Starting phenix.real_space_refine on Sun Dec 29 08:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7y_27238/12_2024/8d7y_27238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7y_27238/12_2024/8d7y_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_27238/12_2024/8d7y_27238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7y_27238/12_2024/8d7y_27238.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7y_27238/12_2024/8d7y_27238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7y_27238/12_2024/8d7y_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-5532/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: 5.92, per 1000 atoms: 0.59 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: 2.27 Conformation dependent library (CDL) restraints added in 1.6 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: 1.79 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: 4.56 Time building geometry restraints manager: 2.68 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: 0.640 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- 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 : 0.003 0.070 10258 Z= 0.216 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 *********************** 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 : 1.178 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: 0.2591 time to fit residues: 36.2271 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 : 1.185 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 10258 Z= 0.651 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 *********************** 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 : 1.117 Fit side-chains REVERT: A 925 ASP cc_start: 0.7714 (p0) cc_final: 0.7472 (p0) REVERT: B 197 VAL cc_start: 0.7240 (m) cc_final: 0.6910 (p) REVERT: B 259 LYS cc_start: 0.7048 (ptpt) cc_final: 0.6484 (mtpt) REVERT: B 380 TRP cc_start: 0.2853 (OUTLIER) cc_final: 0.2419 (p90) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.2314 time to fit residues: 33.0201 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 : 1.221 ------------------------------------------------------------------------------- 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 74 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.0030 chunk 133 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10258 Z= 0.204 Angle : 0.521 7.198 14034 Z= 0.276 Chirality : 0.045 0.143 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.293 42.296 1555 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.50 % Favored : 93.29 % 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 (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: -1.98 (0.22), residues: 1476 helix: 0.30 (0.42), residues: 167 sheet: -1.11 (0.22), residues: 577 loop : -1.84 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE A 641 TYR 0.011 0.001 TYR A 42 ARG 0.005 0.000 ARG A 111 *********************** 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 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.203 Fit side-chains REVERT: A 876 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: A 938 MET cc_start: 0.8131 (mmm) cc_final: 0.7883 (mmp) REVERT: A 1095 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 197 VAL cc_start: 0.7342 (m) cc_final: 0.7000 (p) REVERT: B 259 LYS cc_start: 0.6930 (ptpt) cc_final: 0.6472 (mtpt) REVERT: B 317 LYS cc_start: 0.8580 (ttmm) cc_final: 0.7844 (mptt) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.2465 time to fit residues: 36.6759 Evaluate side-chains 95 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 232 ILE 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 132 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10258 Z= 0.269 Angle : 0.532 7.612 14034 Z= 0.279 Chirality : 0.045 0.141 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.010 17.481 1553 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.32 % Favored : 92.48 % Rotamer: Outliers : 2.54 % Allowed : 16.55 % Favored : 80.92 % 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: -1.93 (0.22), residues: 1476 helix: 0.44 (0.43), residues: 166 sheet: -1.06 (0.22), residues: 566 loop : -1.84 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.002 0.001 HIS A 805 PHE 0.013 0.001 PHE A1030 TYR 0.010 0.001 TYR A 91 ARG 0.003 0.000 ARG A 111 *********************** 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 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.143 Fit side-chains REVERT: A 872 SER cc_start: 0.8833 (m) cc_final: 0.8621 (m) REVERT: A 876 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: A 938 MET cc_start: 0.8117 (mmm) cc_final: 0.7883 (mmp) REVERT: A 1095 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 197 VAL cc_start: 0.7475 (m) cc_final: 0.7115 (p) REVERT: B 259 LYS cc_start: 0.7006 (ptpt) cc_final: 0.6500 (mtpt) REVERT: B 312 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6022 (mm) outliers start: 21 outliers final: 12 residues processed: 107 average time/residue: 0.2515 time to fit residues: 37.9373 Evaluate side-chains 106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 224 GLU 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 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 Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 394 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 B 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10258 Z= 0.423 Angle : 0.601 7.601 14034 Z= 0.315 Chirality : 0.047 0.172 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.304 18.171 1553 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.06 % Favored : 91.73 % Rotamer: Outliers : 2.78 % Allowed : 17.51 % Favored : 79.71 % 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: 0.30 (0.43), residues: 166 sheet: -1.14 (0.22), residues: 565 loop : -1.89 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.005 0.001 HIS A 803 PHE 0.018 0.002 PHE A 169 TYR 0.013 0.002 TYR A 91 ARG 0.004 0.001 ARG A 111 *********************** 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 114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.267 Fit side-chains REVERT: A 54 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 207 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.8262 (p-90) REVERT: A 872 SER cc_start: 0.8851 (m) cc_final: 0.8589 (m) REVERT: A 876 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: A 1014 MET cc_start: 0.8495 (mmp) cc_final: 0.8291 (mmp) REVERT: A 1095 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 197 VAL cc_start: 0.7386 (m) cc_final: 0.7079 (p) REVERT: B 260 GLN cc_start: 0.6434 (tm-30) cc_final: 0.6158 (tm-30) REVERT: B 312 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6055 (mm) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.2581 time to fit residues: 39.5273 Evaluate side-chains 107 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 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 47 optimal weight: 50.0000 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 40.0000 chunk 118 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10258 Z= 0.311 Angle : 0.553 7.911 14034 Z= 0.288 Chirality : 0.046 0.140 1671 Planarity : 0.004 0.054 1874 Dihedral : 4.120 18.492 1553 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.59 % Favored : 92.21 % Rotamer: Outliers : 3.02 % Allowed : 18.36 % 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: -2.02 (0.22), residues: 1476 helix: 0.44 (0.42), residues: 166 sheet: -1.21 (0.22), residues: 568 loop : -1.84 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 726 ARG 0.004 0.000 ARG A 111 *********************** 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 118 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.159 Fit side-chains REVERT: A 54 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: A 207 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.8229 (p-90) REVERT: A 280 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 782 PHE cc_start: 0.7435 (t80) cc_final: 0.7214 (t80) REVERT: A 872 SER cc_start: 0.8832 (m) cc_final: 0.8560 (m) REVERT: A 876 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: A 1095 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 197 VAL cc_start: 0.7350 (m) cc_final: 0.7034 (p) REVERT: B 260 GLN cc_start: 0.6382 (tm-30) cc_final: 0.6037 (tm-30) REVERT: B 312 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6076 (mm) REVERT: B 326 CYS cc_start: 0.6899 (t) cc_final: 0.6597 (m) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.2299 time to fit residues: 37.0690 Evaluate side-chains 114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 40.0000 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10258 Z= 0.205 Angle : 0.514 8.618 14034 Z= 0.268 Chirality : 0.045 0.141 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.895 18.360 1553 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.25 % Favored : 92.55 % Rotamer: Outliers : 2.66 % Allowed : 19.20 % Favored : 78.14 % 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: -1.93 (0.22), residues: 1476 helix: 0.56 (0.43), residues: 166 sheet: -1.15 (0.22), residues: 575 loop : -1.80 (0.22), residues: 735 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 0.011 0.001 PHE A 641 TYR 0.010 0.001 TYR A 42 ARG 0.006 0.000 ARG A 111 *********************** 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 118 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.232 Fit side-chains REVERT: A 54 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: A 207 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.8031 (p-90) REVERT: A 782 PHE cc_start: 0.7360 (t80) cc_final: 0.7141 (t80) REVERT: A 872 SER cc_start: 0.8809 (m) cc_final: 0.8509 (m) REVERT: A 876 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: A 1095 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 197 VAL cc_start: 0.7368 (m) cc_final: 0.7001 (p) REVERT: B 260 GLN cc_start: 0.6319 (tm-30) cc_final: 0.5944 (tm-30) REVERT: B 312 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6035 (mm) REVERT: B 326 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7136 (m) outliers start: 22 outliers final: 12 residues processed: 112 average time/residue: 0.2324 time to fit residues: 37.8280 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 : 1.261 ------------------------------------------------------------------------------- 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 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 815 SER 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 56 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10258 Z= 0.262 Angle : 0.530 8.713 14034 Z= 0.276 Chirality : 0.045 0.141 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.925 18.139 1553 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.11 % Favored : 92.68 % 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: -1.94 (0.22), residues: 1476 helix: 0.57 (0.43), residues: 166 sheet: -1.12 (0.22), residues: 573 loop : -1.83 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.003 0.001 HIS A 797 PHE 0.012 0.001 PHE A1030 TYR 0.011 0.001 TYR A 239 ARG 0.006 0.000 ARG A 111 *********************** 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 116 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.213 Fit side-chains REVERT: A 54 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: A 207 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.8053 (p-90) REVERT: A 782 PHE cc_start: 0.7338 (t80) cc_final: 0.7116 (t80) REVERT: A 872 SER cc_start: 0.8843 (m) cc_final: 0.8545 (m) REVERT: A 876 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: A 1095 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 197 VAL cc_start: 0.7549 (m) cc_final: 0.7233 (p) REVERT: B 260 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5958 (tm-30) REVERT: B 312 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.5988 (mm) outliers start: 23 outliers final: 16 residues processed: 109 average time/residue: 0.2284 time to fit residues: 35.9127 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 : 1.214 ------------------------------------------------------------------------------- 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 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 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 394 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 40.0000 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 50.0000 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 119 optimal weight: 0.0980 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10258 Z= 0.153 Angle : 0.495 8.528 14034 Z= 0.256 Chirality : 0.044 0.137 1671 Planarity : 0.004 0.065 1874 Dihedral : 3.684 17.656 1553 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 2.29 % Allowed : 20.05 % 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: -1.83 (0.22), residues: 1476 helix: 0.92 (0.43), residues: 160 sheet: -1.06 (0.22), residues: 565 loop : -1.80 (0.22), residues: 751 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 0.012 0.001 PHE A 641 TYR 0.012 0.001 TYR A 239 ARG 0.007 0.000 ARG A 111 *********************** 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 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.135 Fit side-chains REVERT: A 54 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: A 207 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.7859 (p-90) REVERT: A 782 PHE cc_start: 0.7336 (t80) cc_final: 0.7111 (t80) REVERT: A 872 SER cc_start: 0.8781 (m) cc_final: 0.8496 (m) REVERT: A 876 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: A 1095 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 1129 LEU cc_start: 0.7899 (mm) cc_final: 0.7635 (tp) REVERT: B 194 MET cc_start: 0.9220 (mmp) cc_final: 0.8993 (mmt) REVERT: B 197 VAL cc_start: 0.7356 (m) cc_final: 0.7019 (p) REVERT: B 260 GLN cc_start: 0.6264 (tm-30) cc_final: 0.5910 (tm-30) REVERT: B 312 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5913 (mm) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.2566 time to fit residues: 40.7376 Evaluate side-chains 110 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 50.0000 chunk 134 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10258 Z= 0.224 Angle : 0.516 8.815 14034 Z= 0.267 Chirality : 0.045 0.142 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.741 17.646 1553 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.05 % Favored : 92.82 % Rotamer: Outliers : 2.17 % Allowed : 19.69 % Favored : 78.14 % 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: -1.83 (0.22), residues: 1476 helix: 0.65 (0.43), residues: 166 sheet: -0.98 (0.22), residues: 565 loop : -1.83 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 224 HIS 0.003 0.001 HIS A 778 PHE 0.010 0.001 PHE A1030 TYR 0.012 0.001 TYR A 239 ARG 0.009 0.000 ARG A 111 ********************** 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: 18 poor density : 93 time to evaluate : 1.141 Fit side-chains REVERT: A 54 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6919 (tp30) REVERT: A 207 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.7898 (p-90) REVERT: A 782 PHE cc_start: 0.7358 (t80) cc_final: 0.7149 (t80) REVERT: A 872 SER cc_start: 0.8793 (m) cc_final: 0.8500 (m) REVERT: A 876 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: A 1095 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 1129 LEU cc_start: 0.8043 (mm) cc_final: 0.7744 (tp) REVERT: B 197 VAL cc_start: 0.7346 (m) cc_final: 0.7017 (p) REVERT: B 260 GLN cc_start: 0.6302 (tm-30) cc_final: 0.5928 (tm-30) REVERT: B 312 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5901 (mm) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.2162 time to fit residues: 33.7652 Evaluate side-chains 108 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 338 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.150638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101010 restraints weight = 15858.499| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.08 r_work: 0.3211 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10258 Z= 0.274 Angle : 0.529 8.501 14034 Z= 0.275 Chirality : 0.046 0.148 1671 Planarity : 0.004 0.054 1874 Dihedral : 3.939 23.857 1553 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 2.29 % Allowed : 19.69 % Favored : 78.02 % 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: -1.92 (0.22), residues: 1476 helix: 0.62 (0.43), residues: 166 sheet: -1.07 (0.22), residues: 573 loop : -1.86 (0.22), residues: 737 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 0.012 0.002 PHE A1030 TYR 0.010 0.001 TYR A 726 ARG 0.008 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.65 seconds wall clock time: 38 minutes 15.36 seconds (2295.36 seconds total)