Starting phenix.real_space_refine on Fri Jul 3 01:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oxc_17264/07_2026/8oxc_17264.cif" } resolution = 2.58 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7199 2.51 5 N 1832 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11143 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, 'PIE': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 2.18, per 1000 atoms: 0.20 Number of scatterers: 11143 At special positions: 0 Unit cell: (85.404, 89.933, 178.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2055 8.00 N 1832 7.00 C 7199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.05 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 503.8 milliseconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 51.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.988A pdb=" N PHE A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.721A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 175 Proline residue: A 147 - end of helix removed outlier: 3.711A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.908A pdb=" N GLN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.503A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 331 through 366 removed outlier: 3.635A pdb=" N THR A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 4.117A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 401 through 422 removed outlier: 4.332A pdb=" N TYR A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 4.034A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.026A pdb=" N ARG A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 635 through 649 removed outlier: 3.515A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 removed outlier: 3.750A pdb=" N VAL A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 695 removed outlier: 3.680A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 771 removed outlier: 3.587A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 770 " --> pdb=" O HIS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.633A pdb=" N ASN A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 796' Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 840 through 859 Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.521A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 Processing helix chain 'A' and resid 938 through 969 removed outlier: 3.994A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 981 through 992 removed outlier: 5.190A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1029 through 1057 Proline residue: A1051 - end of helix removed outlier: 3.540A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1092 removed outlier: 3.519A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1114 removed outlier: 3.720A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A1114 " --> pdb=" O TYR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.528A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1140' Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix removed outlier: 3.515A pdb=" N ALA A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1182 Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.763A pdb=" N ILE B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.858A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.660A pdb=" N LYS B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.791A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.671A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.658A pdb=" N ASN B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY B 251 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE B 252 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.619A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.197A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 11.736A pdb=" N THR A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LYS A 203 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 305 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER A 217 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS A 307 