Starting phenix.real_space_refine on Thu May 29 09:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.map" model { file = "/net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed7_28031/05_2025/8ed7_28031.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 226 5.16 5 C 20456 2.51 5 N 5325 2.21 5 O 5511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31518 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7736 Classifications: {'peptide': 954} Link IDs: {'PTRANS': 33, 'TRANS': 920} Chain breaks: 6 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: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 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: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 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: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7766 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 33, 'TRANS': 924} Chain breaks: 6 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'9Z9': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.99, per 1000 atoms: 0.60 Number of scatterers: 31518 At special positions: 0 Unit cell: (140.175, 140.175, 152.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 226 16.00 O 5511 8.00 N 5325 7.00 C 20456 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: 8.07 Conformation dependent library (CDL) restraints added in 4.2 seconds 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 8 sheets defined 67.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.716A pdb=" N LYS A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.188A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.096A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.663A pdb=" N ILE A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.594A pdb=" N THR A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.539A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.915A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.511A pdb=" N VAL A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.899A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.941A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.012A 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 removed outlier: 4.655A pdb=" N ASN A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.561A pdb=" N TRP A 732 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 729 through 733' Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.729A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 783 through 788 removed outlier: 3.518A pdb=" N ILE A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 783 through 788' Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.579A pdb=" N ASN A 869 " --> pdb=" O TYR A 865 " (cutoff:3.500A) 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: 3.689A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.536A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.204A pdb=" N ILE A 980 " --> pdb=" O CYS A 976 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.877A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 3.915A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.848A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 Processing helix chain 'A' and resid 1089 through 1103 removed outlier: 4.099A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.598A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.679A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A1162 " --> pdb=" O MET A1158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 removed outlier: 3.515A pdb=" N LEU A1190 " --> pdb=" O THR A1186 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.600A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.535A pdb=" N LYS B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.990A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.654A pdb=" N ILE B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.816A pdb=" N THR B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.077A pdb=" N LEU B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.521A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.913A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.521A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 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 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.908A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 3.940A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.012A 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 removed outlier: 4.654A pdb=" N ASN B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.564A pdb=" N TRP B 732 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.742A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 783 through 788 removed outlier: 4.042A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 removed outlier: 3.590A pdb=" N ASN B 869 " --> pdb=" O TYR B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.508A pdb=" N LYS B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.528A pdb=" N VAL B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.255A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.877A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1033 removed outlier: 3.859A pdb=" N TYR B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.739A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1053 Processing helix chain 'B' and resid 1089 through 1103 removed outlier: 4.107A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1117 removed outlier: 3.520A pdb=" N ASN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1143 removed outlier: 4.585A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1156 Processing helix chain 'B' and resid 1156 through 1163 removed outlier: 3.853A pdb=" N PHE B1160 " --> pdb=" O MET B1156 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B1163 " --> pdb=" O ILE B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.596A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 228 through 242 removed outlier: 4.195A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 322 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.289A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 removed outlier: 3.715A pdb=" N GLY C 368 " --> pdb=" O ASP C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.679A pdb=" N ILE C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.565A pdb=" N ALA C 410 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.962A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.532A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.900A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.521A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.908A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.939A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.005A 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 690 through 717 removed outlier: 3.631A pdb=" N LEU C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.561A pdb=" N TRP C 732 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 729 through 733' Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.746A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 783 through 788 removed outlier: 4.176A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 removed outlier: 3.583A pdb=" N ASN C 869 " --> pdb=" O TYR C 865 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.564A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 removed outlier: 4.275A pdb=" N ILE C 980 " --> pdb=" O CYS C 976 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.772A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1006 removed outlier: 3.845A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1033 removed outlier: 