Starting phenix.real_space_refine on Wed Mar 4 06:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.map" model { file = "/net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d80_27241/03_2026/8d80_27241.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 226 atoms to isotropic. 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 2 6.06 5 S 59 5.16 5 C 7105 2.51 5 N 1944 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11230 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8028 Classifications: {'peptide': 1132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1091} Chain breaks: 1 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1081 Unresolved non-hydrogen dihedrals: 668 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 26, 'ASP:plan': 18, 'ARG:plan': 14, 'GLN:plan1': 17, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 10, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 424 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2942 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8W7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10198 SG CYS B 323 45.349 122.008 54.411 1.00192.50 S ATOM 10218 SG CYS B 326 46.815 124.353 51.854 1.00195.77 S ATOM 10708 SG CYS B 391 45.263 125.795 55.152 1.00187.34 S ATOM 10727 SG CYS B 394 43.154 124.531 52.447 1.00195.38 S ATOM 11027 SG CYS C 147 30.359 128.003 59.238 1.00246.80 S Time building chain proxies: 2.16, per 1000 atoms: 0.19 Number of scatterers: 11230 At special positions: 0 Unit cell: (94.3, 148.35, 112.7, 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 2 29.99 S 59 16.00 O 2120 8.00 N 1944 7.00 C 7105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 455.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 167 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 163 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 147 " Number of angles added : 6 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 12.6% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... 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 removed outlier: 3.781A pdb=" N GLN A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1059 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 removed outlier: 3.681A pdb=" N ILE A1100 " --> pdb=" O PHE A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1097 through 1100' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.891A pdb=" N ILE A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A1135 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1136 " --> pdb=" O VAL A1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.604A pdb=" N ASN B 203 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.979A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.544A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 Processing helix chain 'B' and resid 276 through 288 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 337 removed outlier: 3.541A pdb=" N THR B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 334 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASN B 335 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 336 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.562A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.822A 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: 3.992A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.816A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.505A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.937A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 290 removed outlier: 4.169A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 296 " --> pdb=" O GLU A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 313 removed outlier: 6.450A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 365 removed outlier: 4.337A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 403 removed outlier: 6.297A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.633A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 457 through 463 removed outlier: 3.605A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 476 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 498 through 503 removed outlier: 6.920A pdb=" N ALA A 511 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA A 501 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 509 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N CYS A 503 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.281A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 569 " --> pdb=" O CYS A 556 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 595 removed outlier: 6.983A pdb=" N ALA A 605 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 591 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 603 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET A 593 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR A 601 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.529A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.529A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.287A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 