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.835A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.380A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A 797 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE A 864 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 799 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A 866 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.807A pdb=" N CYS A 469 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE A 463 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 658 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG A 572 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.863A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.166A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1482 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: 1.87 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1783 1.31 - 1.44: 3165 1.44 - 1.56: 6351 1.56 - 1.69: 7 1.69 - 1.81: 83 Bond restraints: 11389 Sorted by residual: bond pdb=" C31 PIE A1203 " pdb=" O31 PIE A1203 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.590 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C21 PIE A1203 " pdb=" O21 PIE A1203 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C2 PIE A1203 " pdb=" O21 PIE A1203 " ideal model delta sigma weight residual 1.433 1.395 0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C28 PIE A1203 " pdb=" C29 PIE A1203 " ideal model delta sigma weight residual 1.496 1.532 -0.036 2.00e-02 2.50e+03 3.31e+00 ... (remaining 11384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 15338 3.11 - 6.22: 84 6.22 - 9.33: 3 9.33 - 12.44: 1 12.44 - 15.56: 1 Bond angle restraints: 15427 Sorted by residual: angle pdb=" O11 PIE A1203 " pdb=" P PIE A1203 " pdb=" O14 PIE A1203 " ideal model delta sigma weight residual 94.58 110.14 -15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O12 PIE A1203 " pdb=" P PIE A1203 " pdb=" O13 PIE A1203 " ideal model delta sigma weight residual 119.80 108.88 10.92 3.00e+00 1.11e-01 1.33e+01 angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.34 5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" C ASN A 472 " pdb=" CA ASN A 472 " pdb=" CB ASN A 472 " ideal model delta sigma weight residual 110.42 116.17 -5.75 1.99e+00 2.53e-01 8.34e+00 angle pdb=" C32 PIE A1203 " pdb=" C31 PIE A1203 " pdb=" O31 PIE A1203 " ideal model delta sigma weight residual 111.37 119.86 -8.49 3.00e+00 1.11e-01 8.00e+00 ... (remaining 15422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 6397 23.71 - 47.42: 376 47.42 - 71.12: 51 71.12 - 94.83: 10 94.83 - 118.54: 10 Dihedral angle restraints: 6844 sinusoidal: 2852 harmonic: 3992 Sorted by residual: dihedral pdb=" CA THR A 398 " pdb=" C THR A 398 " pdb=" N MET A 399 " pdb=" CA MET A 399 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" O3' PIE A1203 " pdb=" C3' PIE A1203 " pdb=" C4' PIE A1203 " pdb=" O4' PIE A1203 " ideal model delta sinusoidal sigma weight residual 59.37 -59.17 118.54 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C5' PIE A1203 " pdb=" C3' PIE A1203 " pdb=" C4' PIE A1203 " pdb=" O3' PIE A1203 " ideal model delta sinusoidal sigma weight residual 179.61 -62.21 -118.18 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 6841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 1731 1.004 - 2.008: 0 2.008 - 3.012: 0 3.012 - 4.016: 0 4.016 - 5.020: 1 Chirality restraints: 1732 Sorted by residual: chirality pdb=" C2' PIE A1203 " pdb=" C1' PIE A1203 " pdb=" C3' PIE A1203 " pdb=" O2' PIE A1203 " both_signs ideal model delta sigma weight residual False -2.51 2.51 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C2 PIE A1203 " pdb=" C1 PIE A1203 " pdb=" C3 PIE A1203 " pdb=" O21 PIE A1203 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1729 not shown) Planarity restraints: 1941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO A 793 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 170 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 109 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.032 5.00e-02 4.00e+02 ... (remaining 1938 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 8435 