Starting phenix.real_space_refine on Thu May 1 02:55:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7y_27238/05_2025/8d7y_27238.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 6328 2.51 5 N 1780 2.21 5 O 1929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10086 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 7880 Classifications: {'peptide': 1135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 303} Link IDs: {'PTRANS': 41, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 1036 Unresolved non-hydrogen angles: 1319 Unresolved non-hydrogen dihedrals: 834 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 19, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 562 Chain: "B" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2205 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 330} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 825 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 359 Chain: "B" 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 9594 SG CYS B 323 52.867 28.749 20.898 1.00249.67 S ATOM 9892 SG CYS B 394 51.598 27.839 17.266 1.00278.32 S Time building chain proxies: 6.24, per 1000 atoms: 0.62 Number of scatterers: 10086 At special positions: 0 Unit cell: (105.8, 106.95, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 1929 8.00 N 1780 7.00 C 6328 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 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 323 " 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 11.5% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1090 through 1096 removed outlier: 3.765A pdb=" N ILE A1094 " --> pdb=" O ASP A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1123 through 1126 removed outlier: 4.026A pdb=" N ALA A1126 " --> pdb=" O GLU A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1127 through 1138 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.146A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.726A pdb=" N LYS B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.881A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.835A pdb=" N ILE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.249A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER A1027 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS A1009 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.922A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 6.551A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.273A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.476A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 194 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.476A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 190 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 222 removed outlier: 3.572A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 228 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.938A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.514A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 313 through 317 removed outlier: 3.786A pdb=" N CYS A 313 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 333 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AB3, first strand: chain 'A' and resid 396 through 402 removed outlier: 4.890A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.789A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A 478 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 502 through 503 removed outlier: 4.999A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS A 522 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.648A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 588 through 594 removed outlier: 6.858A pdb=" N ALA A 605 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A 591 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 603 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET A 593 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR A 601 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 611 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 629 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 638 through 639 Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.783A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.783A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.230A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 862 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 875 removed outlier: 4.675A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 913 through 917 removed outlier: 6.834A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 956 through 959 removed outlier: 4.232A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC8, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.856A pdb=" N TYR B 144 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 14.771A pdb=" N THR B 119 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N VAL B 80 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ALA B 121 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 123 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 178 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN B 183 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL B 167 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.856A pdb=" N TYR B 144 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 149 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 330 through 332 removed outlier: 7.457A pdb=" N GLU B 330 " --> pdb=" O CYS B 323 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 323 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 332 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS B 322 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.915A