Starting phenix.real_space_refine on Mon Jul 6 04:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ddt_27341/07_2026/8ddt_27341.cif" } resolution = 3.1 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= 0.094 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 232 5.16 5 Na 1 4.78 5 C 20916 2.51 5 N 5376 2.21 5 O 5688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s 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: 32229 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE A 913 " occ=0.47 residue: pdb=" N AMET A1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET A1011 " occ=0.57 residue: pdb=" N APHE B 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE B 913 " occ=0.47 residue: pdb=" N AMET B1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET B1011 " occ=0.57 residue: pdb=" N APHE C 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE C 913 " occ=0.47 residue: pdb=" N AMET C1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET C1011 " occ=0.57 residue: pdb=" N APHE D 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE D 913 " occ=0.47 residue: pdb=" N AMET D1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET D1011 " occ=0.57 Time building chain proxies: 6.46, per 1000 atoms: 0.20 Number of scatterers: 32229 At special positions: 0 Unit cell: (147.96, 147.96, 159.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 16 15.00 Na 1 11.00 O 5688 8.00 N 5376 7.00 C 20916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 973.4 milliseconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 8 sheets defined 66.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.555A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.806A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.120A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.859A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.547A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.634A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.667A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.887A pdb=" N GLN A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 574 through 577 removed outlier: 3.520A pdb=" N THR A 577 " --> pdb=" O CYS A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 577' Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.856A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.074A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.895A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.710A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.642A pdb=" N THR A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.560A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.546A pdb=" N GLY A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.610A pdb=" N VAL A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 895 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.520A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.695A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.134A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1033 removed outlier: 3.592A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1042 Processing helix chain 'A' and resid 1043 through 1054 removed outlier: 4.310A pdb=" N PHE A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.729A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1105 removed outlier: 3.649A pdb=" N ALA A1096 " --> pdb=" O PRO A1092 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.604A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.543A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.565A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.597A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.116A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.256A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.828A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.865A pdb=" N LYS B 401 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.614A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.678A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.761A pdb=" N GLN B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.524A pdb=" N LYS B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 574 through 577 removed outlier: 3.524A pdb=" N THR B 577 " --> pdb=" O CYS B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.862A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.078A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.896A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 690 through 717 Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.671A pdb=" N THR B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.560A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.521A pdb=" N GLY B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 removed outlier: 3.506A pdb=" N LEU B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 789 removed outlier: 3.741A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 Processing helix chain 'B' and resid 870 through 895 removed outlier: 3.604A pdb=" N VAL B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 895 " --> pdb=" O TYR B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 932 through 939 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.650A pdb=" N LEU B 948 " --> pdb=" O ASN B 944 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.362A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.874A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1033 removed outlier: 3.547A pdb=" N VAL B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.869A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 3.695A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1105 removed outlier: 4.412A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.711A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1163 removed outlier: 3.544A pdb=" N MET B1158 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B1159 " --> pdb=" O HIS B1155 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B1160 " --> pdb=" O MET B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.562A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.726A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.124A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.265A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.714A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.833A pdb=" N LYS C 401 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 402 " --> pdb=" O ILE C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 402' Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.629A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.708A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.765A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 574 through 577 removed outlier: 3.519A pdb=" N THR C 577 " --> pdb=" O CYS C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 574 through 577' Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.883A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.077A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.908A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 