Starting phenix.real_space_refine on Thu Aug 6 17:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdu_17621/08_2026/8pdu_17621.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10586 2.51 5 N 2692 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16210 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8082 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 29, 'TRANS': 992} Chain breaks: 5 Chain: "B" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8082 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 29, 'TRANS': 992} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.20 Number of scatterers: 16210 At special positions: 0 Unit cell: (115.486, 156.366, 126.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 2844 8.00 N 2692 7.00 C 10586 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: 1.15 Conformation dependent library (CDL) restraints added in 491.4 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 78.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.734A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.184A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.904A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 removed outlier: 4.125A pdb=" N GLN A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.583A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.562A pdb=" N ALA A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 removed outlier: 3.835A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.515A pdb=" N VAL A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.549A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 removed outlier: 3.576A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.642A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 382 No H-bonds generated for 'chain 'A' and resid 381 through 382' Processing helix chain 'A' and resid 383 through 413 Proline residue: A 408 - end of helix removed outlier: 3.718A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.252A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 5.283A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 572 through 600 removed outlier: 3.830A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.058A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.722A pdb=" N ASP A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 removed outlier: 3.767A pdb=" N LYS A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.628A pdb=" N HIS A 676 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 706 removed outlier: 4.326A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 3.674A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 3.647A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.927A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 780 Processing helix chain 'A' and resid 798 through 858 removed outlier: 4.086A pdb=" N LEU A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.674A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.801A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 920 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.579A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 4.242A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1045 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.735A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.184A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.904A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 removed outlier: 4.125A pdb=" N GLN B 140 " --> pdb=" O HIS B 136 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.584A pdb=" N LEU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.562A pdb=" N ALA B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 251 removed outlier: 3.836A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.515A pdb=" N VAL B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 318 removed outlier: 3.549A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 removed outlier: 3.577A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.643A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 382 No H-bonds generated for 'chain 'B' and resid 381 through 382' Processing helix chain 'B' and resid 383 through 413 Proline residue: B 408 - end of helix removed outlier: 3.717A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 449 through 469 removed outlier: 4.251A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 5.282A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 572 through 600 removed outlier: 3.830A pdb=" N ASP B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.058A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 removed outlier: 3.723A pdb=" N ASP B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 removed outlier: 3.768A pdb=" N LYS B 656 " --> pdb=" O SER B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.628A pdb=" N HIS B 676 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 706 removed outlier: 4.326A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix removed outlier: 3.674A pdb=" N PHE B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 755 removed outlier: 3.647A pdb=" N ALA B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.926A pdb=" N ILE B 759 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 780 Processing helix chain 'B' and resid 798 through 858 removed outlier: 4.086A pdb=" N LEU B 804 " --> pdb=" O LYS B 800 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 807 " --> pdb=" O ARG B 803 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.674A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.801A pdb=" N GLN B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 887 " --> pdb=" O GLY B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 920 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.579A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 removed outlier: 4.242A pdb=" N LYS B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 977 Processing helix chain 'B' and resid 1045 through 1050 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1108 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1123 Processing helix chain 'B' and resid 1128 through 1132 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.211A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.863A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.183A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 removed outlier: 3.755A pdb=" N ALA A1152 " --> pdb=" O ILE A1161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.211A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.863A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.183A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1134 through 1136 removed outlier: 3.754A pdb=" N ALA B1152 " --> pdb=" O ILE B1161 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3456 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: 2.97 Time building geometry restraints manager: 1.45 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: 5126 1.34 - 1.46: 3685 1.46 - 1.58: 7555 1.58 - 1.70: 4 1.70 - 1.82: 158 Bond restraints: 16528 Sorted by residual: bond pdb=" O1A PCG B1401 " pdb=" PA PCG B1401 " ideal model delta sigma weight residual 1.582 1.468 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" O1A PCG A1401 " pdb=" PA PCG A1401 " ideal model delta sigma weight residual 1.582 1.468 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C5 PCG A1401 " pdb=" C6 PCG A1401 " ideal model delta sigma weight residual 1.425 1.329 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5 PCG B1401 " pdb=" C6 PCG B1401 " ideal model delta sigma weight residual 1.425 1.329 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C8 PCG B1401 " pdb=" N9 PCG B1401 " ideal model delta sigma weight residual 1.375 1.327 0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 16523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 22167 2.14 - 4.29: 217 4.29 - 6.43: 18 6.43 - 8.58: 10 8.58 - 10.72: 8 Bond angle restraints: 22420 Sorted by residual: angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 112.96 107.11 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" N VAL B 137 " pdb=" CA VAL B 137 " pdb=" C VAL B 137 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" O1A PCG A1401 " pdb=" PA PCG A1401 " pdb=" O3' PCG A1401 " ideal model delta sigma weight residual 100.83 111.55 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1A PCG B1401 " pdb=" PA PCG B1401 " pdb=" O3' PCG B1401 " ideal model delta sigma weight residual 100.83 111.52 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N ILE B 657 " pdb=" CA ILE B 657 " pdb=" C ILE B 657 " ideal model delta sigma weight residual 111.62 108.84 2.78 7.90e-01 1.60e+00 1.24e+01 ... (remaining 22415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 9728 35.06 - 70.12: 170 70.12 - 105.18: 6 105.18 - 140.24: 4 140.24 - 175.30: 2 Dihedral angle restraints: 9910 sinusoidal: 3960 harmonic: 5950 Sorted by residual: dihedral pdb=" C3' PCG B1401 " pdb=" O3' PCG B1401 " pdb=" PA PCG B1401 " pdb=" O2A PCG B1401 " ideal model delta sinusoidal sigma weight residual -80.91 94.39 -175.30 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3' PCG A1401 " pdb=" O3' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " ideal model delta sinusoidal sigma weight residual -80.91 94.36 -175.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5' PCG A1401 " pdb=" O5' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " ideal model delta sinusoidal sigma weight residual 81.13 -44.80 125.93 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 9907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2636 0.095 - 0.189: 56 0.189 - 0.284: 2 0.284 - 0.379: 0 0.379 - 0.473: 2 Chirality restraints: 2696 Sorted by residual: chirality pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " pdb=" O3' PCG A1401 " pdb=" O5' PCG A1401 " both_signs ideal model delta sigma weight residual True 2.70 -3.17 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" PA PCG B1401 " pdb=" O2A PCG B1401 " pdb=" O3' PCG B1401 " pdb=" O5' PCG B1401 " both_signs ideal model delta sigma weight residual True 2.70 -3.17 -0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" C3' PCG B1401 " pdb=" C2' PCG B1401 " pdb=" C4' PCG B1401 " pdb=" O3' PCG B1401 " both_signs ideal model delta sigma weight residual False -2.45 -2.66 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2693 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 693 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 694 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 693 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 694 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 295 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C ASN A 295 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 295 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 296 " 0.008 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2516 2.76 - 3.29: 16937 3.29 - 3.83: 26005 3.83 - 4.36: 30631 4.36 - 4.90: 53240 Nonbonded interactions: 129329 Sorted by model distance: nonbonded pdb=" SD MET B 602 " pdb=" CG GLU B1115 " model vdw 2.221 3.800 nonbonded pdb=" SD MET A 602 " pdb=" CG GLU A1115 " model vdw 2.221 3.800 nonbonded pdb=" O ASP A 534 " pdb=" OD1 ASP A 534 " model vdw 2.256 3.040 nonbonded pdb=" O ASP B 534 " pdb=" OD1 ASP B 534 " model vdw 2.256 3.040 nonbonded pdb=" O VAL B 115 " pdb=" OG SER B 118 " model vdw 2.262 3.040 ... (remaining 129324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 16528 Z= 0.155 Angle : 0.594 10.721 22420 Z= 0.319 Chirality : 0.040 0.473 2696 Planarity : 0.003 0.049 2748 Dihedral : 13.854 175.299 6050 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2020 helix: 0.96 (0.13), residues: 1464 sheet: -0.31 (0.80), residues: 48 loop : -0.36 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 499 TYR 0.007 0.001 TYR B 309 PHE 0.014 0.001 PHE B 457 TRP 0.011 0.001 TRP B 278 HIS 0.007 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (16528) covalent geometry : angle 0.59363 / 0.32 (22420) hydrogen bonds : bond 0.18975 / 12.95 ( 1174) hydrogen bonds : angle 6.80419 / 5.12 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.426 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: A 76 LYS cc_start: 0.7895 (mttm) cc_final: 0.7611 (mttm) REVERT: A 113 LEU cc_start: 0.7529 (mt) cc_final: 0.7159 (mp) REVERT: A 120 VAL cc_start: 0.6948 (t) cc_final: 0.6513 (p) REVERT: A 125 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 128 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6701 (ptp-110) REVERT: A 154 MET cc_start: 0.8212 (tpp) cc_final: 0.7681 (mmt) REVERT: A 224 LYS cc_start: 0.7931 (pttt) cc_final: 0.7377 (pttt) REVERT: A 233 GLU cc_start: 0.7764 (tt0) cc_final: 0.6784 (pt0) REVERT: A 270 GLN cc_start: 0.7638 (mt0) cc_final: 0.7430 (mt0) REVERT: A 289 PHE cc_start: 0.8010 (m-80) cc_final: 0.7787 (m-80) REVERT: A 296 ASP cc_start: 0.7818 (t0) cc_final: 0.7466 (t0) REVERT: A 300 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 320 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7396 (mm-30) REVERT: A 337 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 377 LEU cc_start: 0.7971 (mt) cc_final: 0.7769 (mt) REVERT: A 384 ASP cc_start: 0.7008 (m-30) cc_final: 0.6709 (m-30) REVERT: A 406 PHE cc_start: 0.6637 (m-80) cc_final: 0.6393 (m-80) REVERT: A 444 ASN cc_start: 0.7251 (m-40) cc_final: 0.6962 (m110) REVERT: A 475 GLN cc_start: 0.7319 (tp40) cc_final: 0.7011 (tp40) REVERT: A 494 MET cc_start: 0.6833 (tpp) cc_final: 0.6543 (mmm) REVERT: A 499 ARG cc_start: 0.7085 (ttt180) cc_final: 0.6839 (ttt180) REVERT: A 503 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 513 LYS cc_start: 0.7775 (mttt) cc_final: 0.7555 (mttp) REVERT: A 517 PHE cc_start: 0.7073 (m-10) cc_final: 0.6688 (m-10) REVERT: A 579 MET cc_start: 0.5493 (mtp) cc_final: 0.5243 (mtp) REVERT: A 580 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6192 (tp30) REVERT: A 608 LEU cc_start: 0.7462 (tp) cc_final: 0.7184 (tp) REVERT: A 609 ARG cc_start: 0.7480 (mtp-110) cc_final: 0.7148 (mtp180) REVERT: A 612 VAL cc_start: 0.6676 (t) cc_final: 0.6467 (m) REVERT: A 613 GLN cc_start: 0.6713 (tt0) cc_final: 0.6506 (tt0) REVERT: A 629 ASP cc_start: 0.7675 (m-30) cc_final: 0.7351 (m-30) REVERT: A 630 ASP cc_start: 0.7867 (m-30) cc_final: 0.7632 (m-30) REVERT: A 643 TRP cc_start: 0.7707 (t60) cc_final: 0.7503 (t60) REVERT: A 647 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7802 (mmtm) REVERT: A 650 ASP cc_start: 0.8099 (m-30) cc_final: 0.7818 (m-30) REVERT: A 678 MET cc_start: 0.7305 (mmm) cc_final: 0.6782 (mmm) REVERT: A 837 TYR cc_start: 0.7523 (m-80) cc_final: 0.7106 (m-80) REVERT: A 877 GLN cc_start: 0.7258 (mt0) cc_final: 0.7038 (mt0) REVERT: A 881 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 931 GLU cc_start: 0.7031 (tt0) cc_final: 0.6755 (tt0) REVERT: A 967 MET cc_start: 0.6351 (mtp) cc_final: 0.5912 (mtp) REVERT: A 971 ASP cc_start: 0.7117 (m-30) cc_final: 0.6662 (m-30) REVERT: A 976 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7262 (mmt-90) REVERT: A 982 PHE cc_start: 0.6890 (m-80) cc_final: 0.6645 (m-10) REVERT: A 986 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6291 (mt-10) REVERT: A 1003 SER cc_start: 0.7970 (t) cc_final: 0.7624 (t) REVERT: A 1122 GLU cc_start: 0.7003 (tp30) cc_final: 0.6351 (tp30) REVERT: A 1125 TYR cc_start: 0.6207 (p90) cc_final: 0.5594 (p90) REVERT: B 76 LYS cc_start: 0.7857 (mttm) cc_final: 0.7583 (mttm) REVERT: B 124 GLU cc_start: 0.6255 (tt0) cc_final: 0.5916 (tm-30) REVERT: B 125 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7356 (mp0) REVERT: B 154 MET cc_start: 0.8053 (tpp) cc_final: 0.7449 (mmt) REVERT: B 187 ASN cc_start: 0.6975 (m-40) cc_final: 0.6752 (m110) REVERT: B 205 MET cc_start: 0.7630 (tpp) cc_final: 0.7205 (mpp) REVERT: B 214 VAL cc_start: 0.7931 (p) cc_final: 0.7675 (m) REVERT: B 224 LYS cc_start: 0.7900 (pttt) cc_final: 0.7368 (pttt) REVERT: B 344 GLU cc_start: 0.7713 (tt0) cc_final: 0.7372 (tm-30) REVERT: B 475 GLN cc_start: 0.7244 (tp40) cc_final: 0.6921 (tp-100) REVERT: B 503 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 513 LYS cc_start: 0.7820 (mttt) cc_final: 0.7605 (mttp) REVERT: B 579 MET cc_start: 0.5597 (mtp) cc_final: 0.5170 (mtp) REVERT: B 580 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6209 (tp30) REVERT: B 584 LEU cc_start: 0.7802 (mt) cc_final: 0.7597 (mm) REVERT: B 608 LEU cc_start: 0.7430 (tp) cc_final: 0.7152 (tp) REVERT: B 609 ARG cc_start: 0.7434 (mtp-110) cc_final: 0.7102 (mtp180) REVERT: B 612 VAL cc_start: 0.6706 (t) cc_final: 0.6492 (m) REVERT: B 630 ASP cc_start: 0.7902 (m-30) cc_final: 0.7656 (m-30) REVERT: B 647 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8023 (mmtm) REVERT: B 650 ASP cc_start: 0.8161 (m-30) cc_final: 0.7871 (m-30) REVERT: B 678 MET cc_start: 0.6973 (mmm) cc_final: 0.6574 (mmm) REVERT: B 684 ILE cc_start: 0.8114 (mp) cc_final: 0.7913 (pt) REVERT: B 810 MET cc_start: 0.6669 (mmm) cc_final: 0.6428 (mmm) REVERT: B 832 GLN cc_start: 0.7292 (tp40) cc_final: 0.6907 (tp40) REVERT: B 866 GLU cc_start: 0.7542 (tt0) cc_final: 0.7141 (tp30) REVERT: B 881 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 923 ASP cc_start: 0.7151 (m-30) cc_final: 0.6792 (p0) REVERT: B 931 GLU cc_start: 0.7058 (tt0) cc_final: 0.6620 (mt-10) REVERT: B 946 SER cc_start: 0.7974 (p) cc_final: 0.7696 (m) REVERT: B 967 MET cc_start: 0.6514 (mtp) cc_final: 0.6237 (mtp) REVERT: B 976 ARG cc_start: 0.7571 (mpt180) cc_final: 0.7305 (tpt170) REVERT: B 986 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6740 (mt-10) REVERT: B 988 ILE cc_start: 0.8241 (mt) cc_final: 0.8032 (mp) REVERT: B 994 GLU cc_start: 0.7380 (tt0) cc_final: 0.7067 (tp30) REVERT: B 999 PHE cc_start: 0.6910 (m-80) cc_final: 0.6627 (m-80) REVERT: B 1003 SER cc_start: 0.7793 (t) cc_final: 0.7355 (t) REVERT: B 1040 ASN cc_start: 0.7280 (m110) cc_final: 0.6704 (m110) REVERT: B 1060 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7070 (tp30) REVERT: B 1125 TYR cc_start: 0.6170 (p90) cc_final: 0.5472 (p90) REVERT: B 1128 ASP cc_start: 0.6943 (m-30) cc_final: 0.5836 (t0) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.1162 time to fit residues: 80.0103 Evaluate side-chains 414 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 597 GLN A 600 HIS A 636 GLN A 886 GLN A1110 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 444 ASN B 600 HIS B 636 GLN B 886 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.172836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143539 restraints weight = 23256.520| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.99 r_work: 0.3625 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16528 Z= 0.169 Angle : 0.581 7.475 22420 Z= 0.309 Chirality : 0.042 0.225 2696 Planarity : 0.004 0.044 2748 Dihedral : 10.168 179.434 2244 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.16 % Allowed : 11.38 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2020 helix: 1.45 (0.13), residues: 1460 sheet: -0.25 (0.62), residues: 66 loop : -0.22 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 TYR 0.019 0.002 TYR B 984 PHE 0.015 0.001 PHE A 159 TRP 0.016 0.002 TRP A 278 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (16528) covalent geometry : angle 0.58121 / 0.31 (22420) hydrogen bonds : bond 0.05521 / 3.73 ( 1174) hydrogen bonds : angle 4.57067 / 3.41 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 433 time to evaluate : 0.569 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: A 76 LYS cc_start: 0.7986 (mttm) cc_final: 0.7722 (mttm) REVERT: A 77 VAL cc_start: 0.8546 (p) cc_final: 0.8321 (t) REVERT: A 103 THR cc_start: 0.8004 (p) cc_final: 0.7719 (p) REVERT: A 214 VAL cc_start: 0.8799 (p) cc_final: 0.8586 (m) REVERT: A 233 GLU cc_start: 0.8064 (tt0) cc_final: 0.7385 (pt0) REVERT: A 296 ASP cc_start: 0.7859 (t0) cc_final: 0.7622 (t0) REVERT: A 300 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 337 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 377 LEU cc_start: 0.8354 (mt) cc_final: 0.8026 (mt) REVERT: A 475 GLN cc_start: 0.7716 (tp40) cc_final: 0.7506 (tp40) REVERT: A 520 ASP cc_start: 0.7943 (p0) cc_final: 0.7254 (p0) REVERT: A 579 MET