pdb=" N LYS B 401 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 387 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR B 384 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 375 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TRP B 386 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG B 373 " --> pdb=" O TRP B 386 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1038 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: 5.13 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3429 1.34 - 1.46: 1707 1.46 - 1.58: 5052 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10258 Sorted by residual: bond pdb=" N ILE B 207 " pdb=" CA ILE B 207 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.19e+00 bond pdb=" N CYS B 205 " pdb=" CA CYS B 205 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N GLU A 215 " pdb=" CA GLU A 215 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.42e-02 4.96e+03 6.37e+00 bond pdb=" N LEU B 97 " pdb=" CA LEU B 97 " ideal model delta sigma weight residual 1.463 1.491 -0.028 1.11e-02 8.12e+03 6.32e+00 bond pdb=" N THR B 96 " pdb=" CA THR B 96 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.30e-02 5.92e+03 5.97e+00 ... (remaining 10253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 13521 1.29 - 2.58: 384 2.58 - 3.86: 96 3.86 - 5.15: 26 5.15 - 6.44: 7 Bond angle restraints: 14034 Sorted by residual: angle pdb=" N LYS B 229 " pdb=" CA LYS B 229 " pdb=" C LYS B 229 " ideal model delta sigma weight residual 114.56 108.54 6.02 1.27e+00 6.20e-01 2.25e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 113.28 107.58 5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N HIS B 233 " pdb=" CA HIS B 233 " pdb=" C HIS B 233 " ideal model delta sigma weight residual 111.28 106.59 4.69 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N ILE A 707 " pdb=" CA ILE A 707 " pdb=" C ILE A 707 " ideal model delta sigma weight residual 112.80 108.89 3.91 1.15e+00 7.56e-01 1.16e+01 angle pdb=" C ASN A1111 " pdb=" N LEU A1112 " pdb=" CA LEU A1112 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5592 17.42 - 34.85: 425 34.85 - 52.27: 87 52.27 - 69.69: 16 69.69 - 87.12: 8 Dihedral angle restraints: 6128 sinusoidal: 1832 harmonic: 4296 Sorted by residual: dihedral pdb=" CA CYS B 323 " pdb=" C CYS B 323 " pdb=" N LYS B 324 " pdb=" CA LYS B 324 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASP A 654 " pdb=" C ASP A 654 " pdb=" N ARG A 655 " pdb=" CA ARG A 655 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA CYS B 391 " pdb=" C CYS B 391 " pdb=" N LYS B 392 " pdb=" CA LYS B 392 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1320 0.052 - 0.103: 270 0.103 - 0.155: 78 0.155 - 0.207: 1 0.207 - 0.259: 2 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA GLU A 277 " pdb=" N GLU A 277 " pdb=" C GLU A 277 " pdb=" CB GLU A 277 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA HIS B 233 " pdb=" N HIS B 233 " pdb=" C HIS B 233 " pdb=" CB HIS B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS B 231 " pdb=" N LYS B 231 " pdb=" C LYS B 231 " pdb=" CB LYS B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.19e-01 ... (remaining 1668 not shown) Planarity restraints: 1874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 225 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLN B 225 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN B 225 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS B 226 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 416 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 417 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 522 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 523 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.020 5.00e-02 4.00e+02 ... (remaining 1871 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2560 2.80 - 3.33: 8646 3.33 - 3.85: 15268 3.85 - 4.38: 16825 4.38 - 4.90: 31275 Nonbonded interactions: 74574 Sorted by model distance: nonbonded pdb=" O GLY A 227 " pdb=" OH TYR A 239 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 36 " pdb=" NZ LYS A 60 " model vdw 2.321 3.120 nonbonded pdb=" CD1 PHE A 782 " pdb=" N GLY A 783 " model vdw 2.325 3.420 nonbonded pdb=" CD1 LEU B 268 " pdb=" OD1 ASP B 270 " model vdw 2.330 3.460 nonbonded pdb=" NZ LYS A 60 " pdb=" O GLY A1001 " model vdw 2.337 3.120 ... (remaining 74569 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 individual isotropic 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.007 0.573 10260 Z= 0.285 Angle : 0.576 6.440 14034 Z= 0.337 Chirality : 0.046 0.259 1671 Planarity : 0.004 0.052 1874 Dihedral : 13.755 87.118 3344 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.78 % Favored : 92.62 % Rotamer: Outliers : 0.72 % Allowed : 5.31 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1476 helix: -0.32 (0.40), residues: 157 sheet: -0.96 (0.23), residues: 590 loop : -1.90 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.001 PHE A 641 TYR 0.008 0.001 TYR B 245 ARG 0.008 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.19003 ( 375) hydrogen bonds : angle 7.52535 ( 1038) metal coordination : bond 0.47731 ( 2) covalent geometry : bond 0.00318 (10258) covalent geometry : angle 0.57607 (14034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.557 Fit side-chains REVERT: A 908 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7659 (p0) REVERT: B 380 TRP cc_start: 0.2232 (OUTLIER) cc_final: 0.2024 (p90) outliers start: 6 outliers final: 1 residues processed: 99 average time/residue: 0.2440 time to fit residues: 33.9853 Evaluate side-chains 92 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 380 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.0040 