862 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.289A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 913 through 917 removed outlier: 7.139A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 936 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.297A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC7, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.867A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 183 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG B 164 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.867A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 183 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG B 164 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AD1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.666A pdb=" N ALA B 347 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 415 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP B 386 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG B 373 " --> pdb=" O TRP B 386 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 388 " --> pdb=" O ILE B 371 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3451 1.33 - 1.46: 1913 1.46 - 1.58: 6000 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 11450 Sorted by residual: bond pdb=" N ASP B 75 " pdb=" CA ASP B 75 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.21e+00 bond pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.18e-02 7.18e+03 6.84e+00 bond pdb=" N LEU A 770 " pdb=" CA LEU A 770 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.38e+00 bond pdb=" N LYS B 324 " pdb=" CA LYS B 324 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.94e+00 bond pdb=" N SER B 77 " pdb=" CA SER B 77 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.84e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 15265 1.90 - 3.79: 302 3.79 - 5.69: 29 5.69 - 7.59: 6 7.59 - 9.48: 3 Bond angle restraints: 15605 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 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.63e+01 angle pdb=" N ASP A1116 " pdb=" CA ASP A1116 " pdb=" C ASP A1116 " ideal model delta sigma weight residual 113.18 104.58 8.60 1.21e+00 6.83e-01 5.05e+01 angle pdb=" N LEU A1112 " pdb=" CA LEU A1112 " pdb=" C LEU A1112 " ideal model delta sigma weight residual 113.19 106.19 7.00 1.19e+00 7.06e-01 3.46e+01 angle pdb=" N LEU A 770 " pdb=" CA LEU A 770 " pdb=" C LEU A 770 " ideal model delta sigma weight residual 113.02 106.20 6.82 1.20e+00 6.94e-01 3.23e+01 angle pdb=" C GLN B 325 " pdb=" N CYS B 326 " pdb=" CA CYS B 326 " ideal model delta sigma weight residual 120.75 127.26 -6.51 1.51e+00 4.39e-01 1.86e+01 ... (remaining 15600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 6654 33.62 - 67.25: 150 67.25 - 100.87: 20 100.87 - 134.49: 5 134.49 - 168.11: 1 Dihedral angle restraints: 6830 sinusoidal: 2363 harmonic: 4467 Sorted by residual: dihedral pdb=" C19 8W7 B 502 " pdb=" C20 8W7 B 502 " pdb=" C21 8W7 B 502 " pdb=" N3 8W7 B 502 " ideal model delta sinusoidal sigma weight residual 46.78 -145.11 -168.11 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C22 8W7 B 502 " pdb=" C23 8W7 B 502 " pdb=" O5 8W7 B 502 " pdb=" C24 8W7 B 502 " ideal model delta sinusoidal sigma weight residual 57.07 -64.18 121.25 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C11 8W7 B 502 " pdb=" C10 8W7 B 502 " pdb=" C9 8W7 B 502 " pdb=" C13 8W7 B 502 " ideal model delta sinusoidal sigma weight residual -53.05 55.22 -108.27 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1406 0.049 - 0.098: 287 0.098 - 0.147: 106 0.147 - 0.196: 6 0.196 - 0.245: 2 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA TYR A1114 " pdb=" N TYR A1114 " pdb=" C TYR A1114 " pdb=" CB TYR A1114 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLN B 325 " pdb=" N GLN B 325 " pdb=" C GLN B 325 " pdb=" CB GLN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU A 770 " pdb=" N LEU A 770 " pdb=" C LEU A 770 " pdb=" CB LEU A 770 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1804 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 8W7 B 502 " -0.175 2.00e-02 2.50e+03 1.93e-01 1.12e+03 pdb=" C2 8W7 B 502 " -0.111 2.00e-02 2.50e+03 pdb=" C3 8W7 B 502 " 0.022 2.00e-02 2.50e+03 pdb=" C4 8W7 B 502 " -0.106 2.00e-02 2.50e+03 pdb=" C5 8W7 B 502 " 0.026 2.00e-02 2.50e+03 pdb=" C6 8W7 B 502 " 0.091 2.00e-02 2.50e+03 pdb=" C7 8W7 B 502 " 0.231 2.00e-02 2.50e+03 pdb=" C8 8W7 B 502 " 0.120 2.00e-02 2.50e+03 pdb=" C9 8W7 B 502 " -0.460 2.00e-02 2.50e+03 pdb=" N1 8W7 B 502 " -0.041 2.00e-02 2.50e+03 pdb=" O1 8W7 B 502 " 0.307 2.00e-02 2.50e+03 pdb=" O4 8W7 B 502 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 8W7 B 502 " -0.013 2.00e-02 2.50e+03 4.88e-02 2.97e+01 pdb=" C12 8W7 B 502 " -0.009 2.00e-02 2.50e+03 pdb=" C13 8W7 B 502 " 0.058 2.00e-02 2.50e+03 pdb=" N2 8W7 B 502 " -0.080 2.00e-02 2.50e+03 pdb=" O3 8W7 B 502 