removed outlier: 3.737A pdb=" N GLN C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 727 removed outlier: 3.646A pdb=" N THR C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 727 " --> pdb=" O LYS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.565A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.527A pdb=" N GLY C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 784 through 789 removed outlier: 3.711A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 870 through 895 removed outlier: 3.612A pdb=" N VAL C 893 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 895 " --> pdb=" O TYR C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.639A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 962 " --> pdb=" O MET C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.125A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1033 removed outlier: 4.125A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1044 Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 3.684A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.333A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.735A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1163 removed outlier: 3.548A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C1160 " --> pdb=" O MET C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.595A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.866A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 279 through 283 removed outlier: 4.121A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.822A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.544A pdb=" N LYS D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 402 " --> pdb=" O ILE D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 398 through 402' Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.620A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.702A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.881A pdb=" N GLN D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.862A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 4.073A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.880A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 689 through 717 removed outlier: 3.773A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.676A pdb=" N THR D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR D 727 " --> pdb=" O LYS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.559A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 765 removed outlier: 3.521A pdb=" N GLY D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 789 removed outlier: 3.748A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 Processing helix chain 'D' and resid 870 through 895 removed outlier: 3.609A pdb=" N VAL D 893 " --> pdb=" O PHE D 889 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 895 " --> pdb=" O TYR D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.621A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.348A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.885A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 4.086A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1054 removed outlier: 3.832A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET D1049 " --> pdb=" O ASN D1045 " (cutoff:3.500A) Proline residue: D1050 - end of helix removed outlier: 3.742A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1105 removed outlier: 4.391A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1117 Processing helix chain 'D' and resid 1118 through 1142 removed outlier: 4.753A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.546A pdb=" N MET D1158 " --> pdb=" O SER D1154 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D1159 " --> pdb=" O HIS D1155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D1160 " --> pdb=" O MET D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 275 removed outlier: 4.187A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 143 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 275 removed outlier: 4.221A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 143 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 364 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 275 removed outlier: 4.169A pdb=" N VAL C 270 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 143 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N PHE C 294 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET C 156 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU C 296 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 158 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP C 298 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 160 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 270 through 275 removed outlier: 4.090A pdb=" N VAL D 270 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 143 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA D 218 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE D 251 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) 1738 hydrogen bonds defined for protein. 5151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 16 1.05 - 1.26: 5064 1.26 - 1.47: 13024 1.47 - 1.69: 14436 1.69 - 1.90: 428 Bond restraints: 32968 Sorted by residual: bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.834 0.700 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 B1402 " pdb=" C74 9Z9 B1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 D1402 " pdb=" C74 9Z9 D1402 " ideal model delta sigma weight residual 1.534 0.836 0.698 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C03 9Z9 C1402 " pdb=" C74 9Z9 C1402 " ideal model delta sigma weight residual 1.534 0.837 0.697 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 D1402 " pdb=" C03 9Z9 D1402 " ideal model delta sigma weight residual 1.544 1.013 0.531 2.00e-02 2.50e+03 7.04e+02 ... (remaining 32963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.27: 44555 10.27 - 20.54: 13 20.54 - 30.81: 8 30.81 - 41.08: 4 41.08 - 51.35: 4 Bond angle restraints: 44584 Sorted by residual: angle pdb=" C74 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" C76 9Z9 B1402 " ideal model delta sigma weight residual 114.05 165.40 -51.35 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C74 9Z9 D1402 " pdb=" C73 9Z9 D1402 " pdb=" C76 9Z9 D1402 " ideal model delta sigma weight residual 114.05 165.40 -51.35 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C74 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" C76 9Z9 C1402 " ideal model delta sigma weight residual 114.05 165.31 -51.26 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 164.65 -50.60 3.00e+00 1.11e-01 2.84e+02 angle pdb=" C76 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" O72 9Z9 A1402 " ideal model delta sigma weight residual 109.02 70.65 38.37 3.00e+00 1.11e-01 1.64e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 18846 25.30 - 50.61: 709 50.61 - 75.91: 87 75.91 - 101.22: 8 101.22 - 126.52: 5 Dihedral angle restraints: 19655 sinusoidal: 8163 harmonic: 11492 Sorted by residual: dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA THR B 356 " pdb=" C THR B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 19652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 4968 0.392 - 0.784: 4 0.784 - 1.176: 4 1.176 - 1.568: 0 1.568 - 1.960: 4 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C03 9Z9 A1402 " pdb=" C02 9Z9 A1402 " pdb=" C04 9Z9 A1402 " pdb=" C74 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.60e+01 chirality pdb=" C03 9Z9 D1402 " pdb=" C02 9Z9 D1402 " pdb=" C04 9Z9 D1402 " pdb=" C74 9Z9 D1402 " both_signs ideal model delta sigma weight residual False 2.78 0.85 1.94 2.00e-01 2.50e+01 9.37e+01 chirality pdb=" C03 9Z9 B1402 " pdb=" C02 9Z9 B1402 " pdb=" C04 9Z9 B1402 " pdb=" C74 9Z9 B1402 " both_signs ideal model delta sigma weight residual False 2.78 0.85 1.94 2.00e-01 2.50e+01 9.36e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 785 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 784 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO B 785 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 785 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 785 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO C 785 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " -0.032 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6816 2.78 - 3.31: 30424 3.31 - 3.84: 50790 3.84 - 4.37: 58040 4.37 - 4.90: 104114 Nonbonded interactions: 250184 Sorted by model distance: nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR D 553 " pdb=" OD2 ASP D 559 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 157 " pdb=" O LEU A 265 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU C 565 " pdb=" OG1 THR C 577 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU B 565 " pdb=" OG1 THR B 577 " model vdw 2.308 3.040 ... (remaining 250179 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 129 through 1403) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.47 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: 3.840 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.015 0.700 32968 Z= 0.746 Angle : 1.011 51.351 44584 Z= 0.398 Chirality : 0.075 1.960 4980 Planarity : 0.004 0.064 5516 Dihedral : 12.812 126.524 12223 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.79 % Allowed : 6.11 % Favored : 91.09 % 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: 0.17 (0.14), residues: 3824 helix: 0.97 (0.11), residues: 2384 sheet: 0.20 (0.37), residues: 216 loop : -1.57 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1206 TYR 0.015 0.001 TYR D1048 PHE 0.007 0.001 PHE D1140 TRP 0.009 0.001 TRP D 763 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.01492 / 0.75 (32968) covalent geometry : angle 1.01082 / 0.40 (44584) hydrogen bonds : bond 0.14573 / 9.64 ( 1738) hydrogen bonds : angle 4.95245 / 3.48 ( 5151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 632 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 266 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7230 (mm) REVERT: A 287 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 417 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7139 (tt) REVERT: A 422 LYS cc_start: 0.7654 (ttmt) cc_final: 0.6923 (tptp) REVERT: A 925 MET cc_start: 0.7466 (ttm) cc_final: 0.7018 (mtt) REVERT: A 1012 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6148 (t80) REVERT: A 1156 MET cc_start: 0.7597 (mtt) cc_final: 0.7343 (mtm) REVERT: B 269 ASP cc_start: 0.6566 (m-30) cc_final: 0.6163 (t0) REVERT: B 291 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8191 (m90) REVERT: B 414 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4210 (t80) REVERT: B 687 MET cc_start: 0.6459 (mmt) cc_final: 0.6031 (mmt) REVERT: B 925 MET cc_start: 0.7474 (ttm) cc_final: 0.7038 (mtt) REVERT: B 1156 MET cc_start: 0.7618 (mtt) cc_final: 0.7356 (mtm) REVERT: C 266 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7510 (mm) REVERT: C 925 MET cc_start: 0.7541 (ttm) cc_final: 0.7100 (mtt) REVERT: C 1012 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6234 (t80) REVERT: C 1156 MET cc_start: 0.7618 (mtt) cc_final: 0.7372 (mtm) REVERT: D 145 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: D 266 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7181 (mm) REVERT: D 925 MET cc_start: 0.7510 (ttm) cc_final: 0.7074 (mtt) REVERT: D 1156 MET cc_start: 0.7575 (mtt) cc_final: 0.7316 (mtm) outliers start: 96 outliers final: 40 residues processed: 703 average time/residue: 0.1907 time to fit residues: 213.8741 Evaluate side-chains 533 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 482 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 632 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 411 GLN A 633 HIS A 697 HIS A 716 GLN A 719 GLN A 739 GLN A 746 HIS A 794 ASN A 978 ASN A 993 ASN A1115 ASN A1116 ASN A1199 GLN A1238 ASN A1242 HIS B 171 HIS B 411 GLN B 633 HIS B 697 HIS B 719 GLN B 739 GLN B 746 HIS B 794 ASN B1115 ASN B1116 ASN B1199 GLN C 171 HIS C 411 GLN C 633 HIS C 697 HIS C 716 GLN C 739 GLN C 746 HIS C 978 ASN C1115 ASN C1116 ASN C1199 GLN C1238 ASN C1242 HIS D 171 HIS D 291 HIS D 411 GLN D 632 ASN D 633 HIS D 697 HIS D 716 GLN D 739 GLN D 746 HIS D1115 ASN D1116 ASN D1199 GLN D1238 ASN D1242 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122512 restraints weight = 38896.842| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.13 r_work: 0.3121 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32968 Z= 0.191 Angle : 0.573 6.778 44584 Z= 0.289 Chirality : 0.040 0.151 4980 Planarity : 0.004 0.058 5516 Dihedral : 9.221 125.197 4590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.61 % Allowed : 10.63 % Favored : 85.76 % 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: 0.43 (0.14), residues: 3824 helix: 1.20 (0.11), residues: 2424 sheet: 0.11 (0.36), residues: 212 loop : -1.57 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1211 TYR 0.013 0.001 TYR A 479 PHE 0.011 0.001 PHE D1013 TRP 0.017 0.001 TRP D 763 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (32968) covalent geometry : angle 0.57323 / 0.29 (44584) hydrogen bonds : bond 0.05951 / 3.90 ( 1738) hydrogen bonds : angle 3.76418 / 2.66 ( 5151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 493 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 256 TRP cc_start: 0.7987 (t-100) cc_final: 0.7360 (t60) REVERT: A 277 MET cc_start: 0.8453 (ttm) cc_final: 0.7936 (tpp) REVERT: A 287 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7607 (mp) REVERT: A 417 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 422 LYS cc_start: 0.7782 (ttmt) cc_final: 0.6717 (tptp) REVERT: A 580 ARG cc_start: 0.7836 (tmm-80) cc_final: 0.7317 (tmm-80) REVERT: A 925 MET cc_start: 0.8196 (ttm) cc_final: 0.7645 (mtt) REVERT: A 1028 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8164 (ttt90) REVERT: A 1162 HIS cc_start: 0.6757 (t-90) cc_final: 0.6542 (t-90) REVERT: A 1232 MET cc_start: 0.7762 (tpp) cc_final: 0.7533 (mtt) REVERT: A 1233 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7154 (tpp80) REVERT: B 141 PHE cc_start: 0.7986 (p90) cc_final: 0.7731 (p90) REVERT: B 172 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 