Starting phenix.real_space_refine on Wed May 14 09:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d80_27241/05_2025/8d80_27241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d80_27241/05_2025/8d80_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_27241/05_2025/8d80_27241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d80_27241/05_2025/8d80_27241.map" model { file = "/net/cci-nas-00/data/ceres_data/8d80_27241/05_2025/8d80_27241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d80_27241/05_2025/8d80_27241.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 17, 'ASP:plan': 18, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 14} 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: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} 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: 6.59, per 1000 atoms: 0.59 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 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: 1.73 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: 4.74 Time building geometry restraints manager: 3.15 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.011 0.001 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.013 0.001 PHE A1030 TYR 0.010 0.001 TYR B 227 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.23353 ( 381) hydrogen bonds : angle 9.45836 ( 1062) metal coordination : bond 0.13731 ( 7) metal coordination : angle 3.94163 ( 6) covalent geometry : bond 0.00371 (11450) covalent geometry : angle 0.63260 (15605) *********************** 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 : 1.334 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: 0.2092 time to fit residues: 33.4678 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 : 1.255 ------------------------------------------------------------------------------- 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 129 optimal weight: 3.9990 chunk 115 optimal weight: 30.0000 chunk 64 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 50.0000 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 B 353 HIS ** B 357 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 = 0.3714 r_free = 0.3714 target = 0.091649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063226 restraints weight = 30207.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065808 restraints weight = 15374.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067456 restraints weight = 10346.073| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11457 Z= 0.203 Angle : 0.584 8.171 15611 Z= 0.302 Chirality : 0.044 0.149 1807 Planarity : 0.004 0.044 2045 Dihedral : 8.920 169.602 1665 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 0.85 % Allowed : 6.79 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1534 helix: 0.50 (0.41), residues: 180 sheet: -0.68 (0.22), residues: 592 loop : -1.73 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.014 0.001 HIS B 397 PHE 0.015 0.001 PHE A 829 TYR 0.013 0.001 TYR A 42 ARG 0.004 0.001 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 381) hydrogen bonds : angle 6.17947 ( 1062) metal coordination : bond 0.00782 ( 7) metal coordination : angle 4.24257 ( 6) covalent geometry : bond 0.00468 (11450) covalent geometry : angle 0.57843 (15605) *********************** 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 : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8679 (ptp) cc_final: 0.8467 (ptm) REVERT: B 64 MET cc_start: 0.5256 (tpp) cc_final: 0.4928 (tpt) REVERT: B 194 MET cc_start: 0.8654 (tpp) cc_final: 0.8311 (mmm) REVERT: C 148 ASN cc_start: 0.7426 (t0) cc_final: 0.7124 (t0) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.1924 time to fit residues: 24.8816 Evaluate side-chains 73 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 101 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 chunk 68 optimal weight: 0.0570 chunk 110 optimal weight: 0.4980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 826 ASN A 852 GLN A 908 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3755 r_free = 0.3755 target = 0.093828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065657 restraints weight = 30302.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068332 restraints weight = 15175.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070008 restraints weight = 10111.433| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1721 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= 0.089 Angle : 0.498 7.301 15611 Z= 0.258 Chirality : 0.043 0.139 1807 Planarity : 0.003 0.046 2045 Dihedral : 8.301 169.580 1662 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 0.94 % Allowed : 8.77 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1534 helix: 0.50 (0.40), residues: 188 sheet: -0.63 (0.22), residues: 578 loop : -1.59 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.009 0.001 HIS B 397 PHE 0.013 0.001 PHE A 829 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 381) hydrogen bonds : angle 5.40431 ( 1062) metal coordination : bond 0.00425 ( 7) metal coordination : angle 3.21242 ( 6) covalent geometry : bond 0.00199 (11450) covalent geometry : angle 