cc_start: 0.6465 (mtp) cc_final: 0.6094 (mtp) REVERT: A 580 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7142 (tp30) REVERT: A 588 LYS cc_start: 0.7510 (tmmt) cc_final: 0.7286 (ttmt) REVERT: A 591 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7940 (mtpp) REVERT: A 629 ASP cc_start: 0.7707 (m-30) cc_final: 0.7373 (m-30) REVERT: A 630 ASP cc_start: 0.7823 (m-30) cc_final: 0.7613 (m-30) REVERT: A 633 LYS cc_start: 0.8037 (mttt) cc_final: 0.7508 (mmtm) REVERT: A 634 SER cc_start: 0.7815 (t) cc_final: 0.7590 (p) REVERT: A 647 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8206 (mmtm) REVERT: A 650 ASP cc_start: 0.8002 (m-30) cc_final: 0.7799 (m-30) REVERT: A 678 MET cc_start: 0.6444 (mmm) cc_final: 0.6040 (mmm) REVERT: A 822 ILE cc_start: 0.8189 (mt) cc_final: 0.7946 (tp) REVERT: A 958 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7566 (ttpp) REVERT: A 967 MET cc_start: 0.7355 (mtp) cc_final: 0.6741 (mtp) REVERT: A 971 ASP cc_start: 0.7715 (m-30) cc_final: 0.7283 (m-30) REVERT: A 976 ARG cc_start: 0.8447 (mpt180) cc_final: 0.7957 (mmt-90) REVERT: A 982 PHE cc_start: 0.7672 (m-80) cc_final: 0.7165 (m-10) REVERT: A 1003 SER cc_start: 0.8736 (t) cc_final: 0.8490 (t) REVERT: A 1038 VAL cc_start: 0.8557 (t) cc_final: 0.8300 (p) REVERT: A 1058 THR cc_start: 0.8032 (t) cc_final: 0.7812 (p) REVERT: A 1122 GLU cc_start: 0.7451 (tp30) cc_final: 0.6912 (tp30) REVERT: B 125 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7776 (mp0) REVERT: B 199 MET cc_start: 0.8018 (mmm) cc_final: 0.7751 (mmm) REVERT: B 214 VAL cc_start: 0.8816 (p) cc_final: 0.8558 (m) REVERT: B 236 LEU cc_start: 0.8079 (mm) cc_final: 0.7721 (mp) REVERT: B 338 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7782 (mtmt) REVERT: B 475 GLN cc_start: 0.7724 (tp40) cc_final: 0.7517 (tp-100) REVERT: B 579 MET cc_start: 0.6583 (mtp) cc_final: 0.6062 (mtp) REVERT: B 580 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7169 (tp30) REVERT: B 588 LYS cc_start: 0.7606 (tmmt) cc_final: 0.7383 (ttmt) REVERT: B 591 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7911 (mtpp) REVERT: B 609 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7172 (mtp180) REVERT: B 632 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7919 (mtpp) REVERT: B 633 LYS cc_start: 0.8132 (mttt) cc_final: 0.7751 (mmtm) REVERT: B 678 MET cc_start: 0.6220 (mmm) cc_final: 0.5749 (mmm) REVERT: B 810 MET cc_start: 0.7061 (mmm) cc_final: 0.6712 (mmm) REVERT: B 823 LEU cc_start: 0.8368 (mt) cc_final: 0.8123 (mm) REVERT: B 832 GLN cc_start: 0.8039 (tp40) cc_final: 0.7696 (tp40) REVERT: B 926 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 955 ASN cc_start: 0.8054 (t0) cc_final: 0.7590 (t0) REVERT: B 958 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7618 (ttpp) REVERT: B 986 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 1007 LYS cc_start: 0.8234 (tttt) cc_final: 0.7910 (tttp) REVERT: B 1104 MET cc_start: 0.6656 (mmm) cc_final: 0.6377 (tpt) REVERT: B 1125 TYR cc_start: 0.6993 (p90) cc_final: 0.6369 (p90) outliers start: 38 outliers final: 22 residues processed: 450 average time/residue: 0.1025 time to fit residues: 69.4897 Evaluate side-chains 430 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 408 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 201 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 135 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.0060 chunk 185 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN A 600 HIS A 886 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN B 600 HIS B 886 GLN B 917 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144298 restraints weight = 23521.547| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.97 r_work: 0.3601 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16528 Z= 0.135 Angle : 0.515 6.879 22420 Z= 0.275 Chirality : 0.040 0.212 2696 Planarity : 0.004 0.043 2748 Dihedral : 9.959 179.994 2244 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.93 % Allowed : 14.11 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 2020 helix: 1.61 (0.13), residues: 1460 sheet: 0.39 (0.64), residues: 62 loop : -0.26 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 491 TYR 0.020 0.001 TYR B 984 PHE 0.019 0.001 PHE B 517 TRP 0.015 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (16528) covalent geometry : angle 0.51516 / 0.28 (22420) hydrogen bonds : bond 0.04679 / 3.17 ( 1174) hydrogen bonds : angle 4.22065 / 3.15 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 413 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.7950 (p) cc_final: 0.7725 (p) REVERT: A 128 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7251 (ptp-110) REVERT: A 154 MET cc_start: 0.8806 (tpp) cc_final: 0.8355 (tpp) REVERT: A 171 LEU cc_start: 0.8270 (tp) cc_final: 0.7956 (mp) REVERT: A 214 VAL cc_start: 0.8851 (p) cc_final: 0.8648 (m) REVERT: A 233 GLU cc_start: 0.8018 (tt0) cc_final: 0.7430 (tm-30) REVERT: A 296 ASP cc_start: 0.7796 (t0) cc_final: 0.7515 (t0) REVERT: A 300 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 305 LEU cc_start: 0.8698 (mt) cc_final: 0.8481 (mp) REVERT: A 337 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 377 LEU cc_start: 0.8346 (mt) cc_final: 0.7988 (mt) REVERT: A 520 ASP cc_start: 0.7923 (p0) cc_final: 0.7290 (p0) REVERT: A 579 MET cc_start: 0.6545 (mtp) cc_final: 0.6260 (mtp) REVERT: A 580 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7146 (tp30) REVERT: A 591 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7917 (mtpp) REVERT: A 629 ASP cc_start: 0.7705 (m-30) cc_final: 0.7380 (m-30) REVERT: A 630 ASP cc_start: 0.7747 (m-30) cc_final: 0.7536 (m-30) REVERT: A 633 LYS cc_start: 0.8070 (mttt) cc_final: 0.7538 (mmtm) REVERT: A 634 SER cc_start: 0.7659 (t) cc_final: 0.7447 (p) REVERT: A 678 MET cc_start: 0.6459 (mmm) cc_final: 0.5961 (mmm) REVERT: A 822 ILE cc_start: 0.8321 (mt) cc_final: 0.8101 (tp) REVERT: A 835 LEU cc_start: 0.8775 (tt) cc_final: 0.8530 (tp) REVERT: A 841 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7880 (mmmt) REVERT: A 958 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7543 (ttpp) REVERT: A 967 MET cc_start: 0.7342 (mtp) cc_final: 0.6738 (mtp) REVERT: A 971 ASP cc_start: 0.7754 (m-30) cc_final: 0.7336 (m-30) REVERT: A 1058 THR cc_start: 0.8131 (t) cc_final: 0.7889 (p) REVERT: A 1122 GLU cc_start: 0.7430 (tp30) cc_final: 0.6891 (tp30) REVERT: B 103 THR cc_start: 0.8002 (p) cc_final: 0.7763 (p) REVERT: B 125 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7812 (mp0) REVERT: B 154 MET cc_start: 0.8621 (tpp) cc_final: 0.8258 (tpp) REVERT: B 171 LEU cc_start: 0.8303 (tp) cc_final: 0.7992 (mp) REVERT: B 236 LEU cc_start: 0.8042 (mm) cc_final: 0.7717 (mp) REVERT: B 269 LEU cc_start: 