Starting phenix.real_space_refine on Mon Jul 6 04:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ddv_27343/07_2026/8ddv_27343.cif" } resolution = 3.2 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= 0.083 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 2 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): 0.02s 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: 32230 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 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: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 171 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PH': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 171 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PH': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 6.23, per 1000 atoms: 0.19 Number of scatterers: 32230 At special positions: 0 Unit cell: (147.96, 147.96, 160.92, 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 2 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 182 helices and 9 sheets defined 65.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 198 through 216 removed outlier: 4.103A pdb=" N GLN A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.603A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.980A 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 308 through 322 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.217A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.160A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.737A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.586A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.698A 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 removed outlier: 3.505A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.986A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.041A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.993A 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 690 through 717 Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.637A pdb=" N THR A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.990A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.588A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.659A 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 790 removed outlier: 3.667A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.886A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.711A 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: 4.152A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1033 removed outlier: 3.867A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1053 removed outlier: 3.696A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix Processing helix chain 'A' and resid 1089 through 1105 removed outlier: 4.411A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1143 removed outlier: 4.602A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A1143 " --> pdb=" O THR A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.511A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1239 removed outlier: 3.641A pdb=" N GLU A1236 " --> pdb=" O MET A1232 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.555A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 216 removed outlier: 4.077A pdb=" N GLN B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 209 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.622A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.622A 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 261 through 265 Processing helix chain 'B' and resid 308 through 322 removed outlier: 3.522A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.609A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.302A pdb=" N TYR B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.792A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.585A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 removed outlier: 3.669A 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 528 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.949A 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 578 through 587 removed outlier: 3.950A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.040A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.979A 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: 3.611A pdb=" N THR B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.573A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.663A pdb=" N GLY B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.674A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 3.588A 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 Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 933 through 939 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.918A pdb=" N LEU B 948 " --> pdb=" O ASN B 944 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.440A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.840A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1033 removed outlier: 3.937A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.705A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 4.002A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1105 removed outlier: 4.443A 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 1143 removed outlier: 4.691A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1161 removed outlier: 3.716A pdb=" N MET B1158 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B1159 " --> pdb=" O HIS B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.509A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.548A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 216 removed outlier: 3.642A pdb=" N GLN C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.565A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.809A 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 308 through 322 removed outlier: 3.510A pdb=" N LEU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.971A pdb=" N LEU C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.293A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.797A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.681A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.567A 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 removed outlier: 3.509A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.898A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.029A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.981A 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 688 through 717 removed outlier: 3.977A pdb=" N SER C 692 " --> pdb=" O VAL C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 727 removed outlier: 3.637A pdb=" N THR C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.581A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.657A 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 790 removed outlier: 3.699A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 868 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.909A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.683A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.710A 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: 4.157A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1033 removed outlier: 3.851A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1046 removed outlier: 3.768A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 3.965A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1105 Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.773A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C1140 " --> pdb=" O LEU C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1161 removed outlier: 3.505A pdb=" N THR C1157 " --> pdb=" O PHE C1153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (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 removed outlier: 3.600A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 216 removed outlier: 3.657A pdb=" N GLN D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 207 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.597A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.993A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 322 removed outlier: 3.510A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 355 removed outlier: 4.120A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.890A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.851A pdb=" N GLN D 400 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 397 through 401' Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 439 through 450 removed outlier: 3.721A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 450 " --> pdb=" O THR D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 476 removed outlier: 3.588A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.645A 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: 3.960A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.965A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.978A 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 688 through 717 removed outlier: 3.953A pdb=" N SER D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.652A pdb=" N THR D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.577A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 765 removed outlier: 3.669A 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 790 removed outlier: 3.672A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.914A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.677A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.229A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.833A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1033 removed outlier: 3.920A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1053 removed outlier: 3.737A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET D1049 " --> pdb=" O ASN D1045 " (cutoff:3.500A) Proline residue: D1050 - end of helix Processing helix chain 'D' and resid 1089 through 1105 removed outlier: 4.427A 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: 4.600A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.358A 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 1161 removed outlier: 3.541A pdb=" N THR D1157 " --> pdb=" O PHE D1153 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D1158 " --> pdb=" O SER D1154 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D1159 " --> pdb=" O HIS D1155 " (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 272 through 275 removed outlier: 6.334A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.512A pdb=" N UNK F 10 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 267 through 275 removed outlier: 7.165A pdb=" N PHE B 141 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 143 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA B 140 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (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 219 through 222 removed outlier: 5.830A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 250 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE C 295 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 252 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA C 297 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 254 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 157 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 189 removed outlier: 6.498A pdb=" N VAL C 361 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE C 430 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 363 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.532A pdb=" N UNK H 10 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 271 through 275 removed outlier: 6.318A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL D 362 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA D 336 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS D 364 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE D 338 " --> pdb=" O CYS D 364 " (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: 6.53 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 16 1.04 - 1.26: 5064 1.26 - 1.47: 12905 1.47 - 1.68: 14555 1.68 - 1.90: 428 Bond restraints: 32968 Sorted by residual: bond pdb=" C03 9Z9 C1401 " pdb=" C74 9Z9 C1401 " ideal model delta sigma weight residual 1.534 0.832 0.702 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 A1404 " pdb=" C74 9Z9 A1404 " ideal model delta sigma weight residual 1.534 0.832 0.702 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 C1403 " pdb=" C74 9Z9 C1403 " ideal model delta sigma weight residual 1.534 0.833 0.701 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.835 0.699 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 C1401 " pdb=" C03 9Z9 C1401 " ideal model delta sigma weight residual 1.544 1.013 0.531 2.00e-02 2.50e+03 7.06e+02 ... (remaining 32963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.22: 44556 10.22 - 20.45: 12 20.45 - 30.67: 8 30.67 - 40.89: 4 40.89 - 51.11: 4 Bond angle restraints: 44584 Sorted by residual: angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 165.16 -51.11 3.00e+00 1.11e-01 2.90e+02 angle pdb=" C74 9Z9 C1401 " pdb=" C73 9Z9 C1401 " pdb=" C76 9Z9 C1401 " ideal model delta sigma weight residual 114.05 164.94 -50.89 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C74 9Z9 C1403 " pdb=" C73 9Z9 C1403 " pdb=" C76 9Z9 C1403 " ideal model delta sigma weight residual 114.05 164.93 -50.88 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C74 9Z9 A1404 " pdb=" C73 9Z9 A1404 " pdb=" C76 9Z9 A1404 " ideal model delta sigma weight residual 114.05 164.89 -50.84 3.00e+00 1.11e-01 2.87e+02 angle pdb=" C76 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" O72 9Z9 A1402 " ideal model delta sigma weight residual 109.02 70.87 38.15 3.00e+00 1.11e-01 1.62e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 18649 22.14 - 44.28: 855 44.28 - 66.42: 136 66.42 - 88.56: 12 88.56 - 110.69: 4 Dihedral angle restraints: 19656 sinusoidal: 8164 harmonic: 11492 Sorted by residual: dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+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 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+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 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 19653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.394: 4968 0.394 - 0.789: 4 0.789 - 1.183: 4 1.183 - 1.578: 0 1.578 - 1.972: 4 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C03 9Z9 C1401 " pdb=" C02 9Z9 C1401 " pdb=" C04 9Z9 C1401 " pdb=" C74 9Z9 C1401 " both_signs ideal model delta sigma weight residual False 2.78 0.81 1.97 2.00e-01 2.50e+01 9.72e+01 chirality pdb=" C03 9Z9 A1404 " pdb=" C02 9Z9 A1404 " pdb=" C04 9Z9 A1404 " pdb=" C74 9Z9 A1404 " both_signs ideal model delta sigma weight residual False 2.78 0.81 1.97 2.00e-01 2.50e+01 9.72e+01 chirality pdb=" C03 9Z9 C1403 " pdb=" C02 9Z9 C1403 " pdb=" C04 9Z9 C1403 " pdb=" C74 9Z9 C1403 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.57e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+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 delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 785 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 785 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.030 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5477 2.77 - 3.30: 30829 3.30 - 3.83: 50834 3.83 - 4.37: 57286 4.37 - 4.90: 102339 Nonbonded interactions: 246765 Sorted by model distance: nonbonded pdb=" OH TYR B 157 " pdb=" O LEU B 265 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.236 3.040 nonbonded pdb=" OG SER D 367 " pdb=" OG SER D 371 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP B 947 " pdb=" OH TYR B 981 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN A 344 " pdb=" OG SER A 347 " model vdw 2.285 3.040 ... (remaining 246760 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 129 through 1243) selection = (chain 'B' and resid 129 through 1243) selection = (chain 'C' and resid 129 through 1243) selection = (chain 'D' and resid 129 through 1243) } 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 27.000 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.702 32968 Z= 0.747 Angle : 0.999 51.115 44584 Z= 0.391 Chirality : 0.075 1.972 4980 Planarity : 0.004 0.056 5516 Dihedral : 12.407 110.695 12224 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.18 % Allowed : 6.87 % Favored : 90.95 % 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: 0.21 (0.13), residues: 3824 helix: 1.15 (0.11), residues: 2340 sheet: -0.08 (0.37), residues: 216 loop : -1.76 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 272 TYR 0.013 0.001 TYR A1048 PHE 0.009 0.001 PHE A 141 TRP 0.008 0.001 TRP D 763 HIS 0.003 0.000 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.01496 / 0.75 (32968) covalent geometry : angle 0.99944 / 0.39 (44584) hydrogen bonds : bond 0.15835 / 11.02 ( 1738) hydrogen bonds : angle 5.35768 / 3.87 ( 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 684 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 609 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ILE cc_start: 0.8039 (mm) cc_final: 0.7773 (mt) REVERT: A 355 ASP cc_start: 0.5257 (t0) cc_final: 0.4991 (t0) REVERT: A 514 MET cc_start: 0.8133 (mmt) cc_final: 0.7901 (mmt) REVERT: A 963 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: A 1013 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 309 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7482 (m) REVERT: B 380 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7064 (p90) REVERT: B 418 MET cc_start: 0.6680 (mmp) cc_final: 0.6461 (mmm) REVERT: B 442 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 492 MET cc_start: 0.8420 (tpp) cc_final: 0.7495 (tpt) REVERT: B 514 MET cc_start: 0.8097 (mmt) cc_final: 0.7827 (mmt) REVERT: B 770 ARG cc_start: 0.6982 (mmt90) cc_final: 0.6744 (mmt90) REVERT: B 932 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8079 (tp) REVERT: C 442 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 496 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 963 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: C 1017 MET cc_start: 0.6879 (tmm) cc_final: 0.6161 (mtm) REVERT: D 346 ILE cc_start: 0.8015 (mm) cc_final: 0.7500 (mm) REVERT: D 496 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 514 MET cc_start: 0.8051 (mmt) cc_final: 0.7810 (mmt) REVERT: D 1233 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7086 (mtp85) outliers start: 75 outliers final: 22 residues processed: 672 average time/residue: 0.1883 time to fit residues: 202.4635 Evaluate side-chains 461 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 429 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 1217 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 746 HIS A1062 GLN A1115 ASN A1199 GLN B 240 HIS B 528 ASN B 633 HIS B 746 HIS B 940 GLN B 978 ASN B1115 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 275 GLN C 314 GLN C 411 GLN C 528 ASN C 746 HIS C1062 GLN C1115 ASN C1238 ASN C1242 HIS D 194 ASN D 314 GLN D 539 HIS D 746 HIS D 978 ASN D1062 GLN D1115 ASN D1242 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106394 restraints weight = 42939.790| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.77 r_work: 0.3165 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1361 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= 0.253 Angle : 0.624 7.576 44584 Z= 0.319 Chirality : 0.042 0.166 4980 Planarity : 0.005 0.050 5516 Dihedral : 8.815 95.542 4557 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.06 % Allowed : 10.45 % Favored : 86.50 % 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: 0.37 (0.14), residues: 3824 helix: 1.32 (0.11), residues: 2396 sheet: -0.36 (0.34), residues: 224 loop : -1.87 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 268 TYR 0.015 0.001 TYR B1098 PHE 0.037 0.002 PHE D 162 TRP 0.016 0.002 TRP B 763 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.25 (32968) covalent geometry : angle 0.62411 / 0.32 (44584) hydrogen bonds : bond 0.06296 / 4.35 ( 1738) hydrogen bonds : angle 4.22156 / 3.04 ( 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 561 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 456 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8511 (mmm) cc_final: 0.8214 (mmm) REVERT: A 204 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8907 (p) REVERT: A 216 THR cc_start: 0.8434 (m) cc_final: 0.8202 (p) REVERT: A 479 TYR cc_start: 0.7227 (t80) cc_final: 0.6946 (t80) REVERT: A 687 MET cc_start: 0.7271 (tpp) cc_final: 0.7058 (tpp) REVERT: A 963 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (mm-40) REVERT: A 1011 MET cc_start: 0.8066 (mmt) cc_final: 0.7796 (mmt) REVERT: A 1207 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 156 MET cc_start: 0.8301 (mtp) cc_final: 0.8067 (mmm) REVERT: B 178 GLN cc_start: 0.8853 (mm110) cc_final: 0.8647 (mm110) REVERT: B 216 THR cc_start: 0.8381 (m) cc_final: 0.8093 (p) REVERT: B 245 ARG cc_start: 0.8061 (mpt180) cc_final: 0.7494 (mmt-90) REVERT: B 272 ARG cc_start: 0.6519 (mmt90) cc_final: 0.5602 (mmt90) REVERT: B 380 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7538 (p90) REVERT: B 983 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: B 1207 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 496 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7905 (mp) REVERT: C 963 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: C 1017 MET cc_start: 0.8297 (tmm) cc_final: 0.6754 (mtm) REVERT: D 216 THR cc_start: 0.8299 (m) cc_final: 0.8069 (p) REVERT: D 346 ILE cc_start: 0.6968 (mm) cc_final: 0.6706 (mt) REVERT: D 355 ASP cc_start: 0.6625 (t0) cc_final: 0.6130 (t0) REVERT: D 496 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7914 (mp) REVERT: D 1207 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8191 (tm-30) REVERT: D 1230 MET cc_start: 0.8924 (ttp) cc_final: 0.8719 (ttm) REVERT: D 1233 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7332 (mtp85) outliers start: 105 outliers final: 69 residues processed: 537 average time/residue: 0.1883 time to fit residues: 160.9521 Evaluate side-chains 493 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 417 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 332 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 GLN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 890 ASN B1115 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109578 restraints weight = 42750.330| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.73 r_work: 0.3213 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32968 Z= 0.127 Angle : 0.521 8.508 44584 Z= 0.265 Chirality : 0.038 0.153 4980 Planarity : 0.004 0.042 5516 Dihedral : 8.233 82.027 4535 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.79 % Allowed : 12.14 % Favored : 85.07 % 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: 0.72 (0.14), residues: 3824 helix: 1.63 (0.11), residues: 2408 sheet: -0.33 (0.34), residues: 220 loop : -1.83 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 522 TYR 0.019 0.001 TYR B 479 PHE 0.041 0.001 PHE D 162 TRP 0.011 0.001 TRP D 763 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32968) covalent geometry : angle 0.52069 / 0.27 (44584) hydrogen bonds : bond 0.05031 / 3.47 ( 1738) hydrogen bonds : angle 3.95108 / 2.85 ( 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 541 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 445 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8380 (mmm) cc_final: 0.8066 (mmm) REVERT: A 245 ARG cc_start: 0.7603 (mtt-85) cc_final: 0.7192 (mtt-85) REVERT: A 346 ILE cc_start: 0.6882 (mm) cc_final: 0.6578 (mm) REVERT: A 687 MET cc_start: 0.7232 (tpp) cc_final: 0.6999 (tpp) REVERT: A 925 MET cc_start: 0.7342 (ttm) cc_final: 0.7127 (mtt) REVERT: A 963 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7248 (mm-40) REVERT: A 983 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 1011 MET cc_start: 0.8022 (mmt) cc_final: 0.7756 (mmt) REVERT: B 178 GLN cc_start: 0.8819 (mm110) cc_final: 0.8595 (mm110) REVERT: B 245 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7392 (mmt-90) REVERT: B 380 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7358 (p90) REVERT: B 925 MET cc_start: 0.7384 (ttm) cc_final: 0.7169 (mtt) REVERT: B 983 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 1189 GLU cc_start: 0.7740 (mp0) cc_final: 0.7472 (mp0) REVERT: C 216 THR cc_start: 0.8211 (m) cc_final: 0.7944 (p) REVERT: C 243 LYS cc_start: 0.7926 (pttt) cc_final: 0.7371 (pttm) REVERT: C 323 LYS cc_start: 0.8777 (tppt) cc_final: 0.8195 (tptt) REVERT: C 496 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7867 (mp) REVERT: C 925 MET cc_start: 0.7389 (ttm) cc_final: 0.7117 (mtt) REVERT: C 963 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6716 (mp10) REVERT: C 983 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: C 1061 ASP cc_start: 0.7567 (p0) cc_final: 0.7351 (p0) REVERT: C 1199 GLN cc_start: 0.8232 (tt0) cc_final: 0.8028 (tt0) REVERT: D 346 ILE cc_start: 0.6862 (mm) cc_final: 0.6583 (mt) REVERT: D 496 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 983 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: D 1001 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: D 1199 GLN cc_start: 0.8167 (tt0) cc_final: 0.7955 (tt0) REVERT: D 1207 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 1232 MET cc_start: 0.7563 (tmm) cc_final: 0.7333 (tmm) REVERT: D 1233 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7163 (mtp85) outliers start: 96 outliers final: 60 residues processed: 514 average time/residue: 0.1851 time to fit residues: 151.3277 Evaluate side-chains 488 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 418 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN A1115 ASN B1115 ASN C 151 HIS C1115 ASN ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106780 restraints weight = 42710.502| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.72 r_work: 0.3179 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32968 Z= 0.192 Angle : 0.559 7.963 44584 Z= 0.284 Chirality : 0.040 0.153 4980 Planarity : 0.004 0.051 5516 Dihedral : 8.030 66.370 4523 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.67 % Allowed : 12.34 % Favored : 83.99 % 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: 0.69 (0.14), residues: 3824 helix: 1.59 (0.11), residues: 2412 sheet: -0.39 (0.34), residues: 220 loop : -1.79 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 522 TYR 0.021 0.001 TYR D 479 PHE 0.041 0.001 PHE B 162 TRP 0.014 0.001 TRP D 763 HIS 0.007 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (32968) covalent geometry : angle 0.55923 / 0.28 (44584) hydrogen bonds : bond 0.05547 / 3.82 ( 1738) hydrogen bonds : angle 3.94562 / 2.84 ( 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 552 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 426 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8418 (mmm) cc_final: 0.8102 (mmm) REVERT: A 346 ILE cc_start: 0.6950 (mm) cc_final: 0.6647 (mm) REVERT: A 687 MET cc_start: 0.7282 (tpp) cc_final: 0.7028 (tpp) REVERT: A 963 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7534 (mm-40) REVERT: A 983 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: A 1011 MET cc_start: 0.8044 (mmt) cc_final: 0.7804 (mmt) REVERT: A 1207 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 216 THR cc_start: 0.8285 (m) cc_final: 0.8065 (p) REVERT: B 245 ARG cc_start: 0.7983 (mpt180) cc_final: 0.7302 (mmt-90) REVERT: B 380 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7501 (p90) REVERT: B 542 ARG cc_start: 0.8128 (ptt-90) cc_final: 0.7883 (ptt180) REVERT: B 963 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7743 (mm-40) REVERT: B 983 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 1189 GLU cc_start: 0.7757 (mp0) cc_final: 0.7480 (mp0) REVERT: B 1230 MET cc_start: 0.8709 (ttm) cc_final: 0.8508 (ttp) REVERT: C 216 THR cc_start: 0.8282 (m) cc_final: 0.7983 (p) REVERT: C 243 LYS cc_start: 0.7931 (pttt) cc_final: 0.7365 (pttm) REVERT: C 496 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7784 (mp) REVERT: C 963 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7386 (mm-40) REVERT: C 983 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: C 1061 ASP cc_start: 0.7535 (p0) cc_final: 0.7262 (p0) REVERT: C 1199 GLN cc_start: 0.8233 (tt0) cc_final: 0.8029 (tt0) REVERT: C 1207 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 1232 MET cc_start: 0.7901 (tmm) cc_final: 0.7691 (tmm) REVERT: D 496 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 963 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: D 983 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: D 1199 GLN cc_start: 0.8164 (tt0) cc_final: 0.7937 (tt0) REVERT: D 1207 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 1232 MET cc_start: 0.7587 (tmm) cc_final: 0.7341 (tmm) outliers start: 126 outliers final: 89 residues processed: 518 average time/residue: 0.1915 time to fit residues: 158.6202 Evaluate side-chains 509 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 409 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 963 GLN Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 242 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 338 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 375 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 482 GLN B1115 ASN C1115 ASN D 151 HIS ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 GLN D1115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106985 restraints weight = 42809.829| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.72 r_work: 0.3180 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32968 Z= 0.188 Angle : 0.550 6.909 44584 Z= 0.280 Chirality : 0.039 0.151 4980 Planarity : 0.004 0.045 5516 Dihedral : 7.892 59.536 4521 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.84 % Allowed : 12.81 % Favored : 83.35 % 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: 0.71 (0.14), residues: 3824 helix: 1.62 (0.11), residues: 2412 sheet: -0.39 (0.34), residues: 220 loop : -1.80 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.022 0.001 TYR B 479 PHE 0.042 0.001 PHE C 162 TRP 0.014 0.001 TRP D 763 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (32968) covalent geometry : angle 0.55032 / 0.28 (44584) hydrogen bonds : bond 0.05474 / 3.77 ( 1738) hydrogen bonds : angle 3.92493 / 2.83 ( 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 547 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 415 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8423 (mmm) cc_final: 0.8094 (mmm) REVERT: A 245 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.6895 (mtt-85) REVERT: A 346 ILE cc_start: 0.6950 (mm) cc_final: 0.6604 (mm) REVERT: A 687 MET cc_start: 0.7340 (tpp) cc_final: 0.7073 (tpp) REVERT: A 963 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: A 983 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: A 1011 MET cc_start: 0.8052 (mmt) cc_final: 0.7836 (mmt) REVERT: A 1207 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 178 GLN cc_start: 0.8782 (mm110) cc_final: 0.8574 (mm110) REVERT: B 216 THR cc_start: 0.8287 (m) cc_final: 0.8081 (p) REVERT: B 245 ARG cc_start: 0.7997 (mpt180) cc_final: 0.7332 (mmt-90) REVERT: B 354 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: B 380 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7564 (p90) REVERT: B 963 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7640 (mm-40) REVERT: B 983 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 1189 GLU cc_start: 0.7755 (mp0) cc_final: 0.7546 (mp0) REVERT: B 1206 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7157 (ttp80) REVERT: B 1207 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 216 THR cc_start: 0.8241 (m) cc_final: 0.8004 (p) REVERT: C 243 LYS cc_start: 0.7981 (pttt) cc_final: 0.7412 (pttm) REVERT: C 354 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8160 (mtp180) REVERT: C 496 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 963 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: C 983 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: C 1061 ASP cc_start: 0.7539 (p0) cc_final: 0.7252 (p0) REVERT: C 1232 MET cc_start: 0.7858 (tmm) cc_final: 0.7540 (tmm) REVERT: D 354 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7887 (mtp180) REVERT: D 496 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7839 (mp) REVERT: D 983 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: D 1207 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 1232 MET cc_start: 0.7728 (tmm) cc_final: 0.7517 (tmm) outliers start: 132 outliers final: 96 residues processed: 512 average time/residue: 0.1879 time to fit residues: 154.8424 Evaluate side-chains 516 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 410 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 963 GLN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 275 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 259 optimal weight: 0.3980 chunk 198 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS A1062 GLN B1115 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN D 151 HIS D 171 HIS ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 746 HIS D1062 GLN D1115 ASN D1199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105600 restraints weight = 42761.353| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.71 r_work: 0.3165 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32968 Z= 0.236 Angle : 0.585 7.677 44584 Z= 0.298 Chirality : 0.041 0.157 4980 Planarity : 0.004 0.047 5516 Dihedral : 7.894 59.284 4521 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.87 % Allowed : 13.50 % Favored : 82.63 % 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: 0.61 (0.14), residues: 3824 helix: 1.52 (0.11), residues: 2416 sheet: -0.51 (0.34), residues: 220 loop : -1.81 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 272 TYR 0.023 0.001 TYR D 479 PHE 0.044 0.002 PHE C 162 TRP 0.015 0.001 TRP D 763 HIS 0.018 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (32968) covalent geometry : angle 0.58508 / 0.30 (44584) hydrogen bonds : bond 0.05884 / 4.05 ( 1738) hydrogen bonds : angle 3.99639 / 2.88 ( 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 559 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 426 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8438 (mmm) cc_final: 0.8101 (mmm) REVERT: A 193 GLN cc_start: 0.7073 (pp30) cc_final: 0.6814 (pp30) REVERT: A 200 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8219 (mmmt) REVERT: A 346 ILE cc_start: 0.6937 (mm) cc_final: 0.6618 (mm) REVERT: A 687 MET cc_start: 0.7382 (tpp) cc_final: 0.7099 (tpp) REVERT: A 963 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: A 983 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 1207 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 216 THR cc_start: 0.8352 (m) cc_final: 0.8118 (p) REVERT: B 245 ARG cc_start: 0.8001 (mpt180) cc_final: 0.7344 (mmt-90) REVERT: B 380 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7666 (p90) REVERT: B 1232 MET cc_start: 0.7425 (tmm) cc_final: 0.7074 (tmm) REVERT: C 216 THR cc_start: 0.8326 (m) cc_final: 0.8023 (p) REVERT: C 243 LYS cc_start: 0.7999 (pttt) cc_final: 0.7425 (pttm) REVERT: C 260 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: C 354 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8161 (mtp180) REVERT: C 496 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7756 (mp) REVERT: C 963 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6927 (mp10) REVERT: C 983 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: C 1061 ASP cc_start: 0.7539 (p0) cc_final: 0.7252 (p0) REVERT: C 1133 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8405 (ttp80) REVERT: C 1207 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7750 (tm-30) REVERT: C 1232 MET cc_start: 0.7777 (tmm) cc_final: 0.7563 (tmm) REVERT: D 194 ASN cc_start: 0.8181 (t0) cc_final: 0.7927 (m110) REVERT: D 354 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7813 (mtp180) REVERT: D 355 ASP cc_start: 0.6995 (t0) cc_final: 0.6325 (m-30) REVERT: D 496 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 983 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: D 1232 MET cc_start: 0.7867 (tmm) cc_final: 0.7640 (tmm) outliers start: 133 outliers final: 102 residues processed: 523 average time/residue: 0.2030 time to fit residues: 169.2424 Evaluate side-chains 522 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 410 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1133 ARG Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 286 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 329 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 316 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN C1199 GLN D 151 HIS ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 GLN D1115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108590 restraints weight = 42664.291| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.72 r_work: 0.3200 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32968 Z= 0.132 Angle : 0.519 6.786 44584 Z= 0.265 Chirality : 0.038 0.152 4980 Planarity : 0.004 0.043 5516 Dihedral : 7.707 59.501 4519 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.58 % Allowed : 14.23 % Favored : 82.19 % 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: 1.74 (0.11), residues: 2412 sheet: -0.44 (0.34), residues: 220 loop : -1.76 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 700 TYR 0.023 0.001 TYR D 479 PHE 0.046 0.001 PHE C 162 TRP 0.011 0.001 TRP D 763 HIS 0.013 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (32968) covalent geometry : angle 0.51938 / 0.27 (44584) hydrogen bonds : bond 0.04998 / 3.43 ( 1738) hydrogen bonds : angle 3.83646 / 2.76 ( 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 552 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 429 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8425 (mmm) cc_final: 0.8092 (mmm) REVERT: A 200 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8218 (mmmt) REVERT: A 245 ARG cc_start: 0.7729 (mtt-85) cc_final: 0.7067 (mmt-90) REVERT: A 346 ILE cc_start: 0.6892 (mm) cc_final: 0.6593 (mm) REVERT: A 482 GLN cc_start: 0.8712 (mp-120) cc_final: 0.8487 (mp10) REVERT: A 963 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7447 (mm-40) REVERT: A 983 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 1207 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 245 ARG cc_start: 0.7992 (mpt180) cc_final: 0.7294 (mmt-90) REVERT: B 380 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7616 (p90) REVERT: B 746 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8652 (t70) REVERT: B 983 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: B 1232 MET cc_start: 0.7379 (tmm) cc_final: 0.7033 (tmm) REVERT: C 216 THR cc_start: 0.8258 (m) cc_final: 0.7986 (p) REVERT: C 243 LYS cc_start: 0.7988 (pttt) cc_final: 0.7395 (pttm) REVERT: C 260 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: C 323 LYS cc_start: 0.8728 (tppt) cc_final: 0.8286 (tptt) REVERT: C 354 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8199 (mtp180) REVERT: C 496 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7848 (mp) REVERT: C 746 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8616 (t70) REVERT: C 963 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: C 983 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: C 1017 MET cc_start: 0.8264 (tmm) cc_final: 0.6639 (mtt) REVERT: C 1061 