269 ASP cc_start: 0.7074 (m-30) cc_final: 0.6242 (t0) REVERT: B 277 MET cc_start: 0.8429 (ttm) cc_final: 0.7911 (tpp) REVERT: B 291 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8619 (m90) REVERT: B 414 PHE cc_start: 0.5034 (OUTLIER) cc_final: 0.4275 (t80) REVERT: B 421 MET cc_start: 0.7414 (mmp) cc_final: 0.6912 (mmt) REVERT: B 422 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7093 (tppt) REVERT: B 769 MET cc_start: 0.7464 (ptm) cc_final: 0.7221 (ptm) REVERT: B 925 MET cc_start: 0.8170 (ttm) cc_final: 0.7626 (mtt) REVERT: B 1057 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: B 1162 HIS cc_start: 0.6739 (t-90) cc_final: 0.6528 (t-90) REVERT: B 1232 MET cc_start: 0.7784 (tpp) cc_final: 0.7522 (mtt) REVERT: C 172 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8408 (tp) REVERT: C 256 TRP cc_start: 0.7982 (t-100) cc_final: 0.7333 (t60) REVERT: C 277 MET cc_start: 0.8466 (ttm) cc_final: 0.7696 (tpp) REVERT: C 347 SER cc_start: 0.8291 (t) cc_final: 0.7967 (p) REVERT: C 354 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7741 (mtt90) REVERT: C 422 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7449 (mtpp) REVERT: C 925 MET cc_start: 0.8171 (ttm) cc_final: 0.7621 (mtt) REVERT: C 1162 HIS cc_start: 0.6770 (t-90) cc_final: 0.6557 (t-90) REVERT: D 172 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (tp) REVERT: D 256 TRP cc_start: 0.8232 (t60) cc_final: 0.8007 (t-100) REVERT: D 269 ASP cc_start: 0.6927 (m-30) cc_final: 0.6004 (t70) REVERT: D 277 MET cc_start: 0.8424 (ttm) cc_final: 0.7647 (tpp) REVERT: D 287 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7660 (mp) REVERT: D 925 MET cc_start: 0.8199 (ttm) cc_final: 0.7651 (mtt) REVERT: D 1162 HIS cc_start: 0.6829 (t-90) cc_final: 0.6614 (t-90) outliers start: 124 outliers final: 75 residues processed: 572 average time/residue: 0.1792 time to fit residues: 164.8626 Evaluate side-chains 536 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 450 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1115 ASN B 171 HIS B 978 ASN B1115 ASN B1229 ASN C 171 HIS C1115 ASN D 171 HIS D 291 HIS D 293 HIS D1115 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125018 restraints weight = 38782.879| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.06 r_work: 0.3177 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32968 Z= 0.127 Angle : 0.506 7.094 44584 Z= 0.255 Chirality : 0.038 0.149 4980 Planarity : 0.004 0.051 5516 Dihedral : 8.552 113.154 4558 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.93 % Allowed : 11.82 % Favored : 84.25 % 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: 0.85 (0.14), residues: 3824 helix: 1.57 (0.11), residues: 2420 sheet: 0.15 (0.36), residues: 212 loop : -1.49 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 354 TYR 0.012 0.001 TYR C 981 PHE 0.010 0.001 PHE B1047 TRP 0.013 0.001 TRP D 763 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (32968) covalent geometry : angle 0.50640 / 0.25 (44584) hydrogen bonds : bond 0.04992 / 3.28 ( 1738) hydrogen bonds : angle 3.53423 / 2.49 ( 5151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 485 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7886 (pm20) cc_final: 0.7592 (pm20) REVERT: A 178 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8522 (mm-40) REVERT: A 245 ARG cc_start: 0.7478 (mtt90) cc_final: 0.7222 (mtt-85) REVERT: A 277 MET cc_start: 0.8320 (ttm) cc_final: 0.7918 (tpp) REVERT: A 287 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 347 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 417 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6357 (tt) REVERT: A 422 LYS cc_start: 0.7830 (ttmt) cc_final: 0.6614 (tppt) REVERT: B 141 PHE cc_start: 0.8094 (p90) cc_final: 0.7806 (p90) REVERT: B 172 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8365 (tp) REVERT: B 269 ASP cc_start: 0.7197 (m-30) cc_final: 0.6358 (t0) REVERT: B 277 MET cc_start: 0.8311 (ttm) cc_final: 0.7925 (tpp) REVERT: B 287 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7643 (mp) REVERT: B 291 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8652 (m90) REVERT: B 414 PHE cc_start: 0.4827 (OUTLIER) cc_final: 0.4263 (t80) REVERT: B 421 MET cc_start: 0.7235 (mmp) cc_final: 0.6902 (mmt) REVERT: B 422 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7110 (tppt) REVERT: B 546 LYS cc_start: 0.6514 (mtmt) cc_final: 0.6033 (mttm) REVERT: B 769 MET cc_start: 0.7808 (ptm) cc_final: 0.7589 (ptm) REVERT: B 1067 CYS cc_start: 0.6246 (p) cc_final: 0.5976 (m) REVERT: C 145 GLU cc_start: 0.7841 (pm20) cc_final: 0.7555 (pm20) REVERT: C 172 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8371 (tp) REVERT: C 193 GLN cc_start: 0.6297 (pm20) cc_final: 0.6058 (pm20) REVERT: C 256 TRP cc_start: 0.7973 (t-100) cc_final: 0.7355 (t60) REVERT: C 277 MET cc_start: 0.8363 (ttm) cc_final: 0.7909 (tpp) REVERT: C 347 SER cc_start: 0.8340 (t) cc_final: 0.8065 (p) REVERT: C 768 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8170 (ttm110) REVERT: C 769 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7637 (ptm) REVERT: D 172 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8281 (tp) REVERT: D 277 MET cc_start: 0.8353 (ttm) cc_final: 0.7902 (tpp) REVERT: D 287 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7746 (mp) REVERT: D 421 MET cc_start: 0.7477 (mmp) cc_final: 0.7090 (mmt) REVERT: D 1162 HIS cc_start: 0.6655 (t-90) cc_final: 0.6452 (t-90) outliers start: 135 outliers final: 86 residues processed: 566 average time/residue: 0.1846 time to fit residues: 169.6114 Evaluate side-chains 559 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 462 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 187 optimal weight: 0.0370 chunk 285 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 240 HIS A 734 ASN A1115 ASN B 171 HIS B 978 ASN B1115 ASN C 171 HIS C 794 ASN C1115 ASN C1229 ASN D 171 HIS D 291 HIS D 719 GLN D 734 ASN D 794 ASN D1115 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117946 restraints weight = 39121.517| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.14 r_work: 0.3040 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 32968 Z= 0.367 Angle : 0.717 8.231 44584 Z= 0.364 Chirality : 0.047 0.164 4980 Planarity : 0.005 0.065 5516 Dihedral : 8.608 110.976 4554 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.57 % Allowed : 13.28 % Favored : 82.15 % 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 (0.13), residues: 3824 helix: 0.99 (0.10), residues: 2420 sheet: -0.21 (0.35), residues: 220 loop : -1.72 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 354 TYR 0.019 0.002 TYR A 885 PHE 0.017 0.002 PHE B 503 TRP 0.022 0.002 TRP B 763 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.37 (32968) covalent geometry : angle 0.71701 / 0.36 (44584) hydrogen bonds : bond 0.07717 / 5.06 ( 1738) hydrogen bonds : angle 3.98244 / 2.82 ( 5151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 475 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7947 (pm20) cc_final: 0.7662 (pm20) REVERT: A 172 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 269 ASP cc_start: 0.7039 (m-30) cc_final: 0.6030 (t0) REVERT: A 277 MET cc_start: 0.8458 (ttm) cc_final: 0.8090 (tpp) REVERT: A 287 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 347 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 417 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6290 (tt) REVERT: A 422 LYS cc_start: 0.7936 (ttmt) cc_final: 0.6906 (tptt) REVERT: A 462 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 475 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: A 1115 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8635 (t0) REVERT: A 1232 MET cc_start: 0.7941 (tpp) cc_final: 0.7667 (mtt) REVERT: B 141 PHE cc_start: 0.8292 (p90) cc_final: 0.7918 (p90) REVERT: B 193 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 269 ASP cc_start: 0.7037 (m-30) cc_final: 0.6251 (t0) REVERT: B 277 MET cc_start: 0.8413 (ttm) cc_final: 0.8032 (tpp) REVERT: B 287 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 291 HIS cc_start: 0.9242 (OUTLIER) cc_final: 0.8929 (m90) REVERT: B 414 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.4073 (t80) REVERT: B 421 MET cc_start: 0.7381 (mmp) cc_final: 0.7013 (mmt) REVERT: B 462 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 482 GLN cc_start: 0.7422 (mp10) cc_final: 0.7161 (tm-30) REVERT: B 580 ARG cc_start: 0.7996 (tmm-80) cc_final: 0.7552 (ttt-90) REVERT: B 769 MET cc_start: 0.7934 (ptm) cc_final: 0.7583 (ptm) REVERT: B 1001 MET cc_start: 0.8838 (mtt) cc_final: 0.8591 (mtm) REVERT: B 1057 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: B 1232 MET cc_start: 0.8012 (tpp) cc_final: 0.7724 (mtt) REVERT: C 145 GLU cc_start: 0.7915 (pm20) cc_final: 0.7634 (pm20) REVERT: C 172 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8602 (tp) REVERT: C 269 ASP cc_start: 0.7069 (m-30) cc_final: 0.6056 (t0) REVERT: C 277 MET cc_start: 0.8427 (ttm) cc_final: 0.8011 (tpp) REVERT: C 347 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 421 MET cc_start: 0.7117 (mmp) cc_final: 0.6837 (mmm) REVERT: C 462 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8178 (mp) REVERT: C 979 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8901 (tt) REVERT: D 145 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: D 172 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8580 (tp) REVERT: D 256 TRP cc_start: 0.8454 (t60) cc_final: 0.7642 (t60) REVERT: D 269 ASP cc_start: 0.7012 (m-30) cc_final: 0.6062 (t0) REVERT: D 277 MET cc_start: 0.8398 (ttm) cc_final: 0.7972 (tpp) REVERT: D 287 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7902 (mp) REVERT: D 421 MET cc_start: 0.7492 (mmp) cc_final: 0.7089 (mmt) REVERT: D 462 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (mp) REVERT: D 475 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: D 580 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7533 (ttt-90) REVERT: D 1162 HIS cc_start: 0.6596 (t-90) cc_final: 0.6386 (t-90) outliers start: 157 outliers final: 94 residues processed: 588 average time/residue: 0.1885 time to fit residues: 181.8475 Evaluate side-chains 574 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 459 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 115 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 278 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 186 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 338 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 375 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 291 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 240 HIS B 437 HIS B 734 ASN B 978 ASN B1115 ASN C 171 HIS C 437 HIS C 734 ASN C 890 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 171 HIS D 437 HIS D 890 ASN D 978 ASN D1115 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123522 restraints weight = 38521.741| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.08 r_work: 0.3152 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32968 Z= 0.118 Angle : 0.521 7.216 44584 Z= 0.264 Chirality : 0.038 0.138 4980 Planarity : 0.004 0.052 5516 Dihedral : 8.062 99.101 4544 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.78 % Allowed : 14.41 % Favored : 81.80 % 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: 0.86 (0.14), residues: 3824 helix: 1.63 (0.11), residues: 2416 sheet: -0.02 (0.36), residues: 212 loop : -1.54 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.016 0.001 TYR A 981 PHE 0.010 0.001 PHE A1140 TRP 0.012 0.001 TRP D 763 HIS 0.017 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (32968) covalent geometry : angle 0.52139 / 0.26 (44584) hydrogen bonds : bond 0.04909 / 3.23 ( 1738) hydrogen bonds : angle 3.56400 / 2.52 ( 5151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 481 time to evaluate : 1.276 Fit side-chains REVERT: A 145 GLU cc_start: 0.7968 (pm20) cc_final: 0.7575 (pm20) REVERT: A 178 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8560 (mm-40) REVERT: A 245 ARG cc_start: 0.7527 (mtt90) cc_final: 0.7241 (mtt-85) REVERT: A 277 MET cc_start: 0.8306 (ttm) cc_final: 0.7997 (tpp) REVERT: A 287 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 347 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8002 (p) REVERT: A 417 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6222 (tt) REVERT: A 422 LYS cc_start: 0.7761 (ttmt) cc_final: 0.6718 (tptp) REVERT: A 1138 MET cc_start: 0.8419 (mmm) cc_final: 0.8179 (mmt) REVERT: B 135 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7131 (mm) REVERT: B 141 PHE cc_start: 0.8070 (p90) cc_final: 0.7811 (p90) REVERT: B 193 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7665 (mm-40) REVERT: B 269 ASP cc_start: 0.7245 (m-30) cc_final: 0.6401 (t0) REVERT: B 277 MET cc_start: 0.8324 (ttm) cc_final: 0.8008 (tpp) REVERT: B 291 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8685 (m90) REVERT: B 414 PHE cc_start: 0.4573 (OUTLIER) cc_final: 0.3598 (t80) REVERT: B 421 MET cc_start: 0.7405 (mmp) cc_final: 0.7128 (mmt) REVERT: C 145 GLU cc_start: 0.7866 (pm20) cc_final: 0.7595 (pm20) REVERT: C 172 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8433 (tp) REVERT: C 277 MET cc_start: 0.8362 (ttm) cc_final: 0.8005 (tpp) REVERT: C 347 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8054 (p) REVERT: C 422 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7408 (mtpp) REVERT: C 1047 PHE cc_start: 0.7885 (t80) cc_final: 0.7681 (t80) REVERT: D 145 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: D 172 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8387 (tp) REVERT: D 277 MET cc_start: 0.8364 (ttm) cc_final: 0.7996 (tpp) REVERT: D 287 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7819 (mp) REVERT: D 421 MET cc_start: 0.7453 (mmp) cc_final: 0.7244 (mmt) REVERT: D 475 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: D 775 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7846 (mm) outliers start: 130 outliers final: 86 residues processed: 569 average time/residue: 0.1896 time to fit residues: 176.4517 Evaluate side-chains 559 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 460 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 240 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 437 HIS B1115 ASN C 171 HIS C 437 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 171 HIS D 291 HIS D 437 HIS D1115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120807 restraints weight = 38724.703| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.11 r_work: 0.3087 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 32968 Z= 0.231 Angle : 0.598 7.258 44584 Z= 0.301 Chirality : 0.042 0.134 4980 Planarity : 0.004 0.051 5516 Dihedral : 8.039 95.056 4544 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.05 % Allowed : 14.44 % Favored : 81.51 % 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: 0.65 (0.14), residues: 3824 helix: 1.45 (0.11), residues: 2416 sheet: -0.04 (0.36), residues: 212 loop : -1.63 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.012 0.001 TYR A 885 PHE 0.014 0.001 PHE B1140 TRP 0.017 0.002 TRP B 763 HIS 0.008 0.001 HIS B1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.23 (32968) covalent geometry : angle 0.59801 / 0.30 (44584) hydrogen bonds : bond 0.06164 / 4.04 ( 1738) hydrogen bonds : angle 3.67703 / 2.60 ( 5151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 465 time to evaluate : 1.217 Fit side-chains REVERT: A 145 GLU cc_start: 0.7977 (pm20) cc_final: 0.7648 (pm20) REVERT: A 172 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8507 (tp) REVERT: A 178 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8606 (mm-40) REVERT: A 277 MET cc_start: 0.8392 (ttm) cc_final: 0.8128 (tpp) REVERT: A 287 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7830 (mp) REVERT: A 347 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 417 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6221 (tt) REVERT: A 422 LYS cc_start: 0.7839 (ttmt) cc_final: 0.6797 (tptp) REVERT: B 135 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6852 (mm) REVERT: B 141 PHE cc_start: 0.8160 (p90) cc_final: 0.7871 (p90) REVERT: B 269 ASP cc_start: 0.7160 (m-30) cc_final: 0.6362 (t0) REVERT: B 277 MET cc_start: 0.8370 (ttm) cc_final: 0.8103 (tpp) REVERT: B 287 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 291 HIS cc_start: 0.9184 (OUTLIER) cc_final: 0.8817 (m90) REVERT: B 414 PHE cc_start: 0.4516 (OUTLIER) cc_final: 0.3614 (t80) REVERT: B 421 MET cc_start: 0.7554 (mmp) cc_final: 0.7227 (mmt) REVERT: B 1057 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: C 145 GLU cc_start: 0.7911 (pm20) cc_final: 0.7617 (pm20) REVERT: C 172 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (tp) REVERT: C 277 MET cc_start: 0.8399 (ttm) cc_final: 0.8091 (tpp) REVERT: C 347 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8019 (p) REVERT: C 422 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7379 (mtpp) REVERT: D 145 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: D 245 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7528 (mmt90) REVERT: D 277 MET cc_start: 0.8367 (ttm) cc_final: 0.8056 (tpp) REVERT: D 287 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7858 (mp) REVERT: D 475 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: D 580 ARG cc_start: 0.7853 (tmm-80) cc_final: 0.7628 (tpt-90) REVERT: D 775 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7842 (mm) outliers start: 139 outliers final: 102 residues processed: 563 average time/residue: 0.1881 time to fit residues: 173.3441 Evaluate side-chains 574 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 456 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1199 GLN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 157 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 270 optimal weight: 0.9980 chunk 286 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 329 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B1115 ASN C 171 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 171 HIS D1115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124428 restraints weight = 38784.753| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.08 r_work: 0.3158 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32968 Z= 0.117 Angle : 0.519 7.184 44584 Z= 0.261 Chirality : 0.038 0.135 4980 Planarity : 0.004 0.051 5516 Dihedral : 7.704 87.758 4542 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.76 % Allowed : 14.91 % Favored : 81.34 % 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: 1.04 (0.14), residues: 3824 helix: 1.78 (0.11), residues: 2416 sheet: 0.05 (0.36), residues: 212 loop : -1.51 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.015 0.001 TYR A 981 PHE 0.011 0.001 PHE D1114 TRP 0.012 0.001 TRP B 763 HIS 0.011 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (32968) covalent geometry : angle 0.51924 / 0.26 (44584) hydrogen bonds : bond 0.04777 / 3.14 ( 1738) hydrogen bonds : angle 3.48645 / 2.46 ( 5151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 471 time to evaluate : 1.071 Fit side-chains REVERT: A 145 GLU cc_start: 0.7901 (pm20) cc_final: 0.7529 (pm20) REVERT: A 172 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 287 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 347 SER cc_start: 0.8238 (t) cc_final: 0.7944 (p) REVERT: A 417 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6106 (tt) REVERT: A 422 LYS cc_start: 0.7838 (ttmt) cc_final: 0.6788 (tptp) REVERT: A 768 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8103 (ttm110) REVERT: A 1138 MET cc_start: 0.8410 (mmm) cc_final: 0.8165 (mmt) REVERT: B 135 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7131 (mm) REVERT: B 141 PHE cc_start: 0.8003 (p90) cc_final: 0.7749 (p90) REVERT: B 269 ASP cc_start: 0.7263 (m-30) cc_final: 0.6433 (t0) REVERT: B 277 MET cc_start: 0.8336 (ttm) cc_final: 0.8086 (tpp) REVERT: B 287 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 291 HIS cc_start: 0.9118 (OUTLIER) cc_final: 0.8685 (m90) REVERT: B 414 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.3554 (t80) REVERT: B 421 MET cc_start: 0.7517 (mmp) cc_final: 0.7249 (mmt) REVERT: B 422 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7067 (tppt) REVERT: C 145 GLU cc_start: 0.7883 (pm20) cc_final: 0.7547 (pm20) REVERT: C 172 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 193 GLN cc_start: 0.6703 (mm-40) cc_final: 0.5931 (pm20) REVERT: C 277 MET cc_start: 0.8373 (ttm) cc_final: 0.8090 (tpp) REVERT: C 347 SER cc_start: 0.8291 (t) cc_final: 0.8027 (p) REVERT: C 422 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7434 (mtpp) REVERT: C 1138 MET cc_start: 0.8416 (mmm) cc_final: 0.8189 (mmt) REVERT: D 145 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 170 LEU cc_start: 0.8482 (tt) cc_final: 0.8105 (mt) REVERT: D 172 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8356 (tp) REVERT: D 245 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7425 (mmt90) REVERT: D 277 MET cc_start: 0.8378 (ttm) cc_final: 0.8174 (tpp) REVERT: D 287 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 421 MET cc_start: 0.7663 (mmp) cc_final: 0.7085 (mmt) REVERT: D 475 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: D 546 LYS cc_start: 0.6953 (ptpt) cc_final: 0.6485 (pttp) REVERT: D 768 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8172 (ttm110) REVERT: D 775 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (mm) outliers start: 129 outliers final: 90 residues processed: 562 average time/residue: 0.1774 time to fit residues: 163.2208 Evaluate side-chains 560 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 456 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1199 GLN Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 719 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 437 HIS B1115 ASN C 171 HIS C 437 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 171 HIS D 437 HIS D 890 ASN D1115 ASN D1229 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117640 restraints weight = 39059.345| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.15 r_work: 0.3037 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 32968 Z= 0.362 Angle : 0.712 8.300 44584 Z= 0.361 Chirality : 0.047 0.160 4980 Planarity : 0.005 0.059 5516 Dihedral : 8.206 84.628 4542 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.08 % Allowed : 14.70 % Favored : 81.22 % 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 (0.13), residues: 3824 helix: 1.13 (0.10), residues: 2416 sheet: -0.15 (0.35), residues: 220 loop : -1.76 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 354 TYR 0.019 0.002 TYR B 885 PHE 0.018 0.002 PHE B 503 TRP 0.019 0.002 TRP D 763 HIS 0.008 0.001 HIS C1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.36 (32968) covalent geometry : angle 0.71247 / 0.36 (44584) hydrogen bonds : bond 0.07570 / 4.97 ( 1738) hydrogen bonds : angle 3.91675 / 2.77 ( 5151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 476 time to evaluate : 1.220 Fit side-chains REVERT: A 145 GLU cc_start: 0.7931 (pm20) cc_final: 0.7594 (pm20) REVERT: A 172 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 176 GLU cc_start: 0.6861 (mp0) cc_final: 0.6629 (mp0) REVERT: A 256 TRP cc_start: 0.8326 (t60) cc_final: 0.7980 (t-100) REVERT: A 269 ASP cc_start: 0.7050 (m-30) cc_final: 0.6169 (t0) REVERT: A 287 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 417 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6371 (tt) REVERT: A 422 LYS cc_start: 0.7895 (ttmt) cc_final: 0.6925 (tptp) REVERT: A 462 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 724 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 135 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6840 (mm) REVERT: B 141 PHE cc_start: 0.8206 (p90) cc_final: 0.7859 (p90) REVERT: B 193 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 269 ASP cc_start: 0.7088 (m-30) cc_final: 0.6285 (t0) REVERT: B 277 MET cc_start: 0.8388 (ttm) cc_final: 0.8138 (tpp) REVERT: B 287 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 291 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.8837 (m90) REVERT: B 580 ARG cc_start: 0.7914 (tmm-80) cc_final: 0.7697 (tpt-90) REVERT: B 1001 MET cc_start: 0.8891 (mtt) cc_final: 0.8636 (mtm) REVERT: B 1057 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: C 145 GLU cc_start: 0.7861 (pm20) cc_final: 0.7547 (pm20) REVERT: C 277 MET cc_start: 0.8446 (ttm) cc_final: 0.8171 (tpp) REVERT: C 422 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7517 (mtpp) REVERT: C 724 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8814 (mp) REVERT: C 1001 MET cc_start: 0.8863 (mtt) cc_final: 0.8601 (mtm) REVERT: C 1057 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: C 1225 GLU cc_start: 0.8854 (tt0) cc_final: 0.8630 (tt0) REVERT: D 145 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: D 245 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7528 (mmt90) REVERT: D 277 MET cc_start: 0.8400 (ttm) cc_final: 0.8130 (tpp) REVERT: D 287 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7887 (mp) REVERT: D 421 MET cc_start: 0.7598 (mmp) cc_final: 0.6984 (mmt) REVERT: D 475 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: D 546 LYS cc_start: 0.6838 (ptpt) cc_final: 0.6494 (pttp) REVERT: D 580 ARG cc_start: 0.7908 (tmm-80) cc_final: 0.7693 (tpt-90) REVERT: D 768 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8157 (ttm110) REVERT: D 775 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7876 (mm) REVERT: D 1233 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7533 (tpp80) outliers start: 140 outliers final: 103 residues processed: 576 average time/residue: 0.1898 time to fit residues: 177.7910 Evaluate side-chains 583 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 464 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1199 GLN Chi-restraints excluded: chain B residue 1236 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1199 GLN Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 30 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 339 optimal weight: 0.9980 chunk 352 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 171 HIS B 437 HIS B1115 ASN C 171 HIS C 437 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 171 HIS D 437 HIS D 890 ASN D1115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122060 restraints weight = 38400.341| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.07 r_work: 0.3135 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32968 Z= 0.140 Angle : 0.560 8.059 44584 Z= 0.283 Chirality : 0.039 0.152 4980 Planarity : 0.004 0.052 5516 Dihedral : 7.723 85.484 4539 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.41 % Allowed : 15.81 % Favored : 80.79 % 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: 0.81 (0.14), residues: 3824 helix: 1.59 (0.11), residues: 2416 sheet: 0.02 (0.36), residues: 212 loop : -1.60 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 542 TYR 0.015 0.001 TYR A 981 PHE 0.019 0.001 PHE D1114 TRP 0.013 0.001 TRP B 763 HIS 0.018 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (32968) covalent geometry : angle 0.56041 / 0.28 (44584) hydrogen bonds : bond 0.05333 / 3.50 ( 1738) hydrogen bonds : angle 3.61417 / 2.55 ( 5151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 467 time to evaluate : 1.224 Fit side-chains REVERT: A 145 GLU cc_start: 0.7919 (pm20) cc_final: 0.7539 (pm20) REVERT: A 172 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 256 TRP cc_start: 0.8276 (t60) cc_final: 0.7500 (t60) REVERT: A 269 ASP cc_start: 0.7021 (m-30) cc_final: 0.6066 (t0) REVERT: A 287 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 417 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6098 (tt) REVERT: A 422 LYS cc_start: 0.7888 (ttmt) cc_final: 0.6916 (tptp) REVERT: A 768 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8111 (ttm110) REVERT: A 1233 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7402 (tpp80) REVERT: B 135 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7067 (mm) REVERT: B 141 PHE cc_start: 0.7992 (p90) cc_final: 0.7732 (p90) REVERT: B 193 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7792 (mm-40) REVERT: B 269 ASP cc_start: 0.7052 (m-30) cc_final: 0.6280 (t0) REVERT: B 277 MET cc_start: 0.8356 (ttm) cc_final: 0.8111 (tpp) REVERT: B 287 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7793 (mp) REVERT: B 291 HIS cc_start: 0.9159 (OUTLIER) cc_final: 