0.7664 (mt) cc_final: 0.7400 (mm) REVERT: B 280 TYR cc_start: 0.8291 (t80) cc_final: 0.7907 (t80) REVERT: B 347 VAL cc_start: 0.8831 (p) cc_final: 0.8615 (t) REVERT: B 579 MET cc_start: 0.6530 (mtp) cc_final: 0.6120 (mtp) REVERT: B 580 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7128 (tp30) REVERT: B 591 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7963 (mtpp) REVERT: B 609 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7232 (mtp180) REVERT: B 632 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7925 (mtpp) REVERT: B 633 LYS cc_start: 0.8078 (mttt) cc_final: 0.7748 (mmtm) REVERT: B 678 MET cc_start: 0.6190 (mmm) cc_final: 0.5736 (mmm) REVERT: B 810 MET cc_start: 0.7084 (mmm) cc_final: 0.6761 (mmm) REVERT: B 823 LEU cc_start: 0.8439 (mt) cc_final: 0.8228 (mm) REVERT: B 832 GLN cc_start: 0.8050 (tp40) cc_final: 0.7751 (tp40) REVERT: B 866 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7773 (tp30) REVERT: B 887 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7898 (mmm-85) REVERT: B 958 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7729 (ttpp) REVERT: B 986 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 1007 LYS cc_start: 0.8174 (tttt) cc_final: 0.7908 (tmtt) REVERT: B 1115 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7378 (tm-30) outliers start: 34 outliers final: 20 residues processed: 431 average time/residue: 0.1092 time to fit residues: 70.6457 Evaluate side-chains 399 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 379 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 GLN A 600 HIS A 877 GLN A 886 GLN A1110 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 600 HIS B 877 GLN B 981 HIS B1064 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142796 restraints weight = 23530.840| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.00 r_work: 0.3587 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16528 Z= 0.148 Angle : 0.514 7.119 22420 Z= 0.273 Chirality : 0.041 0.232 2696 Planarity : 0.004 0.054 2748 Dihedral : 9.812 178.043 2244 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.50 % Allowed : 14.62 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2020 helix: 1.57 (0.13), residues: 1478 sheet: 0.53 (0.54), residues: 80 loop : -0.25 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 420 TYR 0.019 0.001 TYR B 984 PHE 0.014 0.001 PHE B 517 TRP 0.015 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (16528) covalent geometry : angle 0.51404 / 0.27 (22420) hydrogen bonds : bond 0.04536 / 3.10 ( 1174) hydrogen bonds : angle 4.14155 / 3.08 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 396 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7396 (ptp90) cc_final: 0.7104 (ptp-110) REVERT: A 154 MET cc_start: 0.8775 (tpp) cc_final: 0.8259 (tpp) REVERT: A 171 LEU cc_start: 0.8242 (tp) cc_final: 0.7929 (mp) REVERT: A 233 GLU cc_start: 0.8105 (tt0) cc_final: 0.7418 (tm-30) REVERT: A 300 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7621 (mt-10) REVERT: A 347 VAL cc_start: 0.8869 (p) cc_final: 0.8612 (t) REVERT: A 377 LEU cc_start: 0.8334 (mt) cc_final: 0.7928 (mt) REVERT: A 591 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7923 (mtpp) REVERT: A 633 LYS cc_start: 0.8082 (mttt) cc_final: 0.7604 (mmtm) REVERT: A 647 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8468 (mtmt) REVERT: A 678 MET cc_start: 0.6565 (mmm) cc_final: 0.6038 (mmm) REVERT: A 822 ILE cc_start: 0.8282 (mt) cc_final: 0.8048 (tp) REVERT: A 841 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7858 (mmtt) REVERT: A 863 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5921 (tt) REVERT: A 958 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7600 (ttpp) REVERT: A 967 MET cc_start: 0.7346 (mtp) cc_final: 0.6730 (mtp) REVERT: A 971 ASP cc_start: 0.7723 (m-30) cc_final: 0.7296 (m-30) REVERT: A 1033 GLU cc_start: 0.6217 (tm-30) cc_final: 0.5389 (tm-30) REVERT: A 1034 ASP cc_start: 0.6542 (t0) cc_final: 0.6286 (t0) REVERT: A 1058 THR cc_start: 0.8156 (t) cc_final: 0.7877 (p) REVERT: A 1110 GLN cc_start: 0.6023 (tm130) cc_final: 0.5760 (tm-30) REVERT: A 1122 GLU cc_start: 0.7449 (tp30) cc_final: 0.6885 (tp30) REVERT: B 103 THR cc_start: 0.8011 (p) cc_final: 0.7792 (p) REVERT: B 125 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7734 (mp0) REVERT: B 171 LEU cc_start: 0.8280 (tp) cc_final: 0.7976 (mp) REVERT: B 214 VAL cc_start: 0.8780 (p) cc_final: 0.8467 (m) REVERT: B 236 LEU cc_start: 0.8042 (mm) cc_final: 0.7708 (mp) REVERT: B 269 LEU cc_start: 0.7668 (mt) cc_final: 0.7401 (mm) REVERT: B 280 TYR cc_start: 0.8314 (t80) cc_final: 0.7987 (t80) REVERT: B 347 VAL cc_start: 0.8893 (p) cc_final: 0.8656 (t) REVERT: B 579 MET cc_start: 0.6504 (mtp) cc_final: 0.6177 (mtp) REVERT: B 580 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7158 (tp30) REVERT: B 591 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7990 (mtpp) REVERT: B 605 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: B 609 ARG cc_start: 0.7602 (mtp-110) cc_final: 0.7352 (mtp-110) REVERT: B 632 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7973 (mtpp) REVERT: B 633 LYS cc_start: 0.8131 (mttt) cc_final: 0.7731 (mmtm) REVERT: B 678 MET cc_start: 0.6170 (mmm) cc_final: 0.5713 (mmm) REVERT: B 810 MET cc_start: 0.7104 (mmm) cc_final: 0.6736 (mmm) REVERT: B 823 LEU cc_start: 0.8464 (mt) cc_final: 0.8239 (mm) REVERT: B 967 MET cc_start: 0.7525 (mtp) cc_final: 0.7220 (mmm) REVERT: B 986 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 1007 LYS cc_start: 0.8203 (tttt) cc_final: 0.7975 (tttm) REVERT: B 1185 ARG cc_start: 0.6442 (mmt180) cc_final: 0.5097 (mmt180) outliers start: 44 outliers final: 34 residues processed: 421 average time/residue: 0.1067 time to fit residues: 68.0412 Evaluate side-chains 416 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 381 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 126 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 877 GLN A1120 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 832 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142571 restraints weight = 23381.461| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.99 r_work: 0.3591 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16528 Z= 0.160 Angle : 0.531 9.200 22420 Z= 0.279 Chirality : 0.041 0.254 2696 Planarity : 0.004 0.054 2748 Dihedral : 9.660 174.330 2244 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.79 % Allowed : 15.59 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2020 helix: 1.55 (0.13), residues: 1480 sheet: 0.70 (0.53), residues: 70 loop : -0.35 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 420 TYR 0.019 0.001 TYR B 984 PHE 0.019 0.001 PHE A 254 TRP 0.015 