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 766 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C SER A 766 " -0.053 2.00e-02 2.50e+03 pdb=" O SER A 766 " 0.020 2.00e-02 2.50e+03 pdb=" N SER A 767 " 0.018 2.00e-02 2.50e+03 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1073 2.75 - 3.29: 10554 3.29 - 3.82: 17357 3.82 - 4.36: 20249 4.36 - 4.90: 37219 Nonbonded interactions: 86452 Sorted by model distance: nonbonded pdb=" OD2 ASP B 265 " pdb=" OG SER B 339 " model vdw 2.212 3.040 nonbonded pdb=" CB CYS C 150 " pdb="ZN ZN C 201 " model vdw 2.281 2.630 nonbonded pdb=" NZ LYS A1081 " pdb=" OE2 GLU A1083 " model vdw 2.282 3.120 nonbonded pdb=" O ILE B 301 " pdb=" NH1 ARG B 307 " model vdw 2.287 3.120 nonbonded pdb=" O LEU A 356 " pdb=" OG SER A 379 " model vdw 2.300 3.040 ... (remaining 86447 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 11457 Z= 0.224 Angle : 0.637 9.484 15611 Z= 0.371 Chirality : 0.046 0.245 1807 Planarity : 0.006 0.193 2045 Dihedral : 15.295 168.114 3946 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.67 % Favored : 93.74 % Rotamer: Outliers : 0.75 % Allowed : 0.57 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1534 helix: 0.12 (0.40), residues: 182 sheet: -0.77 (0.22), residues: 587 loop : -1.74 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.010 0.001 TYR B 227 PHE 0.013 0.001 PHE A1030 TRP 0.011 0.001 TRP A 207 HIS 0.003 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00371 (11450) covalent geometry : angle 0.63260 (15605) hydrogen bonds : bond 0.23353 ( 381) hydrogen bonds : angle 9.45836 ( 1062) metal coordination : bond 0.13731 ( 7) metal coordination : angle 3.94163 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8666 (ptp) cc_final: 0.8401 (ptm) REVERT: A 782 PHE cc_start: 0.8393 (t80) cc_final: 0.8160 (t80) REVERT: B 194 MET cc_start: 0.8280 (tpp) cc_final: 0.7996 (mmm) outliers start: 8 outliers final: 1 residues processed: 105 average time/residue: 0.0932 time to fit residues: 15.0105 Evaluate side-chains 69 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0170 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN B 353 HIS B 357 HIS ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.092347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063868 restraints weight = 30572.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066467 restraints weight = 15493.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068152 restraints weight = 10404.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069122 restraints weight = 8181.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069528 restraints weight = 7088.229| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11457 Z= 0.173 Angle : 0.567 7.936 15611 Z= 0.294 Chirality : 0.044 0.146 1807 Planarity : 0.004 0.045 2045 Dihedral : 8.893 169.431 1665 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.52 % Rotamer: Outliers : 0.85 % Allowed : 6.31 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.21), residues: 1534 helix: 0.36 (0.41), residues: 186 sheet: -0.63 (0.22), residues: 590 loop : -1.71 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 171 TYR 0.014 0.001 TYR A1114 PHE 0.016 0.001 PHE A 829 TRP 0.014 0.001 TRP A 207 HIS 0.015 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00397 (11450) covalent geometry : angle 0.56149 (15605) hydrogen bonds : bond 0.03801 ( 381) hydrogen bonds : angle 6.24245 ( 1062) metal coordination : bond 0.00916 ( 7) metal coordination : angle 4.14308 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8647 (ptp) cc_final: 0.8417 (ptm) REVERT: B 64 MET cc_start: 0.5262 (tpp) cc_final: 0.4928 (tpt) REVERT: B 194 MET cc_start: 0.8654 (tpp) cc_final: 0.8298 (mmm) REVERT: C 148 ASN cc_start: 0.7432 (t0) cc_final: 0.7134 (t0) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.0811 time to fit residues: 10.3927 Evaluate side-chains 75 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 68 optimal weight: 0.0980 chunk 143 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 11 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 852 GLN A 908 ASN B 112 ASN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064316 restraints weight = 30470.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.066942 restraints weight = 15294.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068609 restraints weight = 10206.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.069598 restraints weight = 8009.