ASP cc_start: 0.7523 (p0) cc_final: 0.7286 (p0) REVERT: C 1207 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 264 ASP cc_start: 0.7657 (t0) cc_final: 0.7349 (t0) REVERT: D 354 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7863 (mtp180) REVERT: D 496 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7862 (mp) REVERT: D 983 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: D 1232 MET cc_start: 0.7810 (tmm) cc_final: 0.7480 (tmm) outliers start: 123 outliers final: 87 residues processed: 523 average time/residue: 0.2000 time to fit residues: 167.9269 Evaluate side-chains 510 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 411 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 chunk 311 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN B 587 ASN B1115 ASN C1199 GLN D 151 HIS ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105180 restraints weight = 43033.779| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.86 r_work: 0.3109 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 32968 Z= 0.230 Angle : 0.586 7.929 44584 Z= 0.298 Chirality : 0.041 0.155 4980 Planarity : 0.004 0.045 5516 Dihedral : 7.767 61.227 4519 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.52 % Allowed : 14.55 % Favored : 81.93 % 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: 0.67 (0.14), residues: 3824 helix: 1.59 (0.11), residues: 2412 sheet: -0.57 (0.33), residues: 220 loop : -1.79 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 700 TYR 0.025 0.001 TYR D 479 PHE 0.046 0.002 PHE C 162 TRP 0.014 0.001 TRP D 763 HIS 0.016 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (32968) covalent geometry : angle 0.58612 / 0.30 (44584) hydrogen bonds : bond 0.05765 / 3.96 ( 1738) hydrogen bonds : angle 3.95132 / 2.84 ( 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 534 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 413 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8502 (mmm) cc_final: 0.8166 (mmm) REVERT: A 200 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8261 (mmmt) REVERT: A 346 ILE cc_start: 0.7041 (mm) cc_final: 0.6731 (mm) REVERT: A 482 GLN cc_start: 0.8777 (mp-120) cc_final: 0.8575 (mp10) REVERT: A 925 MET cc_start: 0.7033 (mtt) cc_final: 0.6724 (ttm) REVERT: A 963 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7600 (mm-40) REVERT: A 983 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: A 1207 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 245 ARG cc_start: 0.8034 (mpt180) cc_final: 0.7658 (mmt90) REVERT: B 380 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7748 (p90) REVERT: B 925 MET cc_start: 0.7046 (mtt) cc_final: 0.6761 (ttm) REVERT: B 983 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: B 1232 MET cc_start: 0.7456 (tmm) cc_final: 0.7093 (tmm) REVERT: C 216 THR cc_start: 0.8346 (m) cc_final: 0.8063 (p) REVERT: C 260 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: C 496 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7907 (mp) REVERT: C 925 MET cc_start: 0.7068 (mtt) cc_final: 0.6812 (ttm) REVERT: C 963 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7523 (mm-40) REVERT: C 983 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: C 1061 ASP cc_start: 0.7354 (p0) cc_final: 0.7109 (p0) REVERT: D 264 ASP cc_start: 0.7720 (t0) cc_final: 0.7357 (t0) REVERT: D 354 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7889 (mtp180) REVERT: D 355 ASP cc_start: 0.6964 (t0) cc_final: 0.6482 (m-30) REVERT: D 496 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7954 (mp) REVERT: D 983 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: D 1232 MET cc_start: 0.7910 (tmm) cc_final: 0.7572 (tmm) outliers start: 121 outliers final: 96 residues processed: 502 average time/residue: 0.2044 time to fit residues: 163.4622 Evaluate side-chains 512 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 406 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL 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 1217 ASP Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1217 ASP Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1217 ASP Chi-restraints excluded: chain D residue 1227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 105 optimal weight: 6.9990 chunk 259 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 289 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 0.0270 chunk 253 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN D 151 HIS ** D 293 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109694 restraints weight = 42350.630| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.87 r_work: 0.3206 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32968 Z= 0.112 Angle : 0.514 9.046 44584 Z= 0.262 Chirality : 0.037 0.150 4980 Planarity : 0.004 0.043 5516 Dihedral : 7.510 64.147 4519 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.62 % Allowed : 15.54 % Favored : 81.84 % 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: 0.99 (0.14), residues: 3824 helix: 1.85 (0.11), residues: 2408 sheet: -0.38 (0.34), residues: 220 loop : -1.70 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 700 TYR 0.022 0.001 TYR B 479 PHE 0.040 0.001 PHE C 162 TRP 0.009 0.001 TRP C 876 HIS 0.027 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (32968) covalent geometry : angle 0.51438 / 0.26 (44584) hydrogen bonds : bond 0.04552 / 3.12 ( 1738) hydrogen bonds : angle 3.74690 / 2.70 ( 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 519 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 429 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8504 (mmm) cc_final: 0.8186 (mmm) REVERT: A 200 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8167 (mmmt) REVERT: A 260 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6351 (tp30) REVERT: A 346 ILE cc_start: 0.6997 (mm) cc_final: 0.6690 (mm) REVERT: A 482 GLN cc_start: 0.8695 (mp-120) cc_final: 0.8483 (mp10) REVERT: A 925 MET cc_start: 0.6970 (mtt) cc_final: 0.6642 (ttm) REVERT: A 963 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7372 (mm-40) REVERT: A 983 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 245 ARG cc_start: 0.8041 (mpt180) cc_final: 0.7617 (mmt90) REVERT: B 380 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7587 (p90) REVERT: B 642 MET cc_start: 0.8414 (tmm) cc_final: 0.7960 (tpp) REVERT: B 925 MET cc_start: 0.6951 (mtt) cc_final: 0.6660 (ttm) REVERT: B 983 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: B 1206 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7904 (ttp80) REVERT: B 1207 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 