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16528) covalent geometry : angle 0.53071 / 0.28 (22420) hydrogen bonds : bond 0.04501 / 3.08 ( 1174) hydrogen bonds : angle 4.12596 / 3.08 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 411 time to evaluate : 0.390 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: A 128 ARG cc_start: 0.7449 (ptp90) cc_final: 0.7156 (ptp-110) REVERT: A 171 LEU cc_start: 0.8267 (tp) cc_final: 0.7944 (mp) REVERT: A 217 LEU cc_start: 0.8452 (mp) cc_final: 0.8203 (mm) REVERT: A 233 GLU cc_start: 0.8089 (tt0) cc_final: 0.7456 (tm-30) REVERT: A 300 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 347 VAL cc_start: 0.8902 (p) cc_final: 0.8652 (t) REVERT: A 377 LEU cc_start: 0.8340 (mt) cc_final: 0.7950 (mt) REVERT: A 420 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7943 (mtt90) REVERT: A 520 ASP cc_start: 0.8094 (p0) cc_final: 0.7885 (p0) REVERT: A 591 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7974 (mtpp) REVERT: A 609 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7383 (mtp-110) REVERT: A 633 LYS cc_start: 0.8053 (mttt) cc_final: 0.7821 (mttt) REVERT: A 678 MET cc_start: 0.6554 (mmm) cc_final: 0.6035 (mmm) REVERT: A 822 ILE cc_start: 0.8313 (mt) cc_final: 0.8031 (tp) REVERT: A 841 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7797 (mmmt) REVERT: A 931 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 967 MET cc_start: 0.7346 (mtp) cc_final: 0.6757 (mtp) REVERT: A 971 ASP cc_start: 0.7799 (m-30) cc_final: 0.7364 (m-30) REVERT: A 972 PHE cc_start: 0.7884 (t80) cc_final: 0.7538 (t80) REVERT: A 1034 ASP cc_start: 0.6590 (t0) cc_final: 0.6301 (t0) REVERT: A 1058 THR cc_start: 0.8168 (t) cc_final: 0.7912 (p) REVERT: A 1122 GLU cc_start: 0.7423 (tp30) cc_final: 0.6889 (tp30) REVERT: A 1126 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7127 (pt) REVERT: B 125 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7829 (mp0) REVERT: B 171 LEU cc_start: 0.8329 (tp) cc_final: 0.8033 (mp) REVERT: B 214 VAL cc_start: 0.8845 (p) cc_final: 0.8530 (m) REVERT: B 236 LEU cc_start: 0.8088 (mm) cc_final: 0.7713 (mp) REVERT: B 280 TYR cc_start: 0.8354 (t80) cc_final: 0.8070 (t80) REVERT: B 579 MET cc_start: 0.6748 (mtp) cc_final: 0.6317 (mtp) REVERT: B 580 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7207 (tp30) REVERT: B 591 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8009 (mtpp) REVERT: B 633 LYS cc_start: 0.8185 (mttt) cc_final: 0.7795 (mmtm) REVERT: B 678 MET cc_start: 0.6095 (mmm) cc_final: 0.5634 (mmm) REVERT: B 810 MET cc_start: 0.7126 (mmm) cc_final: 0.6766 (mmm) REVERT: B 832 GLN cc_start: 0.8263 (tp40) cc_final: 0.7794 (tp-100) REVERT: B 841 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7842 (mmmt) REVERT: B 866 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 881 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7670 (mp0) REVERT: B 986 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 1007 LYS cc_start: 0.8181 (tttt) cc_final: 0.7867 (tttp) REVERT: B 1185 ARG cc_start: 0.6422 (mmt180) cc_final: 0.5298 (mmt180) outliers start: 49 outliers final: 36 residues processed: 436 average time/residue: 0.1096 time to fit residues: 71.1323 Evaluate side-chains 423 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 386 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 877 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.172006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142767 restraints weight = 23406.500| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.99 r_work: 0.3599 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16528 Z= 0.142 Angle : 0.515 10.347 22420 Z= 0.269 Chirality : 0.041 0.260 2696 Planarity : 0.004 0.056 2748 Dihedral : 9.613 174.359 2244 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.36 % Allowed : 16.15 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2020 helix: 1.61 (0.13), residues: 1480 sheet: 0.63 (0.52), residues: 70 loop : -0.35 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 420 TYR 0.018 0.001 TYR B 984 PHE 0.019 0.001 PHE A 254 TRP 0.013 0.001 TRP A 278 HIS 0.003 0.000 HIS B1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16528) covalent geometry : angle 0.51534 / 0.27 (22420) hydrogen bonds : bond 0.04310 / 2.95 ( 1174) hydrogen bonds : angle 4.07710 / 3.04 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 413 time to evaluate : 0.555 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: symmetry clash REVERT: A 128 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7165 (ptp-110) REVERT: A 171 LEU cc_start: 0.8257 (tp) cc_final: 0.7976 (mp) REVERT: A 197 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6689 (mp0) REVERT: A 214 VAL cc_start: 0.8784 (p) cc_final: 0.8549 (m) REVERT: A 217 LEU cc_start: 0.8439 (mp) cc_final: 0.8229 (mm) REVERT: A 233 GLU cc_start: 0.8065 (tt0) cc_final: 0.7532 (tm-30) REVERT: A 300 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 347 VAL cc_start: 0.8925 (p) cc_final: 0.8662 (t) REVERT: A 377 LEU cc_start: 0.8330 (mt) cc_final: 0.7959 (mt) REVERT: A 390 ILE cc_start: 0.7453 (mm) cc_final: 0.7204 (mt) REVERT: A 591 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7977 (mtpp) REVERT: A 633 LYS cc_start: 0.8060 (mttt) cc_final: 0.7805 (mttt) REVERT: A 678 MET cc_start: 0.6631 (mmm) cc_final: 0.6063 (mmm) REVERT: A 822 ILE cc_start: 0.8342 (mt) cc_final: 0.8060 (tp) REVERT: A 841 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7765 (mmmt) REVERT: A 863 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6162 (tt) REVERT: A 967 MET cc_start: 0.7411 (mtp) cc_final: 0.6849 (mtp) REVERT: A 971 ASP cc_start: 0.7795 (m-30) cc_final: 0.7356 (m-30) REVERT: A 972 PHE cc_start: 0.7848 (t80) cc_final: 0.7537 (t80) REVERT: A 1110 GLN cc_start: 0.6587 (mp10) cc_final: 0.6274 (mp10) REVERT: A 1122 GLU cc_start: 0.7381 (tp30) cc_final: 0.6871 (tp30) REVERT: A 1126 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7058 (pt) REVERT: B 125 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7835 (mp0) REVERT: B 154 MET cc_start: 0.8527 (tpp) cc_final: 0.8195 (mtp) REVERT: B 171 LEU cc_start: 0.8297 (tp) cc_final: 0.7997 (mp) REVERT: B 236 LEU cc_start: 0.8061 (mm) cc_final: 0.7682 (mp) REVERT: B 280 TYR cc_start: 0.8346 (t80) cc_final: 0.8044 (t80) REVERT: B 579 MET cc_start: 0.6683 (mtp) cc_final: 0.6255 (mtp) REVERT: B 591 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8008 (mtpp) REVERT: B 596 LYS cc_start: 0.8300 (mmtp) cc_final: 0.8067 (mttm) REVERT: B 678 MET cc_start: 0.6176 (mmm) cc_final: 0.5645 (mmm) REVERT: B 810 MET cc_start: 0.7106 (mmm) cc_final: 0.6756 (mmm) REVERT: B 832 GLN cc_start: 0.8272 (tp40) cc_final: 0.7827 (tp-100) REVERT: B 841 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7827 (mmmt) REVERT: B 849 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 887 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7882 (mmm-85) REVERT: B 967 MET cc_start: 0.7726 (mmm) cc_final: 0.7483 (mmm) REVERT: B 986 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 1185 ARG cc_start: 0.6435 (mmt180) cc_final: 0.5421 (mmt180) outliers start: 59 outliers final: 43 residues processed: 447 average time/residue: 0.1155 time to fit residues: 76.7504 Evaluate side-chains 438 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 393 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 50 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 190 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 78 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.172678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143192 restraints weight = 23261.983| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.99 r_work: 0.3602 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16528 Z= 0.135 Angle : 0.522 11.085 22420 Z= 0.272 Chirality : 0.040 0.262 2696 Planarity : 0.004 0.048 2748 Dihedral : 9.550 172.808 2244 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.41 % Allowed : 17.29 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 2020 helix: 1.64 (0.13), residues: 1478 sheet: 0.39 (0.57), residues: 62 loop : -0.26 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 491 TYR 0.018 0.001 TYR B 984 PHE 0.019 0.001 PHE A 254 TRP 0.016 0.001 TRP A 635 HIS 0.004 0.001 HIS B1120 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16528) covalent geometry : angle 0.52157 / 0.27 (22420) hydrogen bonds : bond 0.04187 / 2.86 ( 1174) hydrogen bonds : angle 4.08814 / 3.05 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7450 (ptp90) cc_final: 0.7135 (ptp-110) REVERT: A 197 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6642 (mp0) REVERT: A 214 VAL cc_start: 0.8766 (p) cc_final: 0.8521 (m) REVERT: A 217 LEU cc_start: 0.8417 (mp) cc_final: 0.8201 (mm) REVERT: A 233 GLU cc_start: 0.8075 (tt0) cc_final: 0.7569 (tm-30) REVERT: A 300 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 347 VAL cc_start: 0.8915 (p) cc_final: 0.8662 (t) REVERT: A 377 LEU cc_start: 0.8316 (mt) cc_final: 0.7979 (mt) REVERT: A 390 ILE cc_start: 0.7435 (mm) cc_final: 0.7177 (mt) REVERT: A 596 LYS cc_start: 0.8236 (mttp) cc_final: 0.7950 (mtpp) REVERT: A 605 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7070 (ttm-80) REVERT: A 633 LYS cc_start: 0.8013 (mttt) cc_final: 0.7804 (mttt) REVERT: A 678 MET cc_start: 0.6637 (mmm) cc_final: 0.6067 (mmm) REVERT: A 841 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7794 (mmmt) REVERT: A 863 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6132 (tt) REVERT: A 967 MET cc_start: 0.7418 (mtp) cc_final: 0.6881 (mtp) REVERT: A 971 ASP cc_start: 0.7755 (m-30) cc_final: 0.7323 (m-30) REVERT: A 1033 GLU cc_start: 0.6432 (pp20) cc_final: 0.6126 (tm-30) REVERT: A 1058 THR cc_start: 0.8151 (t) cc_final: 0.7873 (p) REVERT: A 1110 GLN cc_start: 0.6663 (mp10) cc_final: 0.6379 (mp10) REVERT: A 1122 GLU cc_start: 0.7361 (tp30) cc_final: 0.6846 (tp30) REVERT: A 1126 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7033 (pt) REVERT: B 125 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7784 (mp0) REVERT: B 154 MET cc_start: 0.8454 (tpp) cc_final: 0.8164 (mtp) REVERT: B 171 LEU cc_start: 0.8276 (tp) cc_final: 0.7997 (mp) REVERT: B 236 LEU cc_start: 0.8030 (mm) cc_final: 0.7664 (mp) REVERT: B 280 TYR cc_start: 0.8308 (t80) cc_final: 0.8045 (t80) REVERT: B 579 MET cc_start: 0.6776 (mtp) cc_final: 0.6350 (mtp) REVERT: B 588 LYS cc_start: 0.7596 (tmmt) cc_final: 0.7384 (ttmt) REVERT: B 591 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7997 (mtpp) REVERT: B 633 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7853 (mmtt) REVERT: B 678 MET cc_start: 0.6217 (mmm) cc_final: 0.5679 (mmm) REVERT: B 810 MET cc_start: 0.7076 (mmm) cc_final: 0.6728 (mmm) REVERT: B 841 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7829 (mmmt) REVERT: B 866 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7596 (tp30) REVERT: B 887 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: B 986 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7388 (mt-10) REVERT: B 1007 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (tttp) REVERT: B 1051 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7776 (pttm) REVERT: B 1185 ARG cc_start: 0.6411 (mmt180) cc_final: 0.5677 (mmt180) outliers start: 60 outliers final: 43 residues processed: 439 average time/residue: 0.1124 time to fit residues: 73.6329 Evaluate side-chains 442 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 394 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 178 optimal weight: 0.1980 chunk 203 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 163 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.4488 > 50:) overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B1110 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.172329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142768 restraints weight = 23399.373| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.99 r_work: 0.3599 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.145 Angle : 0.538 9.651 22420 Z= 0.281 Chirality : 0.041 0.273 2696 Planarity : 0.004 0.050 2748 Dihedral : 9.510 173.061 2244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.24 % Allowed : 17.63 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 2020 helix: 1.63 (0.13), residues: 1478 sheet: 0.30 (0.57), residues: 62 loop : -0.25 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 420 TYR 0.013 0.001 TYR B 984 PHE 0.042 0.001 PHE B 201 TRP 0.016 0.001 TRP A 635 HIS 0.002 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16528) covalent geometry : angle 0.53814 / 0.28 (22420) hydrogen bonds : bond 0.04248 / 2.89 ( 1174) hydrogen bonds : angle 4.09629 / 3.06 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 403 time to evaluate : 0.469 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: A 128 ARG cc_start: 0.7442 (ptp90) cc_final: 0.7144 (ptp-110) REVERT: A 197 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6641 (mp0) REVERT: A 214 VAL cc_start: 0.8756 (p) cc_final: 0.8515 (m) REVERT: A 217 LEU cc_start: 0.8420 (mp) cc_final: 0.8213 (mm) REVERT: A 233 GLU cc_start: 0.8080 (tt0) cc_final: 0.7580 (tm-30) REVERT: A 300 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 347 VAL cc_start: 0.8920 (p) cc_final: 0.8676 (t) REVERT: A 390 ILE cc_start: 0.7439 (mm) cc_final: 0.7184 (mt) REVERT: A 579 MET cc_start: 0.6432 (mpp) cc_final: 0.6068 (mpp) REVERT: A 633 LYS cc_start: 0.8066 (mttt) cc_final: 0.7865 (mttt) REVERT: A 678 MET