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070168 restraints weight = 6925.196| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11457 Z= 0.125 Angle : 0.509 7.071 15611 Z= 0.264 Chirality : 0.043 0.141 1807 Planarity : 0.004 0.046 2045 Dihedral : 8.392 170.083 1662 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.52 % Rotamer: Outliers : 1.23 % Allowed : 8.39 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.21), residues: 1534 helix: 0.48 (0.40), residues: 188 sheet: -0.61 (0.22), residues: 590 loop : -1.67 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.011 0.001 TYR A 42 PHE 0.013 0.001 PHE A 829 TRP 0.014 0.001 TRP A 207 HIS 0.010 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00286 (11450) covalent geometry : angle 0.50526 (15605) hydrogen bonds : bond 0.03054 ( 381) hydrogen bonds : angle 5.50618 ( 1062) metal coordination : bond 0.00482 ( 7) metal coordination : angle 3.24973 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8995 (ttt) cc_final: 0.8697 (ttt) REVERT: B 64 MET cc_start: 0.4987 (tpp) cc_final: 0.4640 (tpt) REVERT: B 288 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8970 (mp) REVERT: B 387 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6231 (p) REVERT: C 148 ASN cc_start: 0.7223 (t0) cc_final: 0.6902 (t0) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 0.0670 time to fit residues: 9.0974 Evaluate side-chains 78 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 5.9990 chunk 57 optimal weight: 40.0000 chunk 58 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.090986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062327 restraints weight = 30737.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.064890 restraints weight = 15565.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066506 restraints weight = 10475.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.067478 restraints weight = 8268.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.067947 restraints weight = 7176.274| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11457 Z= 0.206 Angle : 0.550 13.073 15611 Z= 0.282 Chirality : 0.044 0.146 1807 Planarity : 0.004 0.044 2045 Dihedral : 7.714 168.422 1662 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.26 % Favored : 93.48 % Rotamer: Outliers : 1.23 % Allowed : 10.46 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.21), residues: 1534 helix: 0.29 (0.39), residues: 196 sheet: -0.69 (0.22), residues: 595 loop : -1.72 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.012 0.001 TYR A 91 PHE 0.014 0.001 PHE A1030 TRP 0.014 0.001 TRP A 207 HIS 0.009 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00474 (11450) covalent geometry : angle 0.54739 (15605) hydrogen bonds : bond 0.03232 ( 381) hydrogen bonds : angle 5.36342 ( 1062) metal coordination : bond 0.00566 ( 7) metal coordination : angle 2.87651 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1036 MET cc_start: 0.8998 (ptm) cc_final: 0.8707 (ppp) REVERT: B 64 MET cc_start: 0.4899 (tpp) cc_final: 0.4577 (tpt) REVERT: B 288 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9092 (mp) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.0859 time to fit residues: 11.1195 Evaluate side-chains 71 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 118 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 147 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 GLN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060514 restraints weight = 30898.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063005 restraints weight = 15862.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064564 restraints weight = 10750.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065501 restraints weight = 8535.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066032 restraints weight = 7433.221| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11457 Z= 0.303 Angle : 0.614 11.274 15611 Z= 0.315 Chirality : 0.045 0.149 1807 Planarity : 0.004 0.047 2045 Dihedral : 7.781 167.512 1662 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.71 % Favored : 93.02 % Rotamer: Outliers : 1.60 % Allowed : 12.82 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.21), residues: 1534 helix: 0.05 (0.38), residues: 199 sheet: -0.74 (0.22), residues: 570 loop : -1.84 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.016 0.002 TYR B 355 PHE 0.016 0.002 PHE A1030 TRP 0.017 0.002 TRP A 207 HIS 0.009 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00697 (11450) covalent geometry : angle 0.61116 (15605) hydrogen bonds : bond 0.03541 ( 381) hydrogen bonds : angle 5.52860 ( 1062) metal coordination : bond 0.00667 ( 7) metal coordination : angle 2.89365 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.9000 (ttt) cc_final: 0.8745 (ttt) REVERT: A 1036 MET cc_start: 0.9012 (ptm) cc_final: 0.8775 (ppp) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.0718 time to fit residues: 9.0569 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 40.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.091603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063429 restraints weight = 30753.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066043 restraints weight = 15421.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067688 restraints weight = 10300.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068642 restraints weight = 8096.