3.11 - 3.70: 17408 3.70 - 4.30: 26707 4.30 - 4.90: 43718 Nonbonded interactions: 96368 Sorted by model distance: nonbonded pdb=" O3 NAG C 2 " pdb=" O2 BMA C 3 " model vdw 1.911 3.040 nonbonded pdb=" O GLN A 65 " pdb=" OH TYR A 92 " model vdw 1.945 3.040 nonbonded pdb=" O THR A 978 " pdb=" OH TYR A1069 " model vdw 1.974 3.040 nonbonded pdb=" OG1 THR A 576 " pdb=" O TYR A 588 " model vdw 2.017 3.040 nonbonded pdb=" OD1 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 2.019 3.040 ... (remaining 96363 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=0.00 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.004 0.223 11398 Z= 0.254 Angle : 0.589 15.556 15448 Z= 0.287 Chirality : 0.127 5.020 1732 Planarity : 0.004 0.063 1938 Dihedral : 15.610 118.538 4263 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.08 % Allowed : 0.00 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.23), residues: 1349 helix: 0.03 (0.21), residues: 592 sheet: -0.17 (0.38), residues: 190 loop : -0.86 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.025 0.001 TYR A 588 PHE 0.021 0.001 PHE A 113 TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11389) covalent geometry : angle 0.58419 / 0.29 (15427) SS BOND : bond 0.01170 / 0.44 ( 3) SS BOND : angle 0.94495 / 0.43 ( 6) hydrogen bonds : bond 0.23097 / 14.88 ( 524) hydrogen bonds : angle 8.22257 / 5.83 ( 1482) Misc. bond : bond 0.22308 / 11.74 ( 1) link_BETA1-4 : bond 0.01489 / 0.72 ( 2) link_BETA1-4 : angle 3.18805 / 2.07 ( 6) link_NAG-ASN : bond 0.00202 / 0.10 ( 3) link_NAG-ASN : angle 1.70429 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8334 (mttt) cc_final: 0.7938 (mttt) REVERT: A 195 GLN cc_start: 0.7846 (mt0) cc_final: 0.7436 (mt0) REVERT: A 1055 TYR cc_start: 0.6542 (m-80) cc_final: 0.5657 (m-80) REVERT: A 1091 ASP cc_start: 0.7608 (m-30) cc_final: 0.7257 (m-30) REVERT: B 186 PHE cc_start: 0.7305 (m-80) cc_final: 0.7060 (m-80) REVERT: B 244 ASP cc_start: 0.7393 (t70) cc_final: 0.6580 (t70) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.4864 time to fit residues: 91.0271 Evaluate side-chains 126 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN A 872 GLN A 917 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126336 restraints weight = 11695.627| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.32 r_work: 0.3607 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11398 Z= 0.148 Angle : 0.631 9.259 15448 Z= 0.320 Chirality : 0.044 0.310 1732 Planarity : 0.005 0.059 1938 Dihedral : 10.198 88.921 1645 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.84 % Allowed : 9.69 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.23), residues: 1349 helix: 0.65 (0.21), residues: 623 sheet: 0.04 (0.37), residues: 203 loop : -0.89 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.017 0.002 TYR A 658 PHE 0.021 0.001 PHE A 666 TRP 0.020 0.001 TRP A 669 HIS 0.003 0.001 HIS A 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (11389) covalent geometry : angle 0.62522 / 0.32 (15427) SS BOND : bond 0.00290 / 0.11 ( 3) SS BOND : angle 0.56649 / 0.29 ( 6) hydrogen bonds : bond 0.04834 / 3.16 ( 524) hydrogen bonds : angle 5.41508 / 3.83 ( 1482) Misc. bond : bond 0.00144 / 0.08 ( 1) link_BETA1-4 : bond 0.01603 / 0.76 ( 2) link_BETA1-4 : angle 2.64944 / 1.69 ( 6) link_NAG-ASN : bond 0.02548 / 1.34 ( 3) link_NAG-ASN : angle 3.01589 / 1.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 THR cc_start: 0.7468 (m) cc_final: 0.7163 (p) REVERT: A 190 LYS cc_start: 0.8225 (mttt) cc_final: 0.7786 (mttt) REVERT: A 195 GLN cc_start: 0.7950 (mt0) cc_final: 0.7473 (mt0) REVERT: A 1055 TYR cc_start: 0.6924 (m-10) cc_final: 0.6172 (m-10) REVERT: A 1168 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6480 (pp-130) REVERT: B 146 ASP cc_start: 0.6678 (t70) cc_final: 0.6339 (t0) REVERT: B 225 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8273 (pp20) REVERT: B 246 ASP cc_start: 0.6883 (t0) cc_final: 0.6658 (t0) REVERT: B 307 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7435 (mtp85) outliers start: 22 outliers final: 7 residues processed: 160 average time/residue: 