4.140A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1046 removed outlier: 3.847A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1053 Processing helix chain 'C' and resid 1059 through 1063 removed outlier: 3.676A pdb=" N ILE C1063 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1103 removed outlier: 4.129A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1117 Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.597A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1163 removed outlier: 3.687A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C1160 " --> pdb=" O MET C1156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C1162 " --> pdb=" O MET C1158 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL C1163 " --> pdb=" O ILE C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 removed outlier: 3.529A pdb=" N LEU C1190 " --> pdb=" O THR C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.579A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 228 through 244 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.002A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.668A pdb=" N ILE D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.729A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 453 removed outlier: 3.556A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.909A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.519A pdb=" N VAL D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.906A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.937A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.007A 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 690 through 717 removed outlier: 4.846A pdb=" N ASN D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 729 through 733 removed outlier: 3.531A pdb=" N TRP D 732 " --> pdb=" O LEU D 729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D 733 " --> pdb=" O LYS D 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 729 through 733' Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.712A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 790 removed outlier: 3.803A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 removed outlier: 3.622A pdb=" N ASN D 869 " --> pdb=" O TYR D 865 " (cutoff:3.500A) 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: 3.721A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.257A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.885A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 3.906A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1053 Processing helix chain 'D' and resid 1059 through 1063 removed outlier: 3.672A pdb=" N ILE D1063 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1103 removed outlier: 4.130A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1117 Processing helix chain 'D' and resid 1118 through 1143 removed outlier: 4.593A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.380A 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 1158 Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 3.598A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) 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 271 through 275 removed outlier: 3.564A pdb=" N GLU A 145 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 158 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL A 362 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 336 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N CYS A 364 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE A 338 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.549A pdb=" N GLU B 145 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (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 271 through 275 removed outlier: 3.558A pdb=" N GLU C 145 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 275 removed outlier: 3.542A pdb=" N GLU D 145 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) 1735 hydrogen bonds defined for protein. 5130 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: 10.97 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9954 1.34 - 1.46: 6682 1.46 - 1.58: 15200 1.58 - 1.69: 0 1.69 - 1.81: 402 Bond restraints: 32238 Sorted by residual: bond pdb=" CA THR D 408 " pdb=" CB THR D 408 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" C PRO D1148 " pdb=" N PRO D1149 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.19e-02 7.06e+03 1.13e+00 bond pdb=" C GLN D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.332 1.344 -0.013 1.26e-02 6.30e+03 9.85e-01 bond pdb=" C TYR A1012 " pdb=" O TYR A1012 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.62e-01 bond pdb=" C PRO C1148 " pdb=" N PRO C1149 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.42e-01 ... (remaining 32233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 42961 1.77 - 3.54: 543 3.54 - 5.32: 61 5.32 - 7.09: 35 7.09 - 8.86: 3 Bond angle restraints: 43603 Sorted by residual: angle pdb=" C VAL A 688 " pdb=" N ASP A 689 " pdb=" CA ASP A 689 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C VAL B 688 " pdb=" N ASP B 689 " pdb=" CA ASP B 689 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N PRO B1148 " pdb=" CA PRO B1148 " pdb=" C PRO B1148 " ideal model delta sigma weight residual 110.70 114.68 -3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" N PRO A1148 " pdb=" CA PRO A1148 " pdb=" C PRO A1148 " ideal model delta sigma weight residual 110.70 114.51 -3.81 1.22e+00 6.72e-01 9.74e+00 angle pdb=" N PRO C1148 " pdb=" CA PRO C1148 " pdb=" C PRO C1148 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.49e+00 ... (remaining 43598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 17708 15.42 - 30.83: 1360 30.83 - 46.25: 366 46.25 - 61.66: 99 61.66 - 77.08: 4 Dihedral angle restraints: 19537 sinusoidal: 8187 harmonic: 11350 Sorted by residual: 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 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 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 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 19534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2991 0.032 - 0.065: 1440 0.065 - 0.097: 314 0.097 - 0.129: 142 0.129 - 0.162: 10 Chirality restraints: 4897 Sorted by residual: chirality pdb=" C08 9Z9 A1402 " pdb=" C07 9Z9 A1402 " pdb=" C09 9Z9 A1402 " pdb=" C11 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.45 2.62 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C08 9Z9 B1401 " pdb=" C07 9Z9 B1401 " pdb=" C09 9Z9 B1401 " pdb=" C11 9Z9 B1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C08 9Z9 A1401 " pdb=" C07 9Z9 A1401 " pdb=" C09 9Z9 A1401 " pdb=" C11 9Z9 A1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 4894 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 785 " 0.099 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 C 784 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 785 " -0.098 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 D 784 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO D 785 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.032 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5472 2.76 - 3.30: 31041 3.30 - 3.83: 50871 3.83 - 4.37: 57058 4.37 - 4.90: 101161 Nonbonded interactions: 245603 Sorted by model distance: nonbonded pdb=" O HIS A 240 " pdb=" OG SER A 244 " model vdw 2.230 3.040 nonbonded pdb=" O GLU C 922 " pdb=" OG SER C 926 " model vdw 2.248 3.040 nonbonded pdb=" O ILE C 399 " pdb=" OG1 THR C 402 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP A 947 " pdb=" OH TYR A 981 " model vdw 2.291 3.040 ... (remaining 245598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'B' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'C' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'D' and (resid 129 through 1059 or