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.069217 restraints weight = 7019.186| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11457 Z= 0.100 Angle : 0.504 10.430 15611 Z= 0.258 Chirality : 0.043 0.141 1807 Planarity : 0.003 0.047 2045 Dihedral : 7.417 166.316 1662 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.41 % Favored : 94.33 % Rotamer: Outliers : 1.32 % Allowed : 13.29 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1534 helix: 0.44 (0.40), residues: 196 sheet: -0.81 (0.22), residues: 595 loop : -1.69 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.011 0.001 TYR A 42 PHE 0.013 0.001 PHE A 829 TRP 0.015 0.001 TRP A 207 HIS 0.007 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00226 (11450) covalent geometry : angle 0.50048 (15605) hydrogen bonds : bond 0.02623 ( 381) hydrogen bonds : angle 5.04673 ( 1062) metal coordination : bond 0.00433 ( 7) metal coordination : angle 3.14205 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8833 (ttt) cc_final: 0.8603 (ttt) REVERT: A 1036 MET cc_start: 0.8947 (ptm) cc_final: 0.8737 (ppp) REVERT: B 288 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9170 (mp) REVERT: C 148 ASN cc_start: 0.7360 (t0) cc_final: 0.6849 (t0) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.0737 time to fit residues: 9.0894 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 53 optimal weight: 50.0000 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.088849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060523 restraints weight = 30702.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063009 restraints weight = 15717.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064601 restraints weight = 10616.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065536 restraints weight = 8387.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066057 restraints weight = 7280.039| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11457 Z= 0.305 Angle : 0.615 9.945 15611 Z= 0.314 Chirality : 0.045 0.174 1807 Planarity : 0.004 0.048 2045 Dihedral : 7.471 165.970 1662 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.78 % Favored : 92.96 % Rotamer: Outliers : 1.79 % Allowed : 13.10 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1534 helix: 0.23 (0.38), residues: 196 sheet: -0.77 (0.22), residues: 569 loop : -1.84 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1074 TYR 0.018 0.002 TYR B 221 PHE 0.015 0.002 PHE A1030 TRP 0.015 0.002 TRP A 207 HIS 0.009 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00701 (11450) covalent geometry : angle 0.61232 (15605) hydrogen bonds : bond 0.03395 ( 381) hydrogen bonds : angle 5.33509 ( 1062) metal coordination : bond 0.00655 ( 7) metal coordination : angle 3.20001 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8823 (ttt) cc_final: 0.8618 (ttt) REVERT: B 194 MET cc_start: 0.9015 (mmm) cc_final: 0.8734 (mmm) REVERT: B 288 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9282 (mp) REVERT: B 316 ASN cc_start: 0.8923 (t0) cc_final: 0.8641 (t0) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.0734 time to fit residues: 9.6910 Evaluate side-chains 77 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 48 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 0.0060 chunk 111 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.090049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061867 restraints weight = 30674.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064406 restraints weight = 15541.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066000 restraints weight = 10486.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066975 restraints weight = 8252.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067487 restraints weight = 7142.979| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11457 Z= 0.180 Angle : 0.551 9.417 15611 Z= 0.279 Chirality : 0.044 0.223 1807 Planarity : 0.004 0.049 2045 Dihedral : 7.112 164.609 1662 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.00 % Favored : 93.74 % Rotamer: Outliers : 1.60 % Allowed : 13.67 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.21), residues: 1534 helix: 0.39 (0.39), residues: 196 sheet: -0.81 (0.22), residues: 589 loop : -1.82 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.011 0.001 TYR A 91 PHE 0.013 0.001 PHE A1030 TRP 0.016 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00418 (11450) covalent geometry : angle 0.54694 (15605) hydrogen bonds : bond 0.02906 ( 381) hydrogen bonds : angle 5.13951 ( 1062) metal coordination : bond 0.00555 ( 7) metal coordination : angle 3.30304 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8981 (mmm) cc_final: 0.8668 (mmm) REVERT: B 288 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9196 (mp) REVERT: B 316 ASN cc_start: 0.8885 (t0) cc_final: 0.8589 (t0) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.0849 time to fit residues: 10.7686 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 52 optimal weight: 0.1980 chunk 61 optimal weight: 50.0000 chunk 68 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 397 HIS ** 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 = 0.3712 r_free = 0.3712 target = 0.090889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062880 restraints weight = 30388.