0.49456 (15605) *********************** 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 85 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.8556 (ptp) cc_final: 0.8170 (ptm) REVERT: A 954 MET cc_start: 0.8956 (ttt) cc_final: 0.8651 (ttt) REVERT: B 64 MET cc_start: 0.4884 (tpp) cc_final: 0.4557 (tpt) REVERT: B 194 MET cc_start: 0.8664 (tpp) cc_final: 0.8213 (mmm) REVERT: B 288 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 387 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.6293 (p) REVERT: C 148 ASN cc_start: 0.7202 (t0) cc_final: 0.6899 (t0) outliers start: 10 outliers final: 3 residues processed: 81 average time/residue: 0.1841 time to fit residues: 24.3929 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL 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 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 40 optimal weight: 0.0170 chunk 60 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 overall best weight: 3.1624 ------------------------------------------------------------------------------- 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 A 993 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 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 = 0.3692 r_free = 0.3692 target = 0.090400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061962 restraints weight = 30388.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064377 restraints weight = 16215.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065869 restraints weight = 11201.641| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11457 Z= 0.248 Angle : 0.580 12.170 15611 Z= 0.298 Chirality : 0.045 0.146 1807 Planarity : 0.004 0.045 2045 Dihedral : 7.756 168.737 1662 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.23 % Allowed : 10.74 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1534 helix: 0.40 (0.39), residues: 190 sheet: -0.62 (0.22), residues: 570 loop : -1.75 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.015 0.002 PHE A1030 TYR 0.012 0.001 TYR A 91 ARG 0.003 0.000 ARG A1074 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 381) hydrogen bonds : angle 5.43515 ( 1062) metal coordination : bond 0.00573 ( 7) metal coordination : angle 2.98972 ( 6) covalent geometry : bond 0.00572 (11450) covalent geometry : angle 0.57712 (15605) *********************** 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 80 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 1036 MET cc_start: 0.8995 (ptm) cc_final: 0.8706 (ppp) REVERT: B 64 MET cc_start: 0.5015 (tpp) cc_final: 0.4720 (tpt) REVERT: B 194 MET cc_start: 0.8858 (tpp) cc_final: 0.8525 (mmm) REVERT: B 387 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6176 (m) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.1868 time to fit residues: 23.4008 Evaluate side-chains 73 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 221 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 53 optimal weight: 50.0000 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 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 = 0.3717 r_free = 0.3717 target = 0.091386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063016 restraints weight = 30402.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065583 restraints weight = 15498.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.067197 restraints weight = 10448.155| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11457 Z= 0.147 Angle : 0.513 11.450 15611 Z= 0.264 Chirality : 0.043 0.142 1807 Planarity : 0.003 0.045 2045 Dihedral : 7.538 167.932 1662 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.61 % Favored : 94.13 % Rotamer: Outliers : 1.51 % Allowed : 11.78 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1534 helix: 0.56 (0.40), residues: 190 sheet: -0.70 (0.22), residues: 592 loop : -1.69 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.008 0.001 HIS B 397 PHE 0.013 0.001 PHE A1030 TYR 0.010 0.001 TYR A 42 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 381) hydrogen bonds : angle 5.15141 ( 1062) metal coordination : bond 0.00474 ( 7) metal coordination : angle 2.87287 ( 6) covalent geometry : bond 0.00341 (11450) covalent geometry : angle 0.50952 (15605) *********************** 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 83 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 954 MET cc_start: 0.8932 (ttt) cc_final: 0.8661 (ttt) REVERT: A 1036 MET cc_start: 0.8978 (ptm) cc_final: 0.8742 (ppp) REVERT: B 64 MET cc_start: 0.5345 (tpp) cc_final: 0.4950 (tpt) REVERT: B 288 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9133 (mp) outliers start: 16 outliers final: 7 residues processed: 80 average time/residue: 0.1769 time to fit residues: 23.0635 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 855 ASP Chi-restraints excluded: chain A residue 1040 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 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 = 0.3720 r_free = 0.3720 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063111 restraints weight = 30896.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065716 restraints weight = 15507.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067365 restraints weight = 10386.970| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11457 Z= 0.143 Angle : 0.511 10.407 15611 Z= 0.262 Chirality : 0.043 0.142 1807 Planarity : 0.003 0.047 2045 Dihedral : 7.395 167.502 1662 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.06 % Favored : 93.68 % Rotamer: Outliers : 1.23 % Allowed : 12.91 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1534 helix: 0.42 (0.40), residues: 196 sheet: -0.69 (0.22), residues: 591 loop : -1.69 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.007 0.001 HIS B 397 PHE 0.012 0.001 PHE A1030 TYR 0.010 0.001 TYR A 91 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 381) hydrogen bonds : angle 5.02683 ( 1062) metal coordination : bond 0.00451 ( 7) metal coordination : angle 3.01403 ( 6) covalent geometry : bond 0.00332 (11450) covalent geometry : angle 0.50721 (15605) *********************** 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 79 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 280 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9258 (mp) REVERT: A 954 MET cc_start: 0.8891 (ttt) cc_final: 0.8675 (ttt) REVERT: A 1036 MET cc_start: 0.8971 (ptm) cc_final: 0.8748 (ppp) REVERT: B 64 MET cc_start: 0.5418 (tpp) cc_final: 0.5007 (tpt) REVERT: B 288 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9113 (mp) outliers start: 13 outliers final: 6 residues processed: 76 average time/residue: 0.1784 time to fit residues: 22.1960 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 : 1.180 ------------------------------------------------------------------------------- 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 340 SER Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 122 VAL 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 118 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 101 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 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 = 0.3699 r_free = 0.3699 target = 0.090340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061689 restraints weight = 30979.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064310 restraints weight = 15474.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.065897 restraints weight = 10325.517| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11457 Z= 0.196 Angle : 0.548 9.914 15611 Z= 0.279 Chirality : 0.044 0.181 1807 Planarity : 0.004 0.047 2045 Dihedral : 7.274 166.884 1662 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.87 % Favored : 93.87 % Rotamer: Outliers : 1.51 % Allowed : 12.72 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1534 helix: 0.35 (0.39), residues: 196 sheet: -0.74 (0.22), residues: 591 loop : -1.77 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.007 0.001 HIS B 397 PHE 0.014 0.001 PHE A1030 TYR 0.012 0.001 TYR A 91 ARG 0.003 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 381) hydrogen bonds : angle 5.06950 ( 1062) metal coordination : bond 0.00549 ( 7) metal coordination : angle 3.33329 ( 6) covalent geometry : bond 0.00455 (11450) covalent geometry : angle 0.54411 (15605) *********************** 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 80 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 280 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9337 (mp) REVERT: A 1036 MET cc_start: 0.9023 (ptm) cc_final: 0.8774 (ppp) REVERT: B 288 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9176 (mp) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.1770 time to fit residues: 22.4790 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 122 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 50.0000 chunk 116 optimal weight: 0.0010 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.092547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064571 restraints weight = 31143.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067103 restraints weight = 16121.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068657 restraints weight = 10943.741| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11457 Z= 0.100 Angle : 0.547 15.841 15611 Z= 0.264 Chirality : 0.043 0.190 1807 Planarity : 0.003 0.047 2045 Dihedral : 6.988 165.610 1662 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.48 % Favored : 94.26 % Rotamer: Outliers : 1.23 % Allowed : 13.57 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1534 helix: 0.52 (0.40), residues: 196 sheet: -0.56 (0.22), residues: 571 loop : -1.77 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.006 0.001 HIS B 397 PHE 0.011 0.001 PHE A1030 TYR 0.019 0.001 TYR B 221 ARG 0.005 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.02457 ( 381) hydrogen bonds : angle 4.80594 ( 1062) metal coordination : bond 0.01007 ( 7) metal coordination : angle 9.65920 ( 6) covalent geometry : bond 0.00229 (11450) covalent geometry : angle 0.51342 (15605) *********************** 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: 13 poor density : 69 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8494 (ptp) cc_final: 0.8275 (ptm) REVERT: A 1036 MET cc_start: 0.8951 (ptm) cc_final: 0.8730 (ppp) REVERT: B 288 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9106 (mp) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.2186 time to fit residues: 28.3868 Evaluate side-chains 74 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 78 CYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 406 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.0010 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 115 optimal weight: 30.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.092176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063967 restraints weight = 31212.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066630 restraints weight = 15564.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068286 restraints weight = 10341.122| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11457 Z= 0.117 Angle : 0.551 17.124 15611 Z= 0.263 Chirality : 0.043 0.301 1807 Planarity : 0.003 0.048 2045 Dihedral : 6.529 165.175 1662 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 1.13 % Allowed : 13.95 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1534 helix: 0.51 (0.39), residues: 202 sheet: -0.54 (0.22), residues: 574 loop : -1.80 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.011 0.001 HIS B 397 PHE 0.011 0.001 PHE A1030 TYR 0.009 0.001 TYR A 42 ARG 0.009 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.02536 ( 381) hydrogen bonds : angle 4.72596 ( 1062) metal coordination : bond 0.01357 ( 7) metal coordination : angle 10.31111 ( 6) covalent geometry : bond 0.00273 (11450) covalent geometry : angle 0.51292 (15605) *********************** 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 81 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9131 (mp) REVERT: B 363 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.7209 (m-80) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.2084 time to fit residues: 25.3683 Evaluate side-chains 75 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 406 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 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 = 0.3696 r_free = 0.3696 target = 0.090089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061550 restraints weight = 30647.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064145 restraints weight = 15395.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.065809 restraints weight = 10312.623| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11457 Z= 0.219 Angle : 0.586 15.618 15611 Z= 0.290 Chirality : 0.045 0.331 1807 Planarity : 0.004 0.047 2045 Dihedral : 6.362 164.527 1662 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.45 % Favored : 93.29 % Rotamer: Outliers : 1.04 % Allowed : 14.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1534 helix: 0.58 (0.39), residues: 196 sheet: -0.63 (0.22), residues: 569 loop : -1.77 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.012 0.001 HIS B 397 PHE 0.013 0.001 PHE A1030 TYR 0.013 0.001 TYR A 91 ARG 0.008 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 381) hydrogen bonds : angle 4.96499 ( 1062) metal coordination : bond 0.01013 ( 7) metal coordination : angle 7.87025 ( 6) covalent geometry : bond 0.00510 (11450) covalent geometry : angle 0.56534 (15605) ********************** 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 75 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9207 (mp) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.1873 time to fit residues: 22.3491 Evaluate side-chains 73 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 315 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 406 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 82 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 ASN ** B 357 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 = 0.3733 r_free = 0.3733 target = 0.091996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063929 restraints weight = 30450.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066547 restraints weight = 15349.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068215 restraints weight = 10264.435| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2788 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 : 0.519 8.809 15611 Z= 0.260 Chirality : 0.044 0.301 1807 Planarity : 0.003 0.048 2045 Dihedral : 6.108 164.021 1662 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.54 % Favored : 94.20 % Rotamer: Outliers : 0.85 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1534 helix: 0.67 (0.40), residues: 196 sheet: -0.52 (0.22), residues: 572 loop : -1.75 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 380 HIS 0.009 0.001 HIS B 397 PHE 0.011 0.001 PHE A1030 TYR 0.010 0.001 TYR A 42 ARG 0.006 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.02483 ( 381) hydrogen bonds : angle 4.74166 ( 1062) metal coordination : bond 0.00705 ( 7) metal coordination : angle 4.25019 ( 6) covalent geometry : bond 0.00232 (11450) covalent geometry : angle 0.51209 (15605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.90 seconds wall clock time: 60 minutes 5.49 seconds (3605.49 seconds total)