chunk 133 optimal weight: 10.0000 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A1055 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096950 restraints weight = 16335.497| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.04 r_work: 0.3148 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 10260 Z= 0.403 Angle : 0.742 7.645 14034 Z= 0.387 Chirality : 0.051 0.152 1671 Planarity : 0.005 0.053 1874 Dihedral : 5.098 48.729 1559 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.27 % Favored : 91.40 % Rotamer: Outliers : 2.29 % Allowed : 11.23 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.21), residues: 1476 helix: -0.22 (0.41), residues: 172 sheet: -1.21 (0.22), residues: 566 loop : -1.93 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.006 0.002 HIS A 261 PHE 0.022 0.003 PHE A 169 TYR 0.017 0.002 TYR A 812 ARG 0.004 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 375) hydrogen bonds : angle 5.86312 ( 1038) metal coordination : bond 0.01915 ( 2) covalent geometry : bond 0.00975 (10258) covalent geometry : angle 0.74173 (14034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 2.386 Fit side-chains REVERT: B 197 VAL cc_start: 0.7428 (m) cc_final: 0.7094 (p) REVERT: B 259 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7258 (mtpt) REVERT: B 380 TRP cc_start: 0.2967 (OUTLIER) cc_final: 0.2517 (p90) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.2864 time to fit residues: 41.9757 Evaluate side-chains 97 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 380 TRP Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 50.0000 chunk 82 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.150257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100971 restraints weight = 16274.135| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.09 r_work: 0.3212 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10260 Z= 0.154 Angle : 0.536 7.164 14034 Z= 0.284 Chirality : 0.046 0.144 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.368 42.360 1555 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.95 % Rotamer: Outliers : 1.81 % Allowed : 14.73 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1476 helix: 0.26 (0.42), residues: 167 sheet: -1.16 (0.22), residues: 579 loop : -1.87 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE A 641 TYR 0.010 0.001 TYR A 42 ARG 0.005 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 375) hydrogen bonds : angle 5.14204 ( 1038) metal coordination : bond 0.00671 ( 2) covalent geometry : bond 0.00372 (10258) covalent geometry : angle 0.53637 (14034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.117 Fit side-chains REVERT: A 876 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: A 1095 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 197 VAL cc_start: 0.7586 (m) cc_final: 0.7237 (p) REVERT: B 259 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7287 (mtpt) REVERT: B 260 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 312 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7218 (mm) outliers start: 15 outliers final: 8 residues processed: 109 average time/residue: 0.2775 time to fit residues: 43.5079 Evaluate side-chains 100 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 803 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101769 restraints weight = 16141.550| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.87 r_work: 0.3147 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10260 Z= 0.219 Angle : 0.572 7.822 14034 Z= 0.299 Chirality : 0.046 0.144 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.212 17.688 1553 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.93 % Favored : 91.87 % Rotamer: Outliers : 2.54 % Allowed : 17.27 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1476 helix: 0.32 (0.43), residues: 166 sheet: -1.15 (0.22), residues: 566 loop : -1.89 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.003 0.001 HIS A 797 PHE 0.015 0.002 PHE A1030 TYR 0.012 0.001 TYR A 91 ARG 0.003 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 375) hydrogen bonds : angle 5.10007 ( 1038) metal coordination : bond 0.00604 ( 2) covalent geometry : bond 0.00529 (10258) covalent geometry : angle 0.57173 (14034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.967 Fit side-chains REVERT: A 54 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: A 876 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: A 1095 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 197 VAL cc_start: 0.7576 (m) cc_final: 0.7245 (p) REVERT: B 312 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7326 (mm) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 0.2958 time to fit residues: 45.5834 Evaluate side-chains 101 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 111 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 123 optimal weight: 40.