Starting phenix.real_space_refine on Wed Mar 4 02:27:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_27238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_27238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_27238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_27238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7y_27238/03_2026/8d7y_27238.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 31, 'ASP:plan': 19, 'ARG:plan': 17, 'GLN:plan1': 18, 'HIS:plan': 9, 'TRP:plan': 3, 'ASN:plan1': 14, 'PHE:plan': 9, 'TYR:plan': 8} 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: {'GLU:plan': 17, 'PHE:plan': 9, 'HIS:plan': 5, 'ARG:plan': 10, 'ASP:plan': 9, 'GLN:plan1': 19, 'ASN:plan1': 5, 'TYR:plan': 5, 'TRP:plan': 1} 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: 2.72, per 1000 atoms: 0.27 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: 0.82 Conformation dependent library (CDL) restraints added in 551.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 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: 0.45 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: 2.19 Time building geometry restraints manager: 1.09 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG A 111 TYR 0.008 0.001 TYR B 245 PHE 0.009 0.001 PHE A 641 TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00318 (10258) covalent geometry : angle 0.57607 (14034) hydrogen bonds : bond 0.19003 ( 375) hydrogen bonds : angle 7.52535 ( 1038) metal coordination : bond 0.47731 ( 2) *********************** 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 : 0.366 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: 0.1095 time to fit residues: 14.9415 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 : 0.381 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 978 GLN A1055 GLN B 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097885 restraints weight = 16353.631| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.07 r_work: 0.3162 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 10260 Z= 0.336 Angle : 0.691 7.638 14034 Z= 0.361 Chirality : 0.049 0.146 1671 Planarity : 0.005 0.053 1874 Dihedral : 4.939 48.093 1559 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.20 % Favored : 91.53 % Rotamer: Outliers : 2.05 % Allowed : 10.75 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.21), residues: 1476 helix: -0.12 (0.41), residues: 172 sheet: -1.25 (0.22), residues: 565 loop : -1.87 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1074 TYR 0.016 0.002 TYR A 812 PHE 0.020 0.002 PHE A1030 TRP 0.014 0.002 TRP A 207 HIS 0.005 0.002 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00813 (10258) covalent geometry : angle 0.69072 (14034) hydrogen bonds : bond 0.03887 ( 375) hydrogen bonds : angle 5.69362 ( 1038) metal coordination : bond 0.02201 ( 2) *********************** 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 104 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.440 Fit side-chains REVERT: B 197 VAL cc_start: 0.7403 (m) cc_final: 0.7080 (p) REVERT: B 259 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7234 (mtpt) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.1049 time to fit residues: 14.6206 Evaluate side-chains 94 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 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 394 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 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 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.150118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100202 restraints weight = 16225.058| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.09 r_work: 0.3204 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10260 Z= 0.179 Angle : 0.548 7.315 14034 Z= 0.289 Chirality : 0.046 0.143 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.152 17.768 1553 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.11 % Favored : 92.68 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.22), residues: 1476 helix: 0.26 (0.43), residues: 167 sheet: -1.12 (0.22), residues: 567 loop : -1.86 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.010 0.001 TYR A 42 PHE 0.013 0.001 PHE A1030 TRP 0.014 0.001 TRP A 207 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00432 (10258) covalent geometry : angle 0.54820 (14034) hydrogen bonds : bond 0.03098 ( 375) hydrogen bonds : angle 5.17068 ( 1038) metal coordination : bond 0.00722 ( 2) *********************** 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 108 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.375 Fit side-chains REVERT: A 876 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: A 1095 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 197 VAL cc_start: 0.7407 (m) cc_final: 0.7102 (p) REVERT: B 259 LYS cc_start: 0.7927 (ptpt) cc_final: 0.7308 (mtpt) REVERT: B 260 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 301 ILE cc_start: 0.8141 (mp) cc_final: 0.7800 (mp) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.1109 time to fit residues: 16.0311 Evaluate side-chains 97 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 360 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104057 restraints weight = 16179.126| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.11 r_work: 0.3253 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10260 Z= 0.092 Angle : 0.489 7.222 14034 Z= 0.256 Chirality : 0.044 0.144 1671 Planarity : 0.004 0.055 1874 Dihedral : 3.715 17.058 1553 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.50 % Favored : 93.29 % Rotamer: Outliers : 2.05 % Allowed : 15.22 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1476 helix: 0.54 (0.43), residues: 166 sheet: -0.97 (0.22), residues: 574 loop : -1.78 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 111 TYR 0.011 0.001 TYR A 42 PHE 0.016 0.001 PHE A 782 TRP 0.012 0.001 TRP B 223 HIS 0.003 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00215 (10258) covalent geometry : angle 0.48890 (14034) hydrogen bonds : bond 0.02372 ( 375) hydrogen bonds : angle 4.68120 ( 1038) metal coordination : bond 0.00516 ( 2) *********************** 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 124 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.295 Fit side-chains REVERT: A 211 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: A 876 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: A 1095 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 197 VAL cc_start: 0.7441 (m) cc_final: 0.7059 (p) REVERT: B 210 SER cc_start: 0.7274 (t) cc_final: 0.7031 (p) REVERT: B 259 LYS cc_start: 0.7942 (ptpt) cc_final: 0.7189 (mtpt) REVERT: B 260 GLN cc_start: 0.7487 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 272 SER cc_start: 0.7392 (m) cc_final: 0.7112 (t) REVERT: B 301 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 312 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7114 (mm) outliers start: 17 outliers final: 9 residues processed: 115 average time/residue: 0.1108 time to fit residues: 17.6398 Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 