resid 1085 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 67.860 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.140 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32238 Z= 0.158 Angle : 0.541 8.860 43603 Z= 0.288 Chirality : 0.040 0.162 4897 Planarity : 0.004 0.057 5416 Dihedral : 12.282 77.077 12197 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.92 % Allowed : 8.26 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3770 helix: 1.26 (0.11), residues: 2343 sheet: 0.03 (0.37), residues: 222 loop : -1.29 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.003 0.001 HIS C 240 PHE 0.011 0.001 PHE B 792 TYR 0.010 0.001 TYR A1048 ARG 0.004 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.16363 ( 1735) hydrogen bonds : angle 4.96407 ( 5130) covalent geometry : bond 0.00355 (32238) covalent geometry : angle 0.54106 (43603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 483 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5352 (mm) REVERT: A 479 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.3868 (m-80) REVERT: A 665 MET cc_start: 0.7824 (mtm) cc_final: 0.7423 (mtm) REVERT: A 669 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 772 ASN cc_start: 0.8448 (t0) cc_final: 0.8221 (p0) REVERT: A 778 ILE cc_start: 0.9286 (pt) cc_final: 0.9009 (mt) REVERT: A 924 LEU cc_start: 0.8889 (pp) cc_final: 0.8653 (mt) REVERT: A 925 MET cc_start: 0.7778 (ppp) cc_final: 0.7475 (ppp) REVERT: A 932 LEU cc_start: 0.9255 (tt) cc_final: 0.8951 (mm) REVERT: A 1010 MET cc_start: 0.7232 (tmm) cc_final: 0.6821 (tmm) REVERT: A 1022 MET cc_start: 0.7398 (mtm) cc_final: 0.7154 (mtp) REVERT: A 1049 MET cc_start: 0.6665 (mpp) cc_final: 0.6369 (mpp) REVERT: A 1051 TYR cc_start: 0.8073 (t80) cc_final: 0.6875 (t80) REVERT: A 1055 TYR cc_start: 0.7025 (m-10) cc_final: 0.6342 (m-10) REVERT: A 1103 ASN cc_start: 0.7606 (m-40) cc_final: 0.7147 (m110) REVERT: A 1230 MET cc_start: 0.8487 (ttm) cc_final: 0.8008 (ttm) REVERT: B 409 GLN cc_start: 0.6454 (tp40) cc_final: 0.6074 (mm-40) REVERT: B 412 HIS cc_start: 0.3239 (OUTLIER) cc_final: 0.1783 (m-70) REVERT: B 665 MET cc_start: 0.7784 (mtm) cc_final: 0.7394 (mtm) REVERT: B 669 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 764 MET cc_start: 0.8991 (mmt) cc_final: 0.8725 (mmt) REVERT: B 925 MET cc_start: 0.7509 (ppp) cc_final: 0.7242 (ppp) REVERT: B 948 LEU cc_start: 0.8711 (mt) cc_final: 0.8488 (mt) REVERT: B 958 MET cc_start: 0.6122 (mmm) cc_final: 0.5921 (tmm) REVERT: B 1022 MET cc_start: 0.7154 (mtp) cc_final: 0.6653 (mtm) REVERT: B 1053 MET cc_start: 0.7942 (mtt) cc_final: 0.7618 (mtt) REVERT: B 1095 MET cc_start: 0.7501 (tpp) cc_final: 0.7239 (tpp) REVERT: B 1100 LEU cc_start: 0.9134 (tp) cc_final: 0.8924 (tt) REVERT: B 1230 MET cc_start: 0.8456 (ttm) cc_final: 0.7911 (ttm) REVERT: C 266 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5289 (mm) REVERT: C 633 HIS cc_start: 0.6296 (m90) cc_final: 0.6058 (m90) REVERT: C 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7367 (mtm) REVERT: C 669 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 726 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (m) REVERT: C 769 MET cc_start: 0.7922 (ttm) cc_final: 0.7677 (ttp) REVERT: C 772 ASN cc_start: 0.8778 (t0) cc_final: 0.8491 (p0) REVERT: C 778 ILE cc_start: 0.9143 (pt) cc_final: 0.8870 (mt) REVERT: C 958 MET cc_start: 0.6526 (mmm) cc_final: 0.6258 (tmm) REVERT: C 1053 MET cc_start: 0.7945 (mtt) cc_final: 0.7624 (mtt) REVERT: C 1058 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (p) REVERT: C 1095 MET cc_start: 0.7382 (tpp) cc_final: 0.7102 (tpp) REVERT: C 1230 MET cc_start: 0.8402 (ttm) cc_final: 0.7939 (ttp) REVERT: D 240 HIS cc_start: 0.7572 (t-90) cc_final: 0.7318 (t70) REVERT: D 266 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5302 (mm) REVERT: D 411 GLN cc_start: 0.5565 (OUTLIER) cc_final: 0.5302 (tp-100) REVERT: D 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7363 (mtm) REVERT: D 669 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8779 (mm) REVERT: D 764 MET cc_start: 0.9091 (mmt) cc_final: 0.8711 (mmt) REVERT: D 778 ILE cc_start: 0.9177 (pt) cc_final: 0.8874 (mt) REVERT: D 924 LEU cc_start: 0.8752 (pp) cc_final: 0.8383 (mp) REVERT: D 930 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (tptt) REVERT: D 958 MET cc_start: 0.6797 (mmm) cc_final: 0.6595 (mmm) REVERT: D 1010 MET cc_start: 0.7222 (tmm) cc_final: 0.6867 (tmm) REVERT: D 1022 MET cc_start: 0.7308 (mtm) cc_final: 0.7082 (mtp) REVERT: D 1051 TYR cc_start: 0.8055 (t80) cc_final: 0.7831 (t80) REVERT: D 1053 MET cc_start: 0.7875 (mtt) cc_final: 0.7644 (mtt) REVERT: D 1055 TYR cc_start: 0.7236 (m-80) cc_final: 0.7032 (m-10) REVERT: D 1058 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (p) REVERT: D 1095 MET cc_start: 0.7637 (tpp) cc_final: 0.7288 (tpp) REVERT: D 1099 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 1103 ASN cc_start: 0.7419 (m-40) cc_final: 0.7111 (m110) outliers start: 99 outliers final: 45 residues processed: 560 average time/residue: 0.4120 time to fit residues: 369.0647 Evaluate side-chains 431 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 371 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1099 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 348 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 275 GLN A 279 ASN A 575 ASN A 772 ASN A 933 GLN A 940 GLN A 965 GLN A1115 ASN A1161 GLN B 275 GLN B 279 ASN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1115 ASN B1161 GLN C 275 GLN C 279 ASN C 531 HIS C 575 ASN C 772 ASN C 965 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1161 GLN D 275 GLN D 279 ASN D 965 GLN D1062 GLN D1115 ASN ** D1155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1161 GLN D1199 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087719 restraints weight = 71802.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089869 restraints weight = 45653.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091322 restraints weight = 34287.219| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32238 Z= 0.169 Angle : 0.583 10.189 43603 Z= 0.292 Chirality : 0.040 0.193 4897 Planarity : 0.004 0.053 5416 Dihedral : 7.579 59.812 4688 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.89 % Allowed : 12.39 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3770 helix: 1.70 (0.11), residues: 2402 sheet: 0.30 (0.37), residues: 219 loop : -1.35 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 763 HIS 0.004 0.001 HIS A 151 PHE 0.020 0.001 PHE C1047 TYR 0.011 0.001 TYR C 714 ARG 0.005 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 1735) hydrogen bonds : angle 3.82338 ( 5130) covalent geometry : bond 0.00388 (32238) covalent geometry : angle 0.58336 (43603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 383 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.4205 (m-80) REVERT: A 665 MET cc_start: 0.7755 (mtm) cc_final: 0.7408 (mtm) REVERT: A 669 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8859 (mm) REVERT: A 788 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7424 (pp) REVERT: A 925 MET cc_start: 0.7666 (ppp) cc_final: 0.7295 (ppp) REVERT: A 1010 MET cc_start: 0.7351 (tmm) cc_final: 0.7145 (tmm) REVERT: A 1051 TYR cc_start: 0.8121 (t80) cc_final: 0.6830 (t80) REVERT: A 1055 TYR cc_start: 0.7166 (m-10) cc_final: 0.6355 (m-10) REVERT: A 1103 ASN cc_start: 0.7662 (m-40) cc_final: 0.7259 (m110) REVERT: A 1230 MET cc_start: 0.8605 (ttm) cc_final: 0.8280 (ttm) REVERT: B 266 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5597 (mm) REVERT: B 412 HIS cc_start: 0.2911 (OUTLIER) cc_final: 0.1718 (m-70) REVERT: B 665 MET cc_start: 0.7750 (mtm) cc_final: 0.7401 (mtm) REVERT: B 669 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 764 MET cc_start: 0.9097 (mmt) cc_final: 0.8812 (mmt) REVERT: B 925 MET cc_start: 0.7437 (ppp) cc_final: 0.7158 (ppp) REVERT: B 948 LEU cc_start: 0.8741 (mt) cc_final: 0.8377 (mt) REVERT: B 1049 MET cc_start: 0.6792 (mpp) cc_final: 0.6576 (mpp) REVERT: B 1053 MET cc_start: 0.8037 (mtt) cc_final: 0.7610 (mtt) REVERT: B 1095 MET cc_start: 0.7679 (tpp) cc_final: 0.7250 (tpp) REVERT: B 1230 MET cc_start: 0.8557 (ttm) cc_final: 0.8170 (ttm) REVERT: C 479 TYR cc_start: 0.5252 (OUTLIER) cc_final: 0.3621 (m-80) REVERT: C 665 MET cc_start: 0.7770 (mtm) cc_final: 0.7422 (mtm) REVERT: C 669 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8872 (mm) REVERT: C 778 ILE cc_start: 0.9207 (pt) cc_final: 0.8942 (mt) REVERT: C 1053 MET cc_start: 0.8043 (mtt) cc_final: 0.7608 (mtt) REVERT: C 1095 MET cc_start: 0.7763 (tpp) cc_final: 0.7380 (tpp) REVERT: C 1230 MET cc_start: 0.8548 (ttm) cc_final: 0.7992 (ttm) REVERT: D 633 HIS cc_start: 0.5968 (m90) cc_final: 0.5694 (m90) REVERT: D 665 MET cc_start: 0.7742 (mtm) cc_final: 0.7389 (mtm) REVERT: D 669 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8850 (mm) REVERT: D 764 MET cc_start: 0.9082 (mmt) cc_final: 0.8715 (mmt) REVERT: D 778 ILE cc_start: 0.9220 (pt) cc_final: 0.8954 (mt) REVERT: D 788 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7452 (pp) REVERT: D 958 MET cc_start: 0.7212 (mmm) cc_final: 0.6964 (mmm) REVERT: D 1010 MET cc_start: 0.7311 (tmm) cc_final: 0.6992 (tmm) REVERT: D 1051 TYR cc_start: 0.8154 (t80) cc_final: 0.7795 (t80) REVERT: D 1058 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (p) REVERT: D 1095 MET cc_start: 0.7743 (tpp) cc_final: 0.7224 (tpp) REVERT: D 1099 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 1103 ASN cc_start: 0.7540 (m-40) cc_final: 0.7237 (m110) outliers start: 98 outliers final: 39 residues processed: 452 average time/residue: 0.4017 time to fit residues: 300.2786 Evaluate side-chains 407 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1099 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 279 optimal weight: 0.4980 chunk 312 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 772 ASN A 940 GLN A1115 ASN B 482 GLN B1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D1062 GLN D1155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089260 restraints weight = 71426.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091468 restraints weight = 45103.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092994 restraints weight = 33748.106| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32238 Z= 0.120 Angle : 0.525 8.495 43603 Z= 0.263 Chirality : 0.038 0.165 4897 Planarity : 0.004 0.050 5416 Dihedral : 7.032 61.537 4637 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.51 % Allowed : 13.42 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3770 helix: 1.94 (0.11), residues: 2401 sheet: 0.36 (0.37), residues: 222 loop : -1.28 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 763 HIS 0.008 0.001 HIS B 151 PHE 0.016 0.001 PHE A1047 TYR 0.011 0.001 TYR A1048 ARG 0.002 0.000 ARG B1211 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 1735) hydrogen bonds : angle 3.55719 ( 5130) covalent geometry : bond 0.00265 (32238) covalent geometry : angle 0.52461 (43603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 365 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6624 (t80) cc_final: 0.6385 (t80) REVERT: A 479 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.4090 (m-80) REVERT: A 665 MET cc_start: 0.7739 (mtm) cc_final: 0.7405 (mtm) REVERT: A 669 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 788 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7468 (pp) REVERT: A 1010 MET cc_start: 0.7392 (tmm) cc_final: 0.7116 (tmm) REVERT: A 1051 TYR cc_start: 0.8113 (t80) cc_final: 0.6995 (t80) REVERT: A 1055 TYR cc_start: 0.7185 (m-10) cc_final: 0.6408 (m-10) REVERT: A 1103 ASN cc_start: 0.7566 (m-40) cc_final: 0.7182 (m110) REVERT: A 1230 MET cc_start: 0.8582 (ttm) cc_final: 0.8357 (ttm) REVERT: B 266 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5515 (mm) REVERT: B 412 HIS cc_start: 0.2872 (OUTLIER) cc_final: 0.1737 (m-70) REVERT: B 665 MET cc_start: 0.7736 (mtm) cc_final: 0.7401 (mtm) REVERT: B 669 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 764 MET cc_start: 0.9068 (mmt) cc_final: 0.8721 (mmt) REVERT: B 925 MET cc_start: 0.7459 (ppp) cc_final: 0.7206 (ppp) REVERT: B 948 LEU cc_start: 0.8715 (mt) cc_final: 0.8333 (mt) REVERT: B 1049 MET cc_start: 0.6829 (mpp) cc_final: 0.6591 (mpp) REVERT: B 1053 MET cc_start: 0.8014 (mtt) cc_final: 0.7532 (mtt) REVERT: B 1095 MET cc_start: 0.7686 (tpp) cc_final: 0.7272 (tpp) REVERT: B 1230 MET cc_start: 0.8554 (ttm) cc_final: 0.8163 (ttm) REVERT: C 376 PHE cc_start: 0.6625 (t80) cc_final: 0.6323 (t80) REVERT: C 420 CYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7852 (t) REVERT: C 479 TYR cc_start: 0.5367 (OUTLIER) cc_final: 0.3963 (m-80) REVERT: C 665 MET cc_start: 0.7765 (mtm) cc_final: 0.7437 (mtm) REVERT: C 669 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8829 (mm) REVERT: C 778 ILE cc_start: 0.9209 (pt) cc_final: 0.8964 (mt) REVERT: C 1053 MET cc_start: 0.8016 (mtt) cc_final: 0.7577 (mtt) REVERT: C 1095 MET cc_start: 0.7770 (tpp) cc_final: 0.7259 (tpp) REVERT: C 1230 MET cc_start: 0.8574 (ttm) cc_final: 0.8038 (ttm) REVERT: D 665 MET cc_start: 0.7723 (mtm) cc_final: 0.7388 (mtm) REVERT: D 669 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8807 (mm) REVERT: D 778 ILE cc_start: 0.9181 (pt) cc_final: 0.8938 (mt) REVERT: D 788 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7466 (pp) REVERT: D 958 MET cc_start: 0.7184 (mmm) cc_final: 0.6932 (mmm) REVERT: D 1010 MET cc_start: 0.7466 (tmm) cc_final: 0.7069 (tmm) REVERT: D 1051 TYR cc_start: 0.8101 (t80) cc_final: 0.7776 (t80) REVERT: D 1058 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7377 (p) REVERT: D 1095 MET cc_start: 0.7804 (tpp) cc_final: 0.7277 (tpp) REVERT: D 1099 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 1103 ASN cc_start: 0.7503 (m-40) cc_final: 0.7217 (m110) REVERT: D 1228 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8094 (tm-30) outliers start: 85 outliers final: 43 residues processed: 427 average time/residue: 0.3703 time to fit residues: 266.8765 Evaluate side-chains 413 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1155 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 380 optimal weight: 3.9990 chunk 367 optimal weight: 0.9980 chunk 372 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 321 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 ASN A1115 ASN B1115 ASN C 772 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 575 ASN D1062 GLN D1115 ASN D1155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079351 restraints weight = 74182.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081491 restraints weight = 47315.