0.4712 time to fit residues: 82.3878 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 1168 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 103 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 852 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128633 restraints weight = 11808.342| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.29 r_work: 0.3625 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11398 Z= 0.122 Angle : 0.562 9.541 15448 Z= 0.283 Chirality : 0.043 0.297 1732 Planarity : 0.004 0.060 1938 Dihedral : 8.548 65.732 1645 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.09 % Allowed : 10.78 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.23), residues: 1349 helix: 0.99 (0.21), residues: 620 sheet: 0.08 (0.37), residues: 203 loop : -0.95 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 628 TYR 0.013 0.001 TYR A 588 PHE 0.019 0.001 PHE A 666 TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11389) covalent geometry : angle 0.55391 / 0.28 (15427) SS BOND : bond 0.00529 / 0.26 ( 3) SS BOND : angle 0.80256 / 0.46 ( 6) hydrogen bonds : bond 0.04041 / 2.63 ( 524) hydrogen bonds : angle 4.93907 / 3.50 ( 1482) Misc. bond : bond 0.00033 / 0.02 ( 1) link_BETA1-4 : bond 0.01117 / 0.54 ( 2) link_BETA1-4 : angle 2.28055 / 1.44 ( 6) link_NAG-ASN : bond 0.01187 / 0.62 ( 3) link_NAG-ASN : angle 3.45393 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.7558 (m) cc_final: 0.7265 (p) REVERT: A 190 LYS cc_start: 0.8258 (mttt) cc_final: 0.7833 (mttt) REVERT: A 195 GLN cc_start: 0.7970 (mt0) cc_final: 0.7480 (mt0) REVERT: A 330 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (ptm160) REVERT: A 334 ASP cc_start: 0.7607 (m-30) cc_final: 0.7186 (m-30) REVERT: A 337 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6563 (mmm) REVERT: A 399 MET cc_start: 0.7735 (mmm) cc_final: 0.7476 (mmm) REVERT: A 859 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6562 (tt0) REVERT: A 1055 TYR cc_start: 0.6856 (m-10) cc_final: 0.6275 (m-10) REVERT: A 1168 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6700 (pp-130) REVERT: B 146 ASP cc_start: 0.6625 (t70) cc_final: 0.6315 (t0) REVERT: B 225 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8285 (pp20) REVERT: B 246 ASP cc_start: 0.6837 (t0) cc_final: 0.6578 (t0) outliers start: 37 outliers final: 18 residues processed: 169 average time/residue: 0.5447 time to fit residues: 100.0799 Evaluate side-chains 142 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.0270 chunk 122 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.183303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128377 restraints weight = 11872.990| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.31 r_work: 0.3626 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11398 Z= 0.121 Angle : 0.554 9.605 15448 Z= 0.280 Chirality : 0.043 0.271 1732 Planarity : 0.004 0.060 1938 Dihedral : 8.289 60.540 1645 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.51 % Allowed : 12.03 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.23), residues: 1349 helix: 1.12 (0.21), residues: 624 sheet: 0.34 (0.38), residues: 191 loop : -0.99 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1141 TYR 0.014 0.001 TYR A 658 PHE 0.017 0.001 PHE A 666 TRP 0.017 0.001 TRP A 669 HIS 0.002 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11389) covalent geometry : angle 0.54884 / 0.28 (15427) SS BOND : bond 0.00225 / 0.09 ( 3) SS BOND : angle 0.82848 / 0.48 ( 6) hydrogen bonds : bond 0.03752 / 2.44 ( 524) hydrogen bonds : angle 4.73184 / 3.35 ( 1482) Misc. bond : bond 0.00034 / 0.02 ( 1) link_BETA1-4 : bond 0.01413 / 0.68 ( 2) link_BETA1-4 : angle 2.26191 / 1.43 ( 6) link_NAG-ASN : bond 0.00262 / 0.12 ( 3) link_NAG-ASN : angle 2.52138 / 1.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.7583 (m) cc_final: 0.7346 (p) REVERT: A 190 LYS cc_start: 0.8264 (mttt) cc_final: 0.7846 (mttt) REVERT: A 195 GLN cc_start: 0.7976 (mt0) cc_final: 0.7492 (mt0) REVERT: A 330 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7502 (ptm160) REVERT: A 334 ASP cc_start: 0.7568 (m-30) cc_final: 0.7190 (m-30) REVERT: A 337 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: A 365 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6439 (mt0) REVERT: A 859 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6610 (tt0) REVERT: A 1055 TYR cc_start: 0.6796 (m-10) cc_final: 0.5974 (m-10) REVERT: A 1168 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6754 (pp-130) REVERT: B 146 ASP cc_start: 0.6633 (t70) cc_final: 0.6315 (t0) REVERT: B 246 ASP cc_start: 0.6796 (t0) cc_final: 0.6535 (t0) REVERT: B 307 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7606 (mmt-90) outliers start: 42 outliers final: 22 residues processed: 157 average time/residue: 0.5181 time to fit residues: 88.9418 Evaluate side-chains 147 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126613 restraints weight = 11707.563| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.29 r_work: 0.3603 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11398 Z= 0.144 Angle : 0.577 9.528 15448 Z= 0.291 Chirality : 0.044 0.317 1732 Planarity : 0.004 0.066 1938 Dihedral : 8.014 59.311 1645 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.34 % Allowed : 12.87 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.23), residues: 1349 helix: 1.13 (0.21), residues: 624 sheet: 0.25 (0.37), residues: 193 loop : -1.04 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1141 TYR 0.014 0.001 TYR A 658 PHE 0.017 0.001 PHE A 666 TRP 0.017 0.001 TRP A 669 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (11389) covalent geometry : angle 0.56792 / 0.29 (15427) SS BOND : bond 0.00184 / 0.07 ( 3) SS BOND : angle 0.75768 / 0.43 ( 6) hydrogen bonds : bond 0.03846 / 2.50 ( 524) hydrogen bonds : angle 4.72550 / 3.34 ( 1482) Misc. bond : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : bond 0.01363 / 0.65 ( 2) link_BETA1-4 : angle 2.26639 / 1.42 ( 6) link_NAG-ASN : bond 0.02030 / 1.07 ( 3) link_NAG-ASN : angle 3.74117 / 2.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.7622 (m) cc_final: 0.7369 (p) REVERT: A 190 LYS cc_start: 0.8283 (mttt) cc_final: 0.7856 (mttt) REVERT: A 195 GLN cc_start: 0.7990 (mt0) cc_final: 0.7502 (mt0) REVERT: A 334 ASP cc_start: 0.7606 (m-30) cc_final: 0.7218 (m-30) REVERT: A 337 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6597 (mmm) REVERT: A 399 MET cc_start: 0.7751 (mmm) cc_final: 0.7485 (mmm) REVERT: A 808 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 859 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6614 (tt0) REVERT: A 1055 TYR cc_start: 0.6757 (m-10) cc_final: 0.5593 (m-10) REVERT: A 1168 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6743 (pp-130) REVERT: B 146 ASP cc_start: 0.6645 (t70) cc_final: 0.6322 (t0) REVERT: B 225 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8310 (pp20) REVERT: B 246 ASP cc_start: 0.6797 (t0) cc_final: 0.6516 (t0) outliers start: 40 outliers final: 23 residues processed: 161 average time/residue: 0.5395 time to fit residues: 95.0631 Evaluate side-chains 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN A 796 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124971 restraints weight = 11837.334| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.30 r_work: 0.3581 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11398 Z= 0.161 Angle : 0.581 9.596 15448 Z= 0.295 Chirality : 0.043 0.283 1732 Planarity : 0.004 0.065 1938 Dihedral : 7.625 57.799 1645 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.84 % Allowed : 14.62 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.23), residues: 1349 helix: 1.09 (0.21), residues: 624 sheet: 0.24 (0.37), residues: 195 loop : -1.06 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.015 0.002 TYR A 658 PHE 0.014 0.001 PHE A 666 TRP 0.016 0.001 TRP A 669 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11389) covalent geometry : angle 0.57329 / 0.29 (15427) SS BOND : bond 0.00205 / 0.09 ( 3) SS BOND : angle 0.74449 / 0.42 ( 6) hydrogen bonds : bond 0.03930 / 2.55 ( 524) hydrogen bonds : angle 4.73316 / 3.34 ( 1482) Misc. bond : bond 0.00074 / 0.04 ( 1) link_BETA1-4 : bond 0.01198 / 0.57 ( 2) link_BETA1-4 : angle 2.32627 / 1.45 ( 6) link_NAG-ASN : bond 0.01164 / 0.61 ( 3) link_NAG-ASN : angle 3.50045 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7557 (mtpt) REVERT: A 143 THR cc_start: 0.7622 (m) cc_final: 0.7350 (p) REVERT: A 190 LYS cc_start: 0.8255 (mttt) cc_final: 0.7830 (mttt) REVERT: A 195 GLN cc_start: 0.8000 (mt0) cc_final: 0.7501 (mt0) REVERT: A 252 ARG cc_start: 0.6389 (mpp-170) cc_final: 0.6028 (mmm160) REVERT: A 337 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6591 (mmm) REVERT: A 447 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8549 (mm-40) REVERT: A 808 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 859 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6509 (tt0) REVERT: A 1055 TYR cc_start: 0.6742 (m-10) cc_final: 0.5518 (m-10) REVERT: A 1091 ASP cc_start: 0.7614 (m-30) cc_final: 0.7062 (m-30) REVERT: A 1168 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6737 (pp-130) REVERT: B 146 ASP cc_start: 0.6641 (t70) cc_final: 0.6307 (t0) REVERT: B 225 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8269 (pp20) REVERT: B 246 ASP cc_start: 0.6839 (t0) cc_final: 0.6546 (t0) outliers start: 34 outliers final: 20 residues processed: 149 average time/residue: 0.5497 time to fit residues: 89.6055 Evaluate side-chains 147 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 41 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126614 restraints weight = 11805.735| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.30 r_work: 0.3652 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11398 Z= 0.127 Angle : 0.552 9.513 15448 Z= 0.282 Chirality : 0.042 0.270 1732 Planarity : 0.004 0.065 1938 Dihedral : 7.245 57.406 1645 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 14.95 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.23), residues: 1349 helix: 1.18 (0.21), residues: 626 sheet: 0.35 (0.38), residues: 193 loop : -1.06 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.015 0.001 TYR A 658 PHE 0.013 0.001 PHE A 666 TRP 0.015 0.001 TRP A 669 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11389) covalent geometry : angle 0.54420 / 0.28 (15427) SS BOND : bond 0.00174 / 0.07 ( 3) SS BOND : angle 0.68152 / 0.39 ( 6) hydrogen bonds : bond 0.03668 / 2.38 ( 524) hydrogen bonds : angle 4.64161 / 3.28 ( 1482) Misc. bond : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : bond 0.01145 / 0.55 ( 2) link_BETA1-4 : angle 2.20825 / 1.38 ( 6) link_NAG-ASN : bond 0.01092 / 0.57 ( 3) link_NAG-ASN : angle 3.45329 / 1.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7568 (mtpt) REVERT: A 143 THR cc_start: 0.7615 (m) cc_final: 0.7377 (p) REVERT: A 190 LYS cc_start: 0.8291 (mttt) cc_final: 0.7891 (mttt) REVERT: A 195 GLN cc_start: 0.8025 (mt0) cc_final: 0.7547 (mt0) REVERT: A 252 ARG cc_start: 0.6449 (mpp-170) cc_final: 0.5845 (mmm160) REVERT: A 254 ASP cc_start: 0.7543 (m-30) cc_final: 0.7227 (p0) REVERT: A 334 ASP cc_start: 0.7697 (m-30) cc_final: 0.7294 (m-30) REVERT: A 337 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6670 (mmm) REVERT: A 808 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: A 1055 TYR cc_start: 0.6735 (m-10) cc_final: 0.5506 (m-10) REVERT: A 1091 ASP cc_start: 0.7656 (m-30) cc_final: 0.7128 (m-30) REVERT: A 1168 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6830 (pp-130) REVERT: B 146 ASP cc_start: 0.6591 (t70) cc_final: 0.6282 (t0) REVERT: B 225 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8281 (pp20) REVERT: B 246 ASP cc_start: 0.6913 (t0) cc_final: 0.6621 (t0) outliers start: 33 outliers final: 21 residues processed: 149 average time/residue: 0.5432 time to fit residues: 88.5303 Evaluate side-chains 142 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 7.9990 chunk 122 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125011 restraints weight = 11785.863| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.30 r_work: 0.3593 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11398 Z= 0.161 Angle : 0.585 9.498 15448 Z= 0.299 Chirality : 0.043 0.262 1732 Planarity : 0.004 0.068 1938 Dihedral : 7.052 56.531 