218 MET 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 836 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 803 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.150681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100910 restraints weight = 16227.645| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.09 r_work: 0.3203 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10260 Z= 0.178 Angle : 0.529 7.354 14034 Z= 0.277 Chirality : 0.045 0.143 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.873 17.671 1553 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.98 % Favored : 92.82 % Rotamer: Outliers : 2.90 % Allowed : 16.79 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.22), residues: 1476 helix: 0.58 (0.43), residues: 166 sheet: -0.95 (0.23), residues: 547 loop : -1.78 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.011 0.001 TYR A 91 PHE 0.014 0.002 PHE A1030 TRP 0.010 0.001 TRP A 207 HIS 0.003 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.00427 (10258) covalent geometry : angle 0.52916 (14034) hydrogen bonds : bond 0.02761 ( 375) hydrogen bonds : angle 4.77750 ( 1038) metal coordination : bond 0.00540 ( 2) *********************** 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 116 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.404 Fit side-chains REVERT: A 54 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: A 207 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.8098 (p-90) REVERT: A 876 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: A 938 MET cc_start: 0.8579 (mmt) cc_final: 0.8320 (mmp) REVERT: A 1095 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 197 VAL cc_start: 0.7575 (m) cc_final: 0.7213 (p) REVERT: B 260 GLN cc_start: 0.7473 (tm-30) cc_final: 0.6923 (tm-30) REVERT: B 301 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (mp) REVERT: B 312 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7145 (mm) REVERT: B 326 CYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6940 (m) outliers start: 24 outliers final: 11 residues processed: 107 average time/residue: 0.0963 time to fit residues: 15.0143 Evaluate side-chains 108 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 735 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 293 VAL Chi-restraints excluded: chain B residue 301 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097806 restraints weight = 16349.694| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.08 r_work: 0.3144 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10260 Z= 0.311 Angle : 0.645 9.022 14034 Z= 0.334 Chirality : 0.048 0.165 1671 Planarity : 0.004 0.053 1874 Dihedral : 4.424 18.583 1553 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.33 % Favored : 91.46 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.22), residues: 1476 helix: 0.31 (0.43), residues: 166 sheet: -1.20 (0.22), residues: 570 loop : -1.84 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.015 0.002 TYR A 91 PHE 0.021 0.002 PHE A 169 TRP 0.011 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00744 (10258) covalent geometry : angle 0.64453 (14034) hydrogen bonds : bond 0.03353 ( 375) hydrogen bonds : angle 5.20141 ( 1038) metal coordination : bond 0.00519 ( 2) *********************** 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 113 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.393 Fit side-chains REVERT: A 54 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: A 207 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.8455 (p-90) REVERT: A 876 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: A 1095 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 197 VAL cc_start: 0.7588 (m) cc_final: 0.7268 (p) REVERT: B 260 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 301 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 312 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7444 (mm) REVERT: B 326 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6827 (m) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.0878 time to fit residues: 13.6081 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 : 0.311 ------------------------------------------------------------------------------- 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 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 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 874 VAL 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 301 ILE 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 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 144 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.150859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103947 restraints weight = 15801.947| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.78 r_work: 0.3202 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10260 Z= 0.101 Angle : 0.507 8.963 14034 Z= 0.263 Chirality : 0.045 0.140 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.857 18.594 1553 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.37 % Favored : 93.43 % Rotamer: Outliers : 2.17 % Allowed : 19.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.22), residues: 1476 helix: 0.60 (0.43), residues: 166 sheet: -1.07 (0.22), residues: 574 loop : -1.81 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.010 0.001 TYR A 42 PHE 0.012 0.001 PHE A 641 TRP 0.013 0.001 TRP B 223 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00238 (10258) covalent geometry : angle 0.50656 (14034) hydrogen bonds : bond 0.02497 ( 375) hydrogen bonds : angle 4.69699 ( 1038) metal coordination : bond 0.00444 ( 2) *********************** 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 114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.338 Fit side-chains REVERT: A 54 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: A 207 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.8161 (p-90) REVERT: A 280 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 876 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: A 938 MET cc_start: 0.8621 (mmt) cc_final: 0.8294 (mmp) REVERT: A 1095 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 197 VAL cc_start: 0.7464 (m) cc_final: 0.7099 (p) REVERT: B 260 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 301 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 312 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7179 (mm) REVERT: B 326 CYS cc_start: 0.7174 (t) cc_final: 0.6969 (m) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 0.0870 time to fit residues: 13.7164 Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 280 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 50.0000 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.149703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101618 restraints weight = 15972.843| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.63 r_work: 0.3185 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10260 Z= 0.148 Angle : 0.523 8.112 14034 Z= 0.270 Chirality : 0.045 0.141 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.856 