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082956 restraints weight = 35584.362| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32238 Z= 0.164 Angle : 0.557 10.909 43603 Z= 0.277 Chirality : 0.039 0.169 4897 Planarity : 0.004 0.052 5416 Dihedral : 7.003 64.496 4631 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.24 % Allowed : 13.65 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3770 helix: 2.00 (0.11), residues: 2401 sheet: 0.27 (0.36), residues: 225 loop : -1.22 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.014 0.001 HIS D1155 PHE 0.021 0.001 PHE D1047 TYR 0.012 0.001 TYR B 380 ARG 0.002 0.000 ARG D1143 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 1735) hydrogen bonds : angle 3.58852 ( 5130) covalent geometry : bond 0.00381 (32238) covalent geometry : angle 0.55672 (43603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 369 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6763 (t80) cc_final: 0.6561 (t80) REVERT: A 479 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.4260 (m-80) REVERT: A 665 MET cc_start: 0.7786 (mtm) cc_final: 0.7463 (mtm) REVERT: A 669 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 788 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7413 (pp) REVERT: A 1010 MET cc_start: 0.7639 (tmm) cc_final: 0.7284 (tmm) REVERT: A 1051 TYR cc_start: 0.8196 (t80) cc_final: 0.6886 (t80) REVERT: A 1053 MET cc_start: 0.7892 (ptp) cc_final: 0.7666 (mtp) REVERT: A 1055 TYR cc_start: 0.7091 (m-10) cc_final: 0.6274 (m-10) REVERT: A 1103 ASN cc_start: 0.7488 (m-40) cc_final: 0.7112 (m110) REVERT: B 266 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5579 (mm) REVERT: B 412 HIS cc_start: 0.3282 (OUTLIER) cc_final: 0.2341 (m-70) REVERT: B 665 MET cc_start: 0.7784 (mtm) cc_final: 0.7465 (mtm) REVERT: B 669 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8834 (mm) REVERT: B 764 MET cc_start: 0.9069 (mmt) cc_final: 0.8771 (mmt) REVERT: B 865 TYR cc_start: 0.8334 (t80) cc_final: 0.8127 (t80) REVERT: B 925 MET cc_start: 0.7575 (ppp) cc_final: 0.7326 (ppp) REVERT: B 948 LEU cc_start: 0.8726 (mt) cc_final: 0.8363 (mt) REVERT: B 1049 MET cc_start: 0.6832 (mpp) cc_final: 0.6583 (mpp) REVERT: B 1053 MET cc_start: 0.8012 (mtt) cc_final: 0.7577 (mtt) REVERT: B 1095 MET cc_start: 0.7628 (tpp) cc_final: 0.7197 (tpp) REVERT: B 1230 MET cc_start: 0.8596 (ttm) cc_final: 0.8287 (ttm) REVERT: C 376 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6504 (t80) REVERT: C 479 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.3965 (m-80) REVERT: C 665 MET cc_start: 0.7802 (mtm) cc_final: 0.7492 (mtm) REVERT: C 669 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 778 ILE cc_start: 0.9259 (pt) cc_final: 0.9008 (mt) REVERT: C 948 LEU cc_start: 0.8645 (mt) cc_final: 0.8434 (mt) REVERT: C 1053 MET cc_start: 0.7947 (mtt) cc_final: 0.7531 (mtt) REVERT: C 1095 MET cc_start: 0.7735 (tpp) cc_final: 0.7276 (tpp) REVERT: C 1098 TYR cc_start: 0.8637 (t80) cc_final: 0.8350 (t80) REVERT: C 1138 MET cc_start: 0.8368 (mmt) cc_final: 0.8165 (mpp) REVERT: C 1230 MET cc_start: 0.8574 (ttm) cc_final: 0.8139 (ttm) REVERT: D 665 MET cc_start: 0.7796 (mtm) cc_final: 0.7470 (mtm) REVERT: D 669 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8827 (mm) REVERT: D 778 ILE cc_start: 0.9235 (pt) cc_final: 0.8961 (mt) REVERT: D 788 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7448 (pp) REVERT: D 1010 MET cc_start: 0.7523 (tmm) cc_final: 0.7038 (tmm) REVERT: D 1051 TYR cc_start: 0.8136 (t80) cc_final: 0.7832 (t80) REVERT: D 1095 MET cc_start: 0.7812 (tpp) cc_final: 0.7288 (tpp) REVERT: D 1099 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8504 (mp) REVERT: D 1103 ASN cc_start: 0.7357 (m-40) cc_final: 0.7072 (m110) REVERT: D 1150 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8049 (mt) REVERT: D 1158 MET cc_start: 0.6844 (ptp) cc_final: 0.6396 (ptp) REVERT: D 1228 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 110 outliers final: 61 residues processed: 449 average time/residue: 0.3960 time to fit residues: 300.8405 Evaluate side-chains 437 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 363 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1155 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 155 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN B 575 ASN C 147 GLN C 275 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 ASN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077211 restraints weight = 74558.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080135 restraints weight = 48836.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081161 restraints weight = 34249.306| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 32238 Z= 0.262 Angle : 0.642 9.544 43603 Z= 0.322 Chirality : 0.042 0.238 4897 Planarity : 0.004 0.055 5416 Dihedral : 7.190 71.335 4629 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.83 % Allowed : 14.42 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3770 helix: 1.83 (0.11), residues: 2400 sheet: 0.10 (0.36), residues: 225 loop : -1.28 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 763 HIS 0.005 0.001 HIS D 240 PHE 0.020 0.002 PHE A1047 TYR 0.013 0.002 TYR B 380 ARG 0.006 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 1735) hydrogen bonds : angle 3.84581 ( 5130) covalent geometry : bond 0.00616 (32238) covalent geometry : angle 0.64191 (43603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 372 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 479 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.4121 (m-80) REVERT: A 665 MET cc_start: 0.7889 (mtm) cc_final: 0.7584 (mtm) REVERT: A 669 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 788 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7471 (pp) REVERT: A 1010 MET cc_start: 0.7806 (tmm) cc_final: 0.7426 (tmm) REVERT: A 1051 TYR cc_start: 0.8177 (t80) cc_final: 0.6884 (t80) REVERT: A 1053 MET cc_start: 0.8074 (ptp) cc_final: 0.7868 (mtp) REVERT: A 1055 TYR cc_start: 0.7063 (m-10) cc_final: 0.6170 (m-10) REVERT: A 1103 ASN cc_start: 0.7505 (m-40) cc_final: 0.7237 (m110) REVERT: B 412 HIS cc_start: 0.3220 (OUTLIER) cc_final: 0.2066 (m170) REVERT: B 479 TYR cc_start: 0.5569 (OUTLIER) cc_final: 0.3803 (m-80) REVERT: B 665 MET cc_start: 0.7888 (mtm) cc_final: 0.7585 (mtm) REVERT: B 669 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8756 (mm) REVERT: B 764 MET cc_start: 0.9141 (mmt) cc_final: 0.8914 (mmt) REVERT: B 865 TYR cc_start: 0.8387 (t80) cc_final: 0.8157 (t80) REVERT: B 925 MET cc_start: 0.7603 (ppp) cc_final: 0.7374 (ppp) REVERT: B 948 LEU cc_start: 0.8743 (mt) cc_final: 0.8356 (mt) REVERT: B 1049 MET cc_start: 0.6800 (mpp) cc_final: 0.6567 (mpp) REVERT: B 1053 MET cc_start: 0.7998 (mtt) cc_final: 0.7580 (mtt) REVERT: B 1055 TYR cc_start: 0.7135 (m-10) cc_final: 0.6664 (m-10) REVERT: B 1095 MET cc_start: 0.7659 (tpp) cc_final: 0.7262 (tpp) REVERT: B 1138 MET cc_start: 0.8507 (mmm) cc_final: 0.8234 (mmm) REVERT: B 1155 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5902 (t-170) REVERT: C 376 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.6471 (t80) REVERT: C 479 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.3993 (m-80) REVERT: C 665 MET cc_start: 0.7901 (mtm) cc_final: 0.7588 (mtm) REVERT: C 669 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8738 (mm) REVERT: C 948 LEU cc_start: 0.8675 (mt) cc_final: 0.8446 (mt) REVERT: C 1053 MET cc_start: 0.7972 (mtt) cc_final: 0.7557 (mtm) REVERT: C 1095 MET cc_start: 0.7746 (tpp) cc_final: 0.7316 (tpp) REVERT: C 1230 MET cc_start: 0.8675 (ttm) cc_final: 0.8327 (ttm) REVERT: D 379 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7140 (mmmt) REVERT: D 665 MET cc_start: 0.7889 (mtm) cc_final: 0.7583 (mtm) REVERT: D 669 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8750 (mm) REVERT: D 764 MET cc_start: 0.9192 (mmt) cc_final: 0.8882 (mmt) REVERT: D 778 ILE cc_start: 0.9237 (pt) cc_final: 0.8993 (mt) REVERT: D 788 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7467 (pp) REVERT: D 1010 MET cc_start: 0.7644 (tmm) cc_final: 0.7162 (tmm) REVERT: D 1051 TYR cc_start: 0.8171 (t80) cc_final: 0.7892 (t80) REVERT: D 1095 MET cc_start: 0.7809 (tpp) cc_final: 0.7293 (tpp) REVERT: D 1099 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8533 (mp) REVERT: D 1103 ASN cc_start: 0.7368 (m-40) cc_final: 0.7129 (m110) REVERT: D 1150 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8049 (mp) outliers start: 130 outliers final: 71 residues processed: 469 average time/residue: 0.3986 time to fit residues: 313.0387 Evaluate side-chains 448 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 362 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 295 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 338 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 279 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1115 ASN C 275 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 772 ASN D1062 GLN 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 = 0.3533 r_free = 0.3533 target = 0.099995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080100 restraints weight = 73823.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082314 restraints weight = 47160.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083829 restraints weight = 35270.873| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32238 Z= 0.118 Angle : 0.553 10.122 43603 Z= 0.271 Chirality : 0.039 0.199 4897 Planarity : 0.004 0.053 5416 Dihedral : 6.980 65.586 4629 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.01 % Allowed : 16.22 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.14), residues: 3770 helix: 2.08 (0.11), residues: 2403 sheet: 0.37 (0.37), residues: 219 loop : -1.23 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.011 0.001 HIS D1155 PHE 0.018 0.001 PHE A1047 TYR 0.014 0.001 TYR D 865 ARG 0.004 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1735) hydrogen bonds : angle 3.45712 ( 5130) covalent geometry : bond 0.00260 (32238) covalent geometry : angle 0.55299 (43603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 369 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 479 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.4186 (m-80) REVERT: A 642 MET cc_start: 0.8588 (tpp) cc_final: 0.8318 (tpp) REVERT: A 665 MET cc_start: 0.7775 (mtm) cc_final: 0.7541 (ttp) REVERT: A 669 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8783 (mm) REVERT: A 788 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 985 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.8047 (ttm-80) REVERT: A 1010 MET cc_start: 0.7589 (tmm) cc_final: 0.7270 (tmm) REVERT: A 1051 TYR cc_start: 0.8173 (t80) cc_final: 0.7015 (t80) REVERT: A 1055 TYR cc_start: 0.7111 (m-10) cc_final: 0.6251 (m-10) REVERT: A 1103 ASN cc_start: 0.7482 (m-40) cc_final: 0.7116 (m110) REVERT: B 412 HIS cc_start: 0.3165 (OUTLIER) cc_final: 0.1995 (m-70) REVERT: B 479 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.3807 (m-80) REVERT: B 642 MET cc_start: 0.8572 (tpp) cc_final: 0.8312 (tpp) REVERT: B 665 MET cc_start: 0.7781 (mtm) cc_final: 0.7541 (ttp) REVERT: B 669 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8800 (mm) REVERT: B 764 MET cc_start: 0.9057 (mmt) cc_final: 0.8735 (mmt) REVERT: B 865 TYR cc_start: 0.8351 (t80) cc_final: 0.8096 (t80) REVERT: B 925 MET cc_start: 0.7566 (ppp) cc_final: 0.7280 (ppp) REVERT: B 948 LEU cc_start: 0.8705 (mt) cc_final: 0.8358 (mt) REVERT: B 1049 MET cc_start: 0.6868 (mpp) cc_final: 0.6652 (mpp) REVERT: B 1053 MET cc_start: 0.7970 (mtt) cc_final: 0.7534 (mtt) REVERT: B 1095 MET cc_start: 0.7578 (tpp) cc_final: 0.7177 (tpp) REVERT: B 1155 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.5825 (t-170) REVERT: C 479 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4039 (m-80) REVERT: C 642 MET cc_start: 0.8590 (tpp) cc_final: 0.8319 (tpp) REVERT: C 665 MET cc_start: 0.7791 (mtm) cc_final: 0.7559 (ttp) REVERT: C 669 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 1053 MET cc_start: 0.7906 (mtt) cc_final: 0.7509 (mtt) REVERT: C 1095 MET cc_start: 0.7679 (tpp) cc_final: 0.7205 (tpp) REVERT: C 1098 TYR cc_start: 0.8606 (t80) cc_final: 0.8358 (t80) REVERT: C 1230 MET cc_start: 0.8566 (ttm) cc_final: 0.8237 (ttm) REVERT: D 154 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (mmtt) REVERT: D 379 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6902 (mmmt) REVERT: D 479 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.3893 (m-80) REVERT: D 642 MET cc_start: 0.8586 (tpp) cc_final: 0.8305 (tpp) REVERT: D 665 MET cc_start: 0.7773 (mtm) cc_final: 0.7540 (ttp) REVERT: D 669 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8787 (mm) REVERT: D 764 MET cc_start: 0.9159 (mmt) cc_final: 0.8789 (mmt) REVERT: D 778 ILE cc_start: 0.9220 (pt) cc_final: 0.8959 (mt) REVERT: D 788 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7383 (pp) REVERT: D 1010 MET cc_start: 0.7578 (tmm) cc_final: 0.7056 (tmm) REVERT: D 1051 TYR cc_start: 0.8145 (t80) cc_final: 0.7859 (t80) REVERT: D 1095 MET cc_start: 0.7827 (tpp) cc_final: 0.7407 (tpp) REVERT: D 1103 ASN cc_start: 0.7409 (m-40) cc_final: 0.7141 (m110) REVERT: D 1158 MET cc_start: 0.6738 (ptp) cc_final: 0.6537 (ptp) outliers start: 102 outliers final: 50 residues processed: 444 average time/residue: 0.3739 time to fit residues: 278.3678 Evaluate side-chains 426 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 362 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1155 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 162 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 250 optimal weight: 4.9990 chunk 367 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 308 optimal weight: 0.7980 chunk 320 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1116 ASN D 147 GLN D1062 GLN D1115 ASN D1155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090489 restraints weight = 69133.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092613 restraints weight = 44755.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093894 restraints weight = 34409.964| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32238 Z= 0.124 Angle : 0.562 10.628 43603 Z= 0.273 Chirality : 0.039 0.191 4897 Planarity : 0.004 0.053 5416 Dihedral : 6.815 62.090 4621 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.01 % Allowed : 16.37 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3770 helix: 2.13 (0.11), residues: 2403 sheet: 0.45 (0.37), residues: 219 loop : -1.20 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.006 0.001 HIS B 240 PHE 0.024 0.001 PHE D1047 TYR 0.014 0.001 TYR D 865 ARG 0.015 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1735) hydrogen bonds : angle 3.43489 ( 5130) covalent geometry : bond 0.00279 (32238) covalent geometry : angle 0.56191 (43603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 366 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6495 (t80) REVERT: A 479 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4217 (m-80) REVERT: A 665 MET cc_start: 0.7819 (mtm) cc_final: 0.7560 (ttp) REVERT: A 669 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 788 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7605 (pp) REVERT: A 985 ARG cc_start: 0.8447 (tmm-80) cc_final: 0.8086 (ttm-80) REVERT: A 1010 MET cc_start: 0.7600 (tmm) cc_final: 0.7242 (tmm) REVERT: A 1051 TYR cc_start: 0.8139 (t80) cc_final: 0.7024 (t80) REVERT: A 1053 MET cc_start: 0.7970 (mtp) cc_final: 0.7740 (mtt) REVERT: A 1055 TYR cc_start: 0.7183 (m-10) cc_final: 0.6257 (m-10) REVERT: A 1103 ASN cc_start: 0.7546 (m-40) cc_final: 0.7230 (m110) REVERT: B 266 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5594 (mm) REVERT: B 412 HIS cc_start: 0.3519 (OUTLIER) cc_final: 0.2247 (m-70) REVERT: B 479 TYR cc_start: 0.5269 (OUTLIER) cc_final: 0.3762 (m-80) REVERT: B 665 MET cc_start: 0.7817 (mtm) cc_final: 0.7562 (ttp) REVERT: B 669 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8851 (mm) REVERT: B 764 MET cc_start: 0.9028 (mmt) cc_final: 0.8647 (mmt) REVERT: B 925 MET cc_start: 0.7553 (ppp) cc_final: 0.7330 (ppp) REVERT: B 948 LEU cc_start: 0.8701 (mt) cc_final: 0.8328 (mt) REVERT: B 1053 MET cc_start: 0.7992 (mtt) cc_final: 0.7532 (mtt) REVERT: B 1055 TYR cc_start: 0.7250 (m-10) cc_final: 0.6707 (m-10) REVERT: B 1095 MET cc_start: 0.7646 (tpp) cc_final: 0.7219 (tpp) REVERT: B 1098 TYR cc_start: 0.8593 (t80) cc_final: 0.8316 (t80) REVERT: C 479 TYR cc_start: 0.5203 (OUTLIER) cc_final: 0.3968 (m-80) REVERT: C 665 MET cc_start: 0.7830 (mtm) cc_final: 0.7576 (ttp) REVERT: C 669 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 1053 MET cc_start: 0.7908 (mtt) cc_final: 0.7499 (mtt) REVERT: C 1095 MET cc_start: 0.7767 (tpp) cc_final: 0.7292 (tpp) REVERT: C 1098 TYR cc_start: 0.8646 (t80) cc_final: 0.8373 (t80) REVERT: D 379 LYS cc_start: 0.7310 (ttmt) cc_final: 0.7061 (mmmt) REVERT: D 479 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.3833 (m-80) REVERT: D 665 MET cc_start: 0.7800 (mtm) cc_final: 0.7539 (ttp) REVERT: D 669 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8837 (mm) REVERT: D 764 MET cc_start: 0.9098 (mmt) cc_final: 0.8728 (mmt) REVERT: D 1010 MET cc_start: 0.7560 (tmm) cc_final: 0.7065 (tmm) REVERT: D 1051 TYR cc_start: 0.8165 (t80) cc_final: 0.7883 (t80) REVERT: D 1095 MET cc_start: 0.7999 (tpp) cc_final: 0.7686 (tpp) REVERT: D 1099 LEU cc_start: 0.8802 (mp) cc_final: 0.8396 (mt) REVERT: D 1103 ASN cc_start: 0.7469 (m-40) cc_final: 0.7162 (m110) REVERT: D 1158 MET cc_start: 0.6486 (ptp) cc_final: 0.6138 (ptp) outliers start: 102 outliers final: 61 residues processed: 443 average time/residue: 0.3723 time to fit residues: 275.7304 Evaluate side-chains 434 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1031 ILE Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1155 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 261 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 GLN D1155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093468 restraints weight = 69389.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095895 restraints weight = 44856.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097538 restraints weight = 33138.268| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32238 Z= 0.117 Angle : 0.576 12.984 43603 Z= 0.277 Chirality : 0.038 0.193 4897 Planarity : 0.004 0.075 5416 Dihedral : 6.779 59.560 4621 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.62 % Allowed : 16.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3770 helix: 2.17 (0.11), residues: 2403 sheet: 0.54 (0.37), residues: 219 loop : -1.15 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 763 HIS 0.006 0.001 HIS B 240 PHE 0.034 0.001 PHE A1024 TYR 0.015 0.001 TYR D 865 ARG 0.019 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 1735) hydrogen bonds : angle 3.40062 ( 5130) covalent geometry : bond 0.00258 (32238) covalent geometry : angle 0.57554 (43603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 365 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6820 (t80) cc_final: 0.6530 (t80) REVERT: A 479 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.4200 (m-80) REVERT: A 642 MET cc_start: 0.8578 (tpp) cc_final: 0.8371 (tpp) REVERT: A 665 MET cc_start: 0.7784 (mtm) cc_final: 0.7507 (ttp) REVERT: A 669 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 788 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7589 (pp) REVERT: A 985 ARG cc_start: 0.8467 (tmm-80) cc_final: 0.8067 (ttm-80) REVERT: A 1010 MET cc_start: 0.7569 (tmm) cc_final: 0.7190 (tmm) REVERT: A 1051 TYR cc_start: 0.8172 (t80) cc_final: 0.7161 (t80) REVERT: A 1055 TYR cc_start: 0.7230 (m-10) cc_final: 0.6326 (m-10) REVERT: A 1103 ASN cc_start: 0.7529 (m-40) cc_final: 0.7271 (m110) REVERT: B 266 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5580 (mm) REVERT: B 479 TYR cc_start: 0.5162 (OUTLIER) cc_final: 0.3625 (m-80) REVERT: B 665 MET cc_start: 0.7823 (mtm) cc_final: 0.7543 (ttp) REVERT: B 669 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 764 MET cc_start: 0.9002 (mmt) cc_final: 0.8638 (mmt) REVERT: B 925 MET cc_start: 0.7621 (ppp) cc_final: 0.7365 (ppp) REVERT: B 948 LEU cc_start: 0.8677 (mt) cc_final: 0.8313 (mt) REVERT: B 1053 MET cc_start: 0.8020 (mtt) cc_final: 0.7552 (mtt) REVERT: B 1055 TYR cc_start: 0.7231 (m-10) cc_final: 0.6733 (m-10) REVERT: B 1095 MET cc_start: 0.7703 (tpp) cc_final: 0.7252 (tpp) REVERT: B 1098 TYR cc_start: 0.8585 (t80) cc_final: 0.8329 (t80) REVERT: C 479 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.3874 (m-80) REVERT: C 642 MET cc_start: 0.8590 (tpp) cc_final: 0.8389 (tpp) REVERT: C 665 MET cc_start: 0.7786 (mtm) cc_final: 0.7505 (ttp) REVERT: C 669 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8812 (mm) REVERT: C 1053 MET cc_start: 0.7905 (mtt) cc_final: 0.7482 (mtt) REVERT: C 1095 MET cc_start: 0.7748 (tpp) cc_final: 0.7299 (tpp) REVERT: C 1098 TYR cc_start: 0.8645 (t80) cc_final: 0.8388 (t80) REVERT: C 1103 ASN cc_start: 0.7711 (m-40) cc_final: 0.7346 (m-40) REVERT: C 1138 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: D 379 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6990 (mmmt) REVERT: D 479 TYR cc_start: 0.5137 (OUTLIER) cc_final: 0.4050 (m-80) REVERT: D 642 MET cc_start: 0.8539 (tpp) cc_final: 0.8321 (tpp) REVERT: D 665 MET cc_start: 0.7773 (mtm) cc_final: 0.7481 (ttp) REVERT: D 669 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8793 (mm) REVERT: D 788 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (pp) REVERT: D 1010 MET cc_start: 0.7539 (tmm) cc_final: 0.6993 (tmm) REVERT: D 1051 TYR cc_start: 0.8148 (t80) cc_final: 0.7857 (t80) REVERT: D 1095 MET cc_start: 0.7838 (tpp) cc_final: 0.7446 (tpp) REVERT: D 1099 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 1103 ASN cc_start: 0.7479 (m-40) cc_final: 0.7155 (m110) REVERT: D 1158 MET cc_start: 0.6503 (ptp) cc_final: 0.6172 (ptp) outliers start: 89 outliers final: 59 residues processed: 428 average time/residue: 0.3771 time to fit residues: 268.5696 Evaluate side-chains 429 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 357 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1031 ILE Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 38 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 373 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN A1126 ASN B1115 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092508 restraints weight = 69411.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094375 restraints weight = 45797.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096671 restraints weight = 34576.047| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32238 Z= 0.160 Angle : 0.619 15.220 43603 Z= 0.297 Chirality : 0.039 0.190 4897 Planarity : 0.004 0.055 5416 Dihedral : 6.824 61.297 4615 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.45 % Allowed : 17.10 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.14), residues: 3770 helix: 2.13 (0.11), residues: 2402 sheet: 0.49 (0.37), residues: 219 loop : -1.15 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.009 0.001 HIS D1155 PHE 0.027 0.001 PHE A1024 TYR 0.016 0.001 TYR D 865 ARG 0.005 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 1735) hydrogen bonds : angle 3.50397 ( 5130) covalent geometry : bond 0.00372 (32238) covalent geometry : angle 0.61873 (43603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 358 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6496 (t80) REVERT: A 479 TYR cc_start: 0.5460 (OUTLIER) cc_final: 0.4265 (m-80) REVERT: A 642 MET cc_start: 0.8653 (tpp) cc_final: 0.8386 (tpp) REVERT: A 665 MET cc_start: 0.7848 (mtm) cc_final: 0.7521 (mtm) REVERT: A 669 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8850 (mm) REVERT: A 788 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7610 (pp) REVERT: A 985 ARG cc_start: 0.8496 (tmm-80) cc_final: 0.8068 (ttm-80) REVERT: A 1010 MET cc_start: 0.7618 (tmm) cc_final: 0.7249 (tmm) REVERT: A 1051 TYR cc_start: 0.8138 (t80) cc_final: 0.7051 (t80) REVERT: A 1055 TYR cc_start: 0.7243 (m-10) cc_final: 0.6328 (m-10) REVERT: A 1103 ASN cc_start: 0.7581 (m-40) cc_final: 0.7315 (m110) REVERT: B 266 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5653 (mm) REVERT: B 277 MET cc_start: 0.6141 (mmm) cc_final: 0.5621 (mtt) REVERT: B 479 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.3909 (m-80) REVERT: B 665 MET cc_start: 0.7887 (mtm) cc_final: 0.7563 (mtm) REVERT: B 669 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 764 MET cc_start: 0.8995 (mmt) cc_final: 0.8661 (mmt) REVERT: B 865 TYR cc_start: 0.8505 (t80) cc_final: 0.8228 (t80) REVERT: B 925 MET cc_start: 0.7674 (ppp) cc_final: 0.7440 (ppp) REVERT: B 948 LEU cc_start: 0.8691 (mt) cc_final: 0.8323 (mt) REVERT: B 1053 MET cc_start: 0.8012 (mtt) cc_final: 0.7538 (mtt) REVERT: B 1055 TYR cc_start: 0.7256 (m-10) cc_final: 0.6714 (m-10) REVERT: B 1095 MET cc_start: 0.7732 (tpp) cc_final: 0.7293 (tpp) REVERT: B 1098 TYR cc_start: 0.8656 (t80) cc_final: 0.8398 (t80) REVERT: C 376 PHE cc_start: 0.6883 (t80) cc_final: 0.6672 (t80) REVERT: C 479 TYR cc_start: 0.5210 (OUTLIER) cc_final: 0.3991 (m-80) REVERT: C 642 MET cc_start: 0.8664 (tpp) cc_final: 0.8389 (tpp) REVERT: C 665 MET cc_start: 0.7850 (mtm) cc_final: 0.7569 (ttp) REVERT: C 669 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 1053 MET cc_start: 0.7915 (mtt) cc_final: 0.7517 (mtt) REVERT: C 1095 MET cc_start: 0.7767 (tpp) cc_final: 0.7321 (tpp) REVERT: C 1098 TYR cc_start: 0.8697 (t80) cc_final: 0.8447 (t80) REVERT: C 1103 ASN cc_start: 0.7746 (m-40) cc_final: 0.7387 (m-40) REVERT: D 479 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.3981 (m-80) REVERT: D 642 MET cc_start: 0.8631 (tpp) cc_final: 0.8362 (tpp) REVERT: D 665 MET cc_start: 0.7837 (mtm) cc_final: 0.7518 (mtm) REVERT: D 669 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8859 (mm) REVERT: D 788 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7605 (pp) REVERT: D 1010 MET cc_start: 0.7719 (tmm) cc_final: 0.7218 (tmm) REVERT: D 1051 TYR cc_start: 0.8178 (t80) cc_final: 0.7873 (t80) REVERT: D 1095 MET cc_start: 0.7866 (tpp) cc_final: 0.7494 (tpp) REVERT: D 1099 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8344 (mt) REVERT: D 1103 ASN cc_start: 0.7579 (m-40) cc_final: 0.7231 (m110) outliers start: 83 outliers final: 59 residues processed: 418 average time/residue: 0.3749 time to fit residues: 262.4263 Evaluate side-chains 425 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 353 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 195 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 328 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089550 restraints weight = 69402.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091549 restraints weight = 44905.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092686 restraints weight = 34683.949| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32238 Z= 0.162 Angle : 0.628 12.189 43603 Z= 0.302 Chirality : 0.040 0.202 4897 Planarity : 0.004 0.055 5416 Dihedral : 6.734 62.797 4611 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.39 % Allowed : 17.16 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.14), residues: 3770 helix: 2.10 (0.11), residues: 2398 sheet: 0.50 (0.37), residues: 219 loop : -1.15 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.007 0.001 HIS B 240 PHE 0.026 0.001 PHE A1047 TYR 0.017 0.001 TYR D 865 ARG 0.004 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 1735) hydrogen bonds : angle 3.54288 ( 5130) covalent geometry : bond 0.00376 (32238) covalent geometry : angle 0.62807 (43603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 358 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 TYR cc_start: 0.5200 (OUTLIER) cc_final: 0.4042 (m-80) REVERT: A 642 MET cc_start: 0.8650 (tpp) cc_final: 0.8377 (tpp) REVERT: A 665 MET cc_start: 0.7749 (mtm) cc_final: 0.7414 (mtm) REVERT: A 669 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 788 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (pp) REVERT: A 985 ARG cc_start: 0.8475 (tmm-80) cc_final: 0.8087 (ttm-80) REVERT: A 1010 MET cc_start: 0.7633 (tmm) cc_final: 0.7260 (tmm) REVERT: A 1051 TYR cc_start: 0.8116 (t80) cc_final: 0.6789 (t80) REVERT: A 1055 TYR cc_start: 0.7226 (m-10) cc_final: 0.6259 (m-10) REVERT: A 1103 ASN cc_start: 0.7574 (m-40) cc_final: 0.7286 (m110) REVERT: B 412 HIS cc_start: 0.3538 (OUTLIER) cc_final: 0.2160 (m-70) REVERT: B 479 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.3904 (m-80) REVERT: B 665 MET cc_start: 0.7822 (mtm) cc_final: 0.7572 (ttp) REVERT: B 669 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8870 (mm) REVERT: B 925 MET cc_start: 0.7709 (ppp) cc_final: 0.7451 (ppp) REVERT: B 948 LEU cc_start: 0.8641 (mt) cc_final: 0.8193 (mt) REVERT: B 1053 MET cc_start: 0.7985 (mtt) cc_final: 0.7508 (mtt) REVERT: B 1055 TYR cc_start: 0.7247 (m-10) cc_final: 0.6682 (m-10) REVERT: B 1095 MET cc_start: 0.7682 (tpp) cc_final: 0.7231 (tpp) REVERT: B 1098 TYR cc_start: 0.8644 (t80) cc_final: 0.8408 (t80) REVERT: C 479 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.3986 (m-80) REVERT: C 642 MET cc_start: 0.8649 (tpp) cc_final: 0.8377 (tpp) REVERT: C 665 MET cc_start: 0.7774 (mtm) cc_final: 0.7445 (mtm) REVERT: C 669 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8878 (mm) REVERT: C 1053 MET cc_start: 0.7856 (mtt) cc_final: 0.7452 (mtt) REVERT: C 1095 MET cc_start: 0.7784 (tpp) cc_final: 0.7343 (tpp) REVERT: C 1098 TYR cc_start: 0.8698 (t80) cc_final: 0.8441 (t80) REVERT: C 1103 ASN cc_start: 0.7715 (m-40) cc_final: 0.7368 (m-40) REVERT: D 240 HIS cc_start: 0.7515 (t-90) cc_final: 0.7259 (t-90) REVERT: D 479 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.3984 (m-80) REVERT: D 642 MET cc_start: 0.8643 (tpp) cc_final: 0.8368 (tpp) REVERT: D 665 MET cc_start: 0.7808 (mtm) cc_final: 0.7562 (ttp) REVERT: D 669 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 788 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7585 (pp) REVERT: D 1010 MET cc_start: 0.7576 (tmm) cc_final: 0.7029 (tmm) REVERT: D 1051 TYR cc_start: 0.8178 (t80) cc_final: 0.7866 (t80) REVERT: D 1095 MET cc_start: 0.7852 (tpp) cc_final: 0.7487 (tpp) REVERT: D 1099 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8315 (mt) REVERT: D 1103 ASN cc_start: 0.7570 (m-40) cc_final: 0.7209 (m110) outliers start: 81 outliers final: 60 residues processed: 417 average time/residue: 0.3739 time to fit residues: 261.2778 Evaluate side-chains 424 residues out of total 3391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1150 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 301 optimal weight: 0.0970 chunk 316 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B1115 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081088 restraints weight = 73438.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083254 restraints weight = 46392.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084770 restraints weight = 34716.299| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32238 Z= 0.117 Angle : 0.605 12.095 43603 Z= 0.289 Chirality : 0.038 0.218 4897 Planarity : 0.004 0.054 5416 Dihedral : 6.650 59.583 4611 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.15 % Allowed : 17.34 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.14), residues: 3770 helix: 2.18 (0.11), residues: 2392 sheet: 0.57 (0.37), residues: 220 loop : -1.08 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.006 0.001 HIS B 240 PHE 0.026 0.001 PHE A1024 TYR 0.017 0.001 TYR C 865 ARG 0.009 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1735) hydrogen bonds : angle 3.42187 ( 5130) covalent geometry : bond 0.00259 (32238) covalent geometry : angle 0.60508 (43603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9156.41 seconds wall clock time: 161 minutes 43.04 seconds (9703.04 seconds total)