1645 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.67 % Allowed : 15.62 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.23), residues: 1349 helix: 1.10 (0.21), residues: 626 sheet: 0.37 (0.38), residues: 193 loop : -1.10 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.015 0.002 TYR A 658 PHE 0.013 0.001 PHE A 961 TRP 0.015 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11389) covalent geometry : angle 0.57813 / 0.30 (15427) SS BOND : bond 0.00189 / 0.08 ( 3) SS BOND : angle 0.74880 / 0.43 ( 6) hydrogen bonds : bond 0.03877 / 2.52 ( 524) hydrogen bonds : angle 4.67225 / 3.30 ( 1482) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.01186 / 0.57 ( 2) link_BETA1-4 : angle 2.29499 / 1.43 ( 6) link_NAG-ASN : bond 0.01005 / 0.53 ( 3) link_NAG-ASN : angle 3.40182 / 1.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7512 (mtpt) REVERT: A 143 THR cc_start: 0.7591 (m) cc_final: 0.7340 (p) REVERT: A 190 LYS cc_start: 0.8234 (mttt) cc_final: 0.7808 (mttt) REVERT: A 195 GLN cc_start: 0.8020 (mt0) cc_final: 0.7525 (mt0) REVERT: A 252 ARG cc_start: 0.6384 (mpp-170) cc_final: 0.5773 (mmm160) REVERT: A 254 ASP cc_start: 0.7527 (m-30) cc_final: 0.7202 (p0) REVERT: A 334 ASP cc_start: 0.7654 (m-30) cc_final: 0.7238 (m-30) REVERT: A 337 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6584 (mmm) REVERT: A 808 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 1010 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7962 (mtpt) REVERT: A 1055 TYR cc_start: 0.6629 (m-10) cc_final: 0.5510 (m-10) REVERT: A 1168 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6693 (pp-130) REVERT: B 146 ASP cc_start: 0.6647 (t70) cc_final: 0.6325 (t0) REVERT: B 225 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8285 (pp20) REVERT: B 238 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7881 (pttp) REVERT: B 246 ASP cc_start: 0.6903 (t0) cc_final: 0.6604 (t0) outliers start: 32 outliers final: 19 residues processed: 144 average time/residue: 0.5580 time to fit residues: 87.9508 Evaluate side-chains 144 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.181210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125795 restraints weight = 11728.906| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.30 r_work: 0.3608 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11398 Z= 0.145 Angle : 0.575 9.492 15448 Z= 0.295 Chirality : 0.043 0.262 1732 Planarity : 0.004 0.066 1938 Dihedral : 6.915 59.967 1645 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.23), residues: 1349 helix: 1.17 (0.21), residues: 620 sheet: 0.39 (0.38), residues: 193 loop : -1.07 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.016 0.001 TYR A 658 PHE 0.011 0.001 PHE A 666 TRP 0.015 0.001 TRP A 669 HIS 0.002 0.001 HIS A 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (11389) covalent geometry : angle 0.56807 / 0.29 (15427) SS BOND : bond 0.00290 / 0.14 ( 3) SS BOND : angle 0.71849 / 0.41 ( 6) hydrogen bonds : bond 0.03766 / 2.45 ( 524) hydrogen bonds : angle 4.64430 / 3.28 ( 1482) Misc. bond : bond 0.00068 / 0.04 ( 1) link_BETA1-4 : bond 0.01123 / 0.54 ( 2) link_BETA1-4 : angle 2.19965 / 1.37 ( 6) link_NAG-ASN : bond 0.01001 / 0.53 ( 3) link_NAG-ASN : angle 3.34828 / 1.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7500 (mtpt) REVERT: A 143 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7346 (p) REVERT: A 190 LYS cc_start: 0.8232 (mttt) cc_final: 0.7797 (mttt) REVERT: A 195 GLN cc_start: 0.7996 (mt0) cc_final: 0.7492 (mt0) REVERT: A 252 ARG cc_start: 0.6343 (mpp-170) cc_final: 0.5731 (mmm160) REVERT: A 254 ASP cc_start: 0.7532 (m-30) cc_final: 0.7206 (p0) REVERT: A 334 ASP cc_start: 0.7616 (m-30) cc_final: 0.7197 (m-30) REVERT: A 337 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6459 (mmm) REVERT: A 808 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 1055 TYR cc_start: 0.6569 (m-10) cc_final: 0.5458 (m-10) REVERT: A 1091 ASP cc_start: 0.7550 (m-30) cc_final: 0.7001 (m-30) REVERT: A 1168 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6656 (pp-130) REVERT: B 146 ASP cc_start: 0.6637 (t70) cc_final: 