18.127 1553 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.98 % Favored : 92.82 % Rotamer: Outliers : 2.42 % Allowed : 18.84 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.22), residues: 1476 helix: 0.62 (0.43), residues: 166 sheet: -1.04 (0.22), residues: 572 loop : -1.81 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.010 0.001 TYR A 239 PHE 0.011 0.001 PHE A1030 TRP 0.010 0.001 TRP B 223 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00359 (10258) covalent geometry : angle 0.52265 (14034) hydrogen bonds : bond 0.02675 ( 375) hydrogen bonds : angle 4.70681 ( 1038) metal coordination : bond 0.00459 ( 2) *********************** 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 112 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.220 Fit side-chains REVERT: A 54 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: A 207 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8132 (p-90) REVERT: A 280 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 876 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: A 1095 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 197 VAL cc_start: 0.7530 (m) cc_final: 0.7172 (p) REVERT: B 206 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7154 (mt0) REVERT: B 260 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7124 (tm-30) REVERT: B 301 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7825 (mp) REVERT: B 312 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7194 (mm) outliers start: 20 outliers final: 11 residues processed: 104 average time/residue: 0.0940 time to fit residues: 14.1777 Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 207 TRP Chi-restraints excluded: chain A residue 218 MET 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 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 50 optimal weight: 50.0000 chunk 42 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.148720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100665 restraints weight = 15817.249| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.53 r_work: 0.3164 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2070 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= 0.196 Angle : 0.560 10.472 14034 Z= 0.288 Chirality : 0.046 0.144 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.023 18.418 1553 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.29 % Allowed : 18.96 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1476 helix: 0.58 (0.43), residues: 166 sheet: -1.08 (0.22), residues: 563 loop : -1.82 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.011 0.001 TYR A 726 PHE 0.014 0.002 PHE A1030 TRP 0.010 0.001 TRP A 207 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00475 (10258) covalent geometry : angle 0.55994 (14034) hydrogen bonds : bond 0.02865 ( 375) hydrogen bonds : angle 4.83048 ( 1038) metal coordination : bond 0.00504 ( 2) *********************** 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 110 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.305 Fit side-chains REVERT: A 54 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: A 207 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8223 (p-90) REVERT: A 280 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (tt) REVERT: A 876 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: A 1095 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 1129 LEU cc_start: 0.8273 (mm) cc_final: 0.7897 (tp) REVERT: B 197 VAL cc_start: 0.7590 (m) cc_final: 0.7236 (p) REVERT: B 260 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 301 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 312 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7188 (mm) outliers start: 19 outliers final: 9 residues processed: 103 average time/residue: 0.0902 time to fit residues: 13.4373 Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 50.0000 chunk 137 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.150147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101358 restraints weight = 15882.814| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.63 r_work: 0.3196 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10260 Z= 0.131 Angle : 0.517 10.698 14034 Z= 0.267 Chirality : 0.045 0.147 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.846 18.059 1553 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.98 % Favored : 92.89 % Rotamer: Outliers : 1.81 % Allowed : 19.20 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1476 helix: 0.66 (0.43), residues: 166 sheet: -1.02 (0.22), residues: 572 loop : -1.82 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 111 TYR 0.010 0.001 TYR A 42 PHE 0.011 0.001 PHE A 782 TRP 0.011 0.001 TRP B 223 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00316 (10258) covalent geometry : angle 0.51737 (14034) hydrogen bonds : bond 0.02585 ( 375) hydrogen bonds : angle 4.66602 ( 1038) metal coordination : bond 0.01488 ( 2) ********************** 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 105 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.347 Fit side-chains REVERT: A 54 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7138 (tp30) REVERT: A 207 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.8053 (p-90) REVERT: A 280 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 876 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: A 1095 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 1129 LEU cc_start: 0.8089 (mm) cc_final: 0.7749 (tp) REVERT: B 197 VAL cc_start: 0.7465 (m) cc_final: 0.7114 (p) REVERT: B 260 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 301 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 312 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7115 (mm) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.1020 time to fit residues: 14.4950 Evaluate side-chains 103 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 123 optimal weight: 40.0000 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.149459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101689 restraints weight = 15984.893| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.53 r_work: 0.3182 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10260 Z= 0.161 Angle : 0.535 10.600 14034 Z= 0.276 Chirality : 0.045 0.144 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.895 18.124 1553 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 1.93 % Allowed : 19.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.22), residues: 1476 helix: 0.61 (0.43), residues: 166 sheet: -1.02 (0.23), residues: 555 loop : -1.91 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 111 TYR 0.010 0.001 TYR A 239 PHE 0.012 0.002 PHE A1030 TRP 0.010 0.001 TRP B 224 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00389 (10258) covalent geometry : angle 0.53502 (14034) hydrogen bonds : bond 0.02681 ( 375) hydrogen bonds : angle 4.70930 ( 1038) metal coordination : bond 0.00554 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.21 seconds wall clock time: 38 minutes 58.50 seconds (2338.50 seconds total)