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.065463 restraints weight = 15352.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067085 restraints weight = 10258.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068009 restraints weight = 8076.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068599 restraints weight = 7016.326| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11457 Z= 0.137 Angle : 0.568 18.164 15611 Z= 0.273 Chirality : 0.044 0.361 1807 Planarity : 0.003 0.049 2045 Dihedral : 6.485 163.480 1662 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.41 % Allowed : 14.04 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.21), residues: 1534 helix: 0.54 (0.39), residues: 196 sheet: -0.73 (0.22), residues: 577 loop : -1.81 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.010 0.001 TYR A 42 PHE 0.012 0.001 PHE A 829 TRP 0.014 0.001 TRP A 207 HIS 0.006 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00316 (11450) covalent geometry : angle 0.53049 (15605) hydrogen bonds : bond 0.02693 ( 381) hydrogen bonds : angle 5.00052 ( 1062) metal coordination : bond 0.01832 ( 7) metal coordination : angle 10.40713 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9241 (mp) REVERT: B 288 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9073 (mp) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.0732 time to fit residues: 9.5340 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** B 397 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.091870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.063997 restraints weight = 30844.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066608 restraints weight = 15464.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068220 restraints weight = 10289.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.069214 restraints weight = 8086.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069806 restraints weight = 6988.956| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11457 Z= 0.107 Angle : 0.547 17.556 15611 Z= 0.263 Chirality : 0.044 0.313 1807 Planarity : 0.003 0.049 2045 Dihedral : 6.184 162.771 1662 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 1.13 % Allowed : 14.51 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.21), residues: 1534 helix: 0.55 (0.40), residues: 196 sheet: -0.67 (0.22), residues: 582 loop : -1.80 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.010 0.001 TYR A 42 PHE 0.011 0.001 PHE A 829 TRP 0.013 0.001 TRP B 380 HIS 0.006 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00247 (11450) covalent geometry : angle 0.50889 (15605) hydrogen bonds : bond 0.02507 ( 381) hydrogen bonds : angle 4.80384 ( 1062) metal coordination : bond 0.01443 ( 7) metal coordination : angle 10.24502 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.9391 (OUTLIER) cc_final: 0.7977 (p-90) REVERT: A 1129 LEU cc_start: 0.8882 (mt) cc_final: 0.8600 (mt) REVERT: B 288 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8926 (mp) REVERT: B 409 MET cc_start: 0.4174 (tmm) cc_final: 0.3800 (tmm) REVERT: C 148 ASN cc_start: 0.7407 (t0) cc_final: 0.7189 (t0) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.0788 time to fit residues: 9.2837 Evaluate side-chains 70 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 369 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 151 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.090576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061988 restraints weight = 31269.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064635 restraints weight = 15610.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066325 restraints weight = 10420.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067320 restraints weight = 8176.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067923 restraints weight = 7089.682| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11457 Z= 0.195 Angle : 0.588 16.229 15611 Z= 0.286 Chirality : 0.044 0.306 1807 Planarity : 0.004 0.050 2045 Dihedral : 6.256 163.142 1662 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.26 % Favored : 93.48 % Rotamer: Outliers : 1.04 % Allowed : 14.99 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1534 helix: 0.53 (0.40), residues: 197 sheet: -0.65 (0.22), residues: 579 loop : -1.80 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.012 0.001 TYR A 91 PHE 0.013 0.001 PHE A1030 TRP 0.013 0.001 TRP A 207 HIS 0.012 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00454 (11450) covalent geometry : angle 0.55681 (15605) hydrogen bonds : bond 0.02913 ( 381) hydrogen bonds : angle 4.94601 ( 1062) metal coordination : bond 0.01229 ( 7) metal coordination : angle 9.57540 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1855.85 seconds wall clock time: 32 minutes 46.15 seconds (1966.15 seconds total)