0.6325 (t0) REVERT: B 225 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8293 (pp20) REVERT: B 246 ASP cc_start: 0.6873 (t0) cc_final: 0.6566 (t0) outliers start: 31 outliers final: 19 residues processed: 145 average time/residue: 0.5010 time to fit residues: 79.3444 Evaluate side-chains 143 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 447 GLN A 564 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125800 restraints weight = 11752.825| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.30 r_work: 0.3610 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11398 Z= 0.145 Angle : 0.576 9.490 15448 Z= 0.296 Chirality : 0.043 0.262 1732 Planarity : 0.004 0.065 1938 Dihedral : 6.768 56.053 1645 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.17 % Allowed : 16.71 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.23), residues: 1349 helix: 1.14 (0.21), residues: 623 sheet: 0.43 (0.38), residues: 193 loop : -1.02 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.016 0.001 TYR A 658 PHE 0.011 0.001 PHE A1072 TRP 0.015 0.001 TRP A 669 HIS 0.002 0.001 HIS A 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (11389) covalent geometry : angle 0.56929 / 0.29 (15427) SS BOND : bond 0.00260 / 0.12 ( 3) SS BOND : angle 0.70428 / 0.41 ( 6) hydrogen bonds : bond 0.03761 / 2.44 ( 524) hydrogen bonds : angle 4.63165 / 3.28 ( 1482) Misc. bond : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : bond 0.01082 / 0.52 ( 2) link_BETA1-4 : angle 2.16149 / 1.35 ( 6) link_NAG-ASN : bond 0.00975 / 0.51 ( 3) link_NAG-ASN : angle 3.30284 / 1.87 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7497 (mtpt) REVERT: A 143 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7368 (p) REVERT: A 190 LYS cc_start: 0.8232 (mttt) cc_final: 0.7798 (mttt) REVERT: A 195 GLN cc_start: 0.8004 (mt0) cc_final: 0.7503 (mt0) REVERT: A 252 ARG cc_start: 0.6314 (mpp-170) cc_final: 0.5717 (mmm160) REVERT: A 254 ASP cc_start: 0.7565 (m-30) cc_final: 0.7245 (p0) REVERT: A 334 ASP cc_start: 0.7623 (m-30) cc_final: 0.7210 (m-30) REVERT: A 337 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6493 (mmm) REVERT: A 808 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: A 1055 TYR cc_start: 0.6571 (m-10) cc_final: 0.5463 (m-10) REVERT: A 1091 ASP cc_start: 0.7548 (m-30) cc_final: 0.6999 (m-30) REVERT: A 1168 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6647 (pp-130) REVERT: B 146 ASP cc_start: 0.6646 (t70) cc_final: 0.6334 (t0) REVERT: B 225 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8293 (pp20) REVERT: B 246 ASP cc_start: 0.6887 (t0) cc_final: 0.6615 (t0) outliers start: 26 outliers final: 19 residues processed: 140 average time/residue: 0.5431 time to fit residues: 83.2582 Evaluate side-chains 143 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 SER Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123730 restraints weight = 11884.906| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.29 r_work: 0.3581 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11398 Z= 0.181 Angle : 0.610 9.477 15448 Z= 0.312 Chirality : 0.044 0.260 1732 Planarity : 0.004 0.064 1938 Dihedral : 6.842 57.251 1645 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.17 % Allowed : 16.96 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1349 helix: 1.02 (0.21), residues: 619 sheet: 0.40 (0.37), residues: 193 loop : -1.08 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.016 0.002 TYR A 658 PHE 0.014 0.002 PHE A 961 TRP 0.017 0.002 TRP B 207 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (11389) covalent geometry : angle 0.60328 / 0.31 (15427) SS BOND : bond 0.00161 / 0.06 ( 3) SS BOND : angle 0.66453 / 0.38 ( 6) hydrogen bonds : bond 0.04056 / 2.63 ( 524) hydrogen bonds : angle 4.74249 / 3.35 ( 1482) Misc. bond : bond 0.00097 / 0.05 ( 1) link_BETA1-4 : bond 0.01039 / 0.50 ( 2) link_BETA1-4 : angle 2.19490 / 1.35 ( 6) link_NAG-ASN : bond 0.00958 / 0.50 ( 3) link_NAG-ASN : angle 3.22813 / 1.82 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5222.89 seconds wall clock time: 89 minutes 45.42 seconds (5385.42 seconds total)