination : angle 3.27473 ( 6) covalent geometry : bond 0.00489 ( 9433) covalent geometry : angle 0.62788 (12816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.14 seconds wall clock time: 62 minutes 2.98 seconds (3722.98 seconds total)