0.8748 (m90) REVERT: B 421 MET cc_start: 0.7560 (mmp) cc_final: 0.6953 (mmt) REVERT: B 422 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7078 (tppt) REVERT: C 145 GLU cc_start: 0.7922 (pm20) cc_final: 0.7557 (pm20) REVERT: C 245 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7124 (mmt90) REVERT: C 277 MET cc_start: 0.8394 (ttm) cc_final: 0.8137 (tpp) REVERT: C 347 SER cc_start: 0.8266 (t) cc_final: 0.7950 (p) REVERT: C 422 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7471 (mtpp) REVERT: C 1225 GLU cc_start: 0.8725 (tt0) cc_final: 0.8492 (tt0) REVERT: D 145 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: D 170 LEU cc_start: 0.8457 (tt) cc_final: 0.8072 (mt) REVERT: D 245 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7571 (mmt90) REVERT: D 287 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 421 MET cc_start: 0.7552 (mmp) cc_final: 0.7074 (mmt) REVERT: D 475 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: D 546 LYS cc_start: 0.6860 (ptpt) cc_final: 0.6533 (pttp) REVERT: D 768 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8121 (ttm110) REVERT: D 775 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7737 (mm) outliers start: 117 outliers final: 89 residues processed: 549 average time/residue: 0.1881 time to fit residues: 168.8165 Evaluate side-chains 553 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 452 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1236 GLU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1199 GLN Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 179 optimal weight: 0.0770 chunk 203 optimal weight: 0.1980 chunk 177 optimal weight: 0.5980 chunk 270 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D1115 ASN ** 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 = 0.3898 r_free = 0.3898 target = 0.164783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122684 restraints weight = 38666.655| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 32968 Z= 0.180 Angle : 0.711 59.168 44584 Z= 0.403 Chirality : 0.040 0.394 4980 Planarity : 0.006 0.169 5516 Dihedral : 7.669 85.542 4536 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.97 % Allowed : 15.81 % Favored : 81.22 % Cbeta Deviations : 0.11 % 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: 0.85 (0.14), residues: 3824 helix: 1.63 (0.11), residues: 2416 sheet: 0.03 (0.36), residues: 212 loop : -1.59 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.016 0.001 TYR A 981 PHE 0.015 0.001 PHE D1114 TRP 0.013 0.001 TRP B 763 HIS 0.257 0.005 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (32968) covalent geometry : angle 0.71071 / 0.40 (44584) hydrogen bonds : bond 0.05267 / 3.45 ( 1738) hydrogen bonds : angle 3.61607 / 2.55 ( 5151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 453 time to evaluate : 1.216 Fit side-chains REVERT: A 145 GLU cc_start: 0.7921 (pm20) cc_final: 0.7548 (pm20) REVERT: A 172 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 256 TRP cc_start: 0.8275 (t60) cc_final: 0.7541 (t60) REVERT: A 269 ASP cc_start: 0.7017 (m-30) cc_final: 0.6064 (t0) REVERT: A 287 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 417 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6142 (tt) REVERT: A 422 LYS cc_start: 0.7906 (ttmt) cc_final: 0.6863 (tptp) REVERT: A 768 ARG cc_start: 0.8331 (ttm110) cc_final: 0.8092 (ttm110) REVERT: A 1233 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7407 (tpp80) REVERT: B 135 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7061 (mm) REVERT: B 141 PHE cc_start: 0.7996 (p90) cc_final: 0.7751 (p90) REVERT: B 193 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7793 (mm-40) REVERT: B 269 ASP cc_start: 0.7040 (m-30) cc_final: 0.6287 (t0) REVERT: B 277 MET cc_start: 0.8345 (ttm) cc_final: 0.8106 (tpp) REVERT: B 287 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 291 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8745 (m90) REVERT: B 421 MET cc_start: 0.7507 (mmp) cc_final: 0.6975 (mmt) REVERT: B 422 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7085 (tppt) REVERT: C 145 GLU cc_start: 0.7919 (pm20) cc_final: 0.7564 (pm20) REVERT: C 172 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 245 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7117 (mmt90) REVERT: C 277 MET cc_start: 0.8357 (ttm) cc_final: 0.8102 (tpp) REVERT: C 347 SER cc_start: 0.8294 (t) cc_final: 0.8027 (p) REVERT: C 422 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7468 (mtpp) REVERT: C 1225 GLU cc_start: 0.8702 (tt0) cc_final: 0.8471 (tt0) REVERT: D 145 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: D 170 LEU cc_start: 0.8468 (tt) cc_final: 0.8087 (mt) REVERT: D 245 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7567 (mmt90) REVERT: D 287 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7803 (mp) REVERT: D 421 MET cc_start: 0.7546 (mmp) cc_final: 0.7072 (mmt) REVERT: D 475 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: D 546 LYS cc_start: 0.6940 (ptpt) cc_final: 0.6622 (pttp) REVERT: D 768 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8109 (ttm110) REVERT: D 775 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7743 (mm) outliers start: 102 outliers final: 88 residues processed: 519 average time/residue: 0.2021 time to fit residues: 170.4438 Evaluate side-chains 554 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 453 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 958 MET Chi-restraints excluded: chain C residue 979 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain C residue 1202 GLU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 958 MET Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1199 GLN Chi-restraints excluded: chain D residue 1202 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 212 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 320 optimal weight: 10.0000 chunk 178 optimal weight: 0.0270 chunk 223 optimal weight: 10.0000 chunk 163 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D1115 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.164065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121820 restraints weight = 38598.006| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 32968 Z= 0.180 Angle : 0.711 59.168 44584 Z= 0.403 Chirality : 0.040 0.394 4980 Planarity : 0.006 0.169 5516 Dihedral : 7.669 85.542 4536 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.94 % Allowed : 15.78 % Favored : 81.28 % Cbeta Deviations : 0.11 % 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: 0.85 (0.14), residues: 3824 helix: 1.63 (0.11), residues: 2416 sheet: 0.03 (0.36), residues: 212 loop : -1.59 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.016 0.001 TYR A 981 PHE 0.015 0.001 PHE D1114 TRP 0.013 0.001 TRP B 763 HIS 0.257 0.005 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (32968) covalent geometry : angle 0.71072 / 0.40 (44584) hydrogen bonds : bond 0.05267 / 3.45 ( 1738) hydrogen bonds : angle 3.61607 / 2.55 ( 5151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9276.56 seconds wall clock time: 158 minutes 52.94 seconds (9532.94 seconds total)