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101593 restraints weight = 16096.598| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.57 r_work: 0.3172 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10260 Z= 0.160 Angle : 0.537 9.889 14034 Z= 0.279 Chirality : 0.045 0.140 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.046 18.153 1553 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.32 % Favored : 92.48 % Rotamer: Outliers : 2.66 % Allowed : 18.24 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.22), residues: 1476 helix: 0.44 (0.43), residues: 166 sheet: -1.18 (0.22), residues: 581 loop : -1.85 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS A 803 PHE 0.012 0.001 PHE A1030 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 375) hydrogen bonds : angle 4.90195 ( 1038) metal coordination : bond 0.00488 ( 2) covalent geometry : bond 0.00386 (10258) covalent geometry : angle 0.53668 (14034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.209 Fit side-chains REVERT: A 54 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: A 207 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.8326 (p-90) REVERT: A 876 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: A 938 MET cc_start: 0.8611 (mmt) cc_final: 0.8335 (mmp) REVERT: A 1054 MET cc_start: 0.8469 (ttp) cc_final: 0.8181 (ttp) REVERT: A 1095 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7844 (tm-30) REVERT: B 197 VAL cc_start: 0.7464 (m) cc_final: 0.7183 (p) REVERT: B 260 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 312 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7256 (mm) outliers start: 22 outliers final: 15 residues processed: 110 average time/residue: 0.2406 time to fit residues: 37.5128 Evaluate side-chains 109 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102326 restraints weight = 16063.308| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.79 r_work: 0.3170 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10260 Z= 0.176 Angle : 0.538 8.655 14034 Z= 0.281 Chirality : 0.046 0.142 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.032 18.127 1553 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.25 % Favored : 92.55 % Rotamer: Outliers : 3.26 % Allowed : 18.12 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.22), residues: 1476 helix: 0.44 (0.42), residues: 166 sheet: -1.16 (0.22), residues: 572 loop : -1.86 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.003 0.001 HIS A 803 PHE 0.013 0.002 PHE A1030 TYR 0.010 0.001 TYR A 91 ARG 0.004 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 375) hydrogen bonds : angle 4.85047 ( 1038) metal coordination : bond 0.00485 ( 2) covalent geometry : bond 0.00425 (10258) covalent geometry : angle 0.53827 (14034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.180 Fit side-chains REVERT: A 54 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 207 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8264 (p-90) REVERT: A 876 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: A 938 MET cc_start: 0.8715 (mmt) cc_final: 0.8414 (mmp) REVERT: A 1095 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 197 VAL cc_start: 0.7553 (m) cc_final: 0.7202 (p) REVERT: B 260 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 312 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7287 (mm) REVERT: B 326 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6808 (m) outliers start: 27 outliers final: 18 residues processed: 113 average time/residue: 0.2181 time to fit residues: 36.0920 Evaluate side-chains 112 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 58 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.150785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102005 restraints weight = 16287.865| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.64 r_work: 0.3177 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10260 Z= 0.149 Angle : 0.523 8.222 14034 Z= 0.272 Chirality : 0.045 0.139 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.927 18.241 1553 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.05 % Favored : 92.75 % Rotamer: Outliers : 3.26 % Allowed : 18.84 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1476 helix: 0.56 (0.43), residues: 166 sheet: -1.14 (0.22), residues: 581 loop : -1.83 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.001 PHE A 641 TYR 0.011 0.001 TYR A 239 ARG 0.005 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 375) hydrogen bonds : angle 4.74670 ( 1038) metal coordination : bond 0.00467 ( 2) covalent geometry : bond 0.00359 (10258) covalent geometry : angle 0.52345 (14034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.128 Fit side-chains REVERT: A 54 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: A 207 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8175 (p-90) REVERT: A 280 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8306 (tp) REVERT: A 876 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: A 938 MET cc_start: 0.8726 (mmt) cc_final: 0.8423 (mmp) REVERT: A 1095 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 197 VAL cc_start: 0.7546 (m) cc_final: 0.7281 (p) REVERT: B 260 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7056 (tm-30) REVERT: B 312 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7196 (mm) REVERT: B 326 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6970 (m) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 0.2189 time to fit residues: 36.1364 Evaluate side-chains 109 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099283 restraints weight = 16175.072| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.80 r_work: 0.3135 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10260 Z= 0.249 Angle : 0.593 7.523 14034 Z= 0.309 Chirality : 0.047 0.183 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.236 18.525 1553 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.20 % Favored : 91.60 % Rotamer: Outliers : 3.38 % Allowed : 18.96 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.22), residues: 1476 helix: 0.43 (0.43), residues: 166 sheet: -1.24 (0.22), residues: 574 loop : -1.91 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.004 0.001 HIS A 797 PHE 0.017 0.002 PHE A1030 TYR 0.012 0.002 TYR A 726 ARG 0.005 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 375) hydrogen bonds : angle 5.01701 ( 1038) metal coordination : bond 0.00483 ( 2) covalent geometry : bond 0.00602 (10258) covalent geometry : angle 0.59339 (14034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.193 Fit side-chains REVERT: A 54 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: A 207 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.8352 (p-90) REVERT: A 280 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 876 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: A 938 MET cc_start: 0.8752 (mmt) cc_final: 0.8447 (mmp) REVERT: A 1095 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 197 VAL cc_start: 0.7711 (m) cc_final: 0.7417 (p) REVERT: B 260 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 312 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7306 (mm) REVERT: B 326 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6970 (m) outliers start: 28 outliers final: 17 residues processed: 110 average time/residue: 0.2300 time to fit residues: 36.6773 Evaluate side-chains 110 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 chunk 135 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102008 restraints weight = 16127.951| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.45 r_work: 0.3197 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10260 Z= 0.115 Angle : 0.512 10.646 14034 Z= 0.266 Chirality : 0.045 0.143 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.873 18.222 1553 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 2.42 % Allowed : 20.17 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.99 (0.22), residues: 1476 helix: 0.57 (0.42), residues: 166 sheet: -1.13 (0.22), residues: 574 loop : -1.90 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE A 641 TYR 0.010 0.001 TYR A 239 ARG 0.007 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02587 ( 375) hydrogen bonds : angle 4.68323 ( 1038) metal coordination : bond 0.00417 ( 2) covalent geometry : bond 0.00274 (10258) covalent geometry : angle 0.51196 (14034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.044 Fit side-chains REVERT: A 207 TRP cc_start: 0.9038 (OUTLIER) cc_final: 0.8072 (p-90) REVERT: A 280 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 876 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: A 938 MET cc_start: 0.8732 (mmt) cc_final: 0.8427 (mmp) REVERT: A 1095 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 1129 LEU cc_start: 0.8157 (mm) cc_final: 0.7810 (tp) REVERT: B 197 VAL cc_start: 0.7556 (m) cc_final: 0.7250 (p) REVERT: B 260 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 312 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7154 (mm) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.2111 time to fit residues: 33.3303 Evaluate side-chains 104 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 116 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 50.0000 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099445 restraints weight = 16123.887| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.07 r_work: 0.3185 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10260 Z= 0.226 Angle : 0.583 10.165 14034 Z= 0.301 Chirality : 0.047 0.163 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.119 18.378 1553 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1476 helix: 0.49 (0.43), residues: 166 sheet: -1.23 (0.22), residues: 594 loop : -1.91 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 224 HIS 0.003 0.001 HIS A 803 PHE 0.015 0.002 PHE A1030 TYR 0.011 0.001 TYR A 91 ARG 0.008 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 375) hydrogen bonds : angle 4.90312 ( 1038) metal coordination : bond 0.00519 ( 2) covalent geometry : bond 0.00547 (10258) covalent geometry : angle 0.58253 (14034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.182 Fit side-chains REVERT: A 54 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: A 207 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.8249 (p-90) REVERT: A 280 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 876 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: A 938 MET cc_start: 0.8706 (mmt) cc_final: 0.8424 (mmp) REVERT: A 1095 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 197 VAL cc_start: 0.7746 (m) cc_final: 0.7462 (p) REVERT: B 260 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 312 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7331 (mm) outliers start: 23 outliers final: 16 residues processed: 104 average time/residue: 0.2162 time to fit residues: 33.2172 Evaluate side-chains 108 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 61 optimal weight: 0.0970 chunk 142 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 140 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.149614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100008 restraints weight = 15995.892| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.06 r_work: 0.3194 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10260 Z= 0.200 Angle : 0.564 10.425 14034 Z= 0.292 Chirality : 0.046 0.149 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.113 18.500 1553 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 3.02 % Allowed : 19.08 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.22), residues: 1476 helix: 0.51 (0.43), residues: 166 sheet: -1.20 (0.22), residues: 572 loop : -1.96 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.003 0.001 HIS A 803 PHE 0.013 0.002 PHE A1030 TYR 0.011 0.001 TYR A 726 ARG 0.009 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 375) hydrogen bonds : angle 4.87488 ( 1038) metal coordination : bond 0.00495 ( 2) covalent geometry : bond 0.00483 (10258) covalent geometry : angle 0.56387 (14034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.64 seconds wall clock time: 93 minutes 35.48 seconds (5615.48 seconds total)