1232 MET cc_start: 0.7508 (tmm) cc_final: 0.7153 (tmm) REVERT: C 216 THR cc_start: 0.8290 (m) cc_final: 0.8083 (p) REVERT: C 354 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8180 (mtp180) REVERT: C 700 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7503 (ttp-110) REVERT: C 746 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8706 (t70) REVERT: C 925 MET cc_start: 0.6964 (mtt) cc_final: 0.6692 (ttm) REVERT: C 963 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: C 983 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: C 1017 MET cc_start: 0.8236 (tmm) cc_final: 0.6616 (mtm) REVERT: C 1061 ASP cc_start: 0.7330 (p0) cc_final: 0.7094 (p0) REVERT: C 1207 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 346 ILE cc_start: 0.6949 (mm) cc_final: 0.6684 (mt) REVERT: D 354 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7847 (mtp180) REVERT: D 355 ASP cc_start: 0.6966 (t0) cc_final: 0.6430 (m-30) REVERT: D 983 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: D 1232 MET cc_start: 0.8010 (tmm) cc_final: 0.7670 (tmm) outliers start: 90 outliers final: 60 residues processed: 493 average time/residue: 0.1907 time to fit residues: 151.3567 Evaluate side-chains 477 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 408 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL 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 C residue 151 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1217 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 60 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 356 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 336 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A1115 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN C1115 ASN ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108878 restraints weight = 43014.164| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.73 r_work: 0.3204 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32968 Z= 0.155 Angle : 0.538 8.627 44584 Z= 0.273 Chirality : 0.039 0.148 4980 Planarity : 0.004 0.044 5516 Dihedral : 7.412 66.600 4515 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.47 % Allowed : 15.69 % Favored : 81.84 % 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: 0.92 (0.14), residues: 3824 helix: 1.78 (0.11), residues: 2416 sheet: -0.39 (0.34), residues: 220 loop : -1.70 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 700 TYR 0.026 0.001 TYR D 479 PHE 0.039 0.001 PHE C 162 TRP 0.011 0.001 TRP D 763 HIS 0.007 0.000 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (32968) covalent geometry : angle 0.53836 / 0.27 (44584) hydrogen bonds : bond 0.04893 / 3.36 ( 1738) hydrogen bonds : angle 3.76829 / 2.71 ( 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 493 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 408 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8439 (mmm) cc_final: 0.8102 (mmm) REVERT: A 200 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8138 (mmmt) REVERT: A 346 ILE cc_start: 0.6882 (mm) cc_final: 0.6580 (mm) REVERT: A 482 GLN cc_start: 0.8693 (mp-120) cc_final: 0.8480 (mp10) REVERT: A 642 MET cc_start: 0.8437 (tmm) cc_final: 0.7861 (tpp) REVERT: A 685 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 925 MET cc_start: 0.6907 (mtt) cc_final: 0.6609 (ttm) REVERT: A 963 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7481 (mm-40) REVERT: A 983 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 1207 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 245 ARG cc_start: 0.7966 (mpt180) cc_final: 0.7570 (mmt90) REVERT: B 380 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7579 (p90) REVERT: B 746 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8711 (t70) REVERT: B 925 MET cc_start: 0.6889 (mtt) cc_final: 0.6616 (ttm) REVERT: B 983 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 1207 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 1232 MET cc_start: 0.7433 (tmm) cc_final: 0.7088 (tmm) REVERT: C 216 THR cc_start: 0.8232 (m) cc_final: 0.7987 (p) REVERT: C 260 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: C 354 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8152 (mtp180) REVERT: C 642 MET cc_start: 0.8445 (tmm) cc_final: 0.7574 (tmm) REVERT: C 746 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8681 (t70) REVERT: C 925 MET cc_start: 0.6950 (mtt) cc_final: 0.6691 (ttm) REVERT: C 963 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (mm-40) REVERT: C 983 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: C 1207 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 354 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7821 (mtp180) REVERT: D 355 ASP cc_start: 0.6979 (t0) cc_final: 0.6323 (m-30) REVERT: D 983 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: D 1207 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7740 (tm-30) REVERT: D 1232 MET cc_start: 0.8024 (tmm) cc_final: 0.7677 (tmm) outliers start: 85 outliers final: 71 residues processed: 471 average time/residue: 0.1933 time to fit residues: 145.5622 Evaluate side-chains 487 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 405 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1217 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 49 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 195 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A1115 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN C1115 ASN ** D 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109470 restraints weight = 42720.326| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.88 r_work: 0.3200 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1944 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= 0.124 Angle : 0.524 9.695 44584 Z= 0.266 Chirality : 0.038 0.148 4980 Planarity : 0.004 0.050 5516 Dihedral : 7.352 68.415 4515 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.50 % Allowed : 15.60 % Favored : 81.90 % 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: 1.00 (0.14), residues: 3824 helix: 1.84 (0.11), residues: 2416 sheet: -0.34 (0.34), residues: 220 loop : -1.67 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1206 TYR 0.026 0.001 TYR D 479 PHE 0.038 0.001 PHE C 162 TRP 0.010 0.001 TRP C 876 HIS 0.007 0.000 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (32968) covalent geometry : angle 0.52408 / 0.27 (44584) hydrogen bonds : bond 0.04638 / 3.18 ( 1738) hydrogen bonds : angle 3.73317 / 2.68 ( 5151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7198.43 seconds wall clock time: 124 minutes 11.42 seconds (7451.42 seconds total)