cc_start: 0.6719 (mmm) cc_final: 0.6128 (mmm) REVERT: A 832 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7890 (tm-30) REVERT: A 841 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7765 (mmmt) REVERT: A 881 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7541 (mp0) REVERT: A 967 MET cc_start: 0.7400 (mtp) cc_final: 0.6883 (mtp) REVERT: A 971 ASP cc_start: 0.7753 (m-30) cc_final: 0.7319 (m-30) REVERT: A 986 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 1005 LEU cc_start: 0.7741 (tp) cc_final: 0.7538 (tt) REVERT: A 1110 GLN cc_start: 0.6731 (mp10) cc_final: 0.6403 (mp10) REVERT: A 1122 GLU cc_start: 0.7384 (tp30) cc_final: 0.6862 (tp30) REVERT: A 1126 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7034 (pt) REVERT: B 125 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 140 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7723 (mp10) REVERT: B 171 LEU cc_start: 0.8265 (tp) cc_final: 0.8003 (mp) REVERT: B 186 MET cc_start: 0.5889 (mpp) cc_final: 0.5470 (mmm) REVERT: B 205 MET cc_start: 0.7634 (mpp) cc_final: 0.7401 (mpp) REVERT: B 236 LEU cc_start: 0.8069 (mm) cc_final: 0.7704 (mp) REVERT: B 280 TYR cc_start: 0.8301 (t80) cc_final: 0.8043 (t80) REVERT: B 579 MET cc_start: 0.6713 (mtp) cc_final: 0.6324 (mtp) REVERT: B 591 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8007 (mtpp) REVERT: B 633 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7922 (mmtt) REVERT: B 678 MET cc_start: 0.6101 (mmm) cc_final: 0.5591 (mmm) REVERT: B 810 MET cc_start: 0.6872 (mmm) cc_final: 0.6549 (mmm) REVERT: B 832 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7983 (tm-30) REVERT: B 841 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7773 (mmmm) REVERT: B 866 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 887 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: B 983 ASP cc_start: 0.7630 (t0) cc_final: 0.7384 (t0) REVERT: B 986 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 1007 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7917 (tttm) REVERT: B 1045 MET cc_start: 0.6789 (pmm) cc_final: 0.6490 (tmm) REVERT: B 1051 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7725 (pttp) REVERT: B 1078 ASP cc_start: 0.8225 (m-30) cc_final: 0.8020 (m-30) REVERT: B 1185 ARG cc_start: 0.6440 (mmt180) cc_final: 0.5644 (mmt180) outliers start: 57 outliers final: 46 residues processed: 434 average time/residue: 0.1097 time to fit residues: 71.7641 Evaluate side-chains 435 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 385 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 181 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143741 restraints weight = 23170.268| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.98 r_work: 0.3606 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16528 Z= 0.136 Angle : 0.555 10.155 22420 Z= 0.286 Chirality : 0.041 0.276 2696 Planarity : 0.004 0.058 2748 Dihedral : 9.504 173.755 2244 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.01 % Allowed : 18.32 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2020 helix: 1.70 (0.13), residues: 1466 sheet: 0.34 (0.58), residues: 62 loop : -0.18 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 420 TYR 0.025 0.001 TYR B 267 PHE 0.039 0.001 PHE A 201 TRP 0.014 0.001 TRP A 635 HIS 0.004 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (16528) covalent geometry : angle 0.55481 / 0.29 (22420) hydrogen bonds : bond 0.04152 / 2.82 ( 1174) hydrogen bonds : angle 4.07504 / 3.04 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 389 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7447 (ptp90) cc_final: 0.7145 (ptp-110) REVERT: A 205 MET cc_start: 0.7472 (mpp) cc_final: 0.7042 (mpp) REVERT: A 217 LEU cc_start: 0.8421 (mp) cc_final: 0.8209 (mm) REVERT: A 218 LYS cc_start: 0.8235 (tttt) cc_final: 0.7849 (tttt) REVERT: A 233 GLU cc_start: 0.8073 (tt0) cc_final: 0.7573 (tm-30) REVERT: A 300 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 347 VAL cc_start: 0.8922 (p) cc_final: 0.8667 (t) REVERT: A 377 LEU cc_start: 0.8306 (mt) cc_final: 0.7971 (mt) REVERT: A 390 ILE cc_start: 0.7481 (mm) cc_final: 0.7207 (mt) REVERT: A 600 HIS cc_start: 0.7491 (m-70) cc_final: 0.7289 (m-70) REVERT: A 678 MET cc_start: 0.6833 (mmm) cc_final: 0.6293 (mmm) REVERT: A 832 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7880 (tm-30) REVERT: A 841 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7401 (mmmt) REVERT: A 881 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7582 (mp0) REVERT: A 958 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7435 (ttpp) REVERT: A 967 MET cc_start: 0.7383 (mtp) cc_final: 0.6855 (mtp) REVERT: A 971 ASP cc_start: 0.7730 (m-30) cc_final: 0.7297 (m-30) REVERT: A 986 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 1005 LEU cc_start: 0.7732 (tp) cc_final: 0.7505 (tt) REVERT: A 1110 GLN cc_start: 0.6746 (mp10) cc_final: 0.6447 (mp10) REVERT: A 1126 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6992 (pt) REVERT: A 1128 ASP cc_start: 0.7223 (m-30) cc_final: 0.6956 (m-30) REVERT: B 125 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7812 (mp0) REVERT: B 140 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7674 (mp10) REVERT: B 171 LEU cc_start: 0.8268 (tp) cc_final: 0.8019 (mp) REVERT: B 186 MET cc_start: 0.5998 (mpp) cc_final: 0.5643 (mmm) REVERT: B 236 LEU cc_start: 0.8040 (mm) cc_final: 0.7679 (mp) REVERT: B 280 TYR cc_start: 0.8300 (t80) cc_final: 0.8036 (t80) REVERT: B 517 PHE cc_start: 0.6916 (m-80) cc_final: 0.6326 (m-10) REVERT: B 579 MET cc_start: 0.6726 (mtp) cc_final: 0.6311 (mtp) REVERT: B 591 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7995 (mtpp) REVERT: B 633 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7909 (mmtt) REVERT: B 810 MET cc_start: 0.7026 (mmm) cc_final: 0.6663 (mmm) REVERT: B 832 GLN cc_start: 0.8322 (tp-100) cc_final: 0.8000 (tm-30) REVERT: B 841 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7782 (mmmm) REVERT: B 887 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7839 (mmm-85) REVERT: B 983 ASP cc_start: 0.7627 (t0) cc_final: 0.7284 (t0) REVERT: B 986 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7101 (mt-10) REVERT: B 1007 LYS cc_start: 0.8002 (tttt) cc_final: 0.7746 (tttp) REVERT: B 1051 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (pttp) REVERT: B 1078 ASP cc_start: 0.8239 (m-30) cc_final: 0.8029 (m-30) REVERT: B 1185 ARG cc_start: 0.6421 (mmt180) cc_final: 0.5642 (mmt180) outliers start: 53 outliers final: 45 residues processed: 419 average time/residue: 0.1147 time to fit residues: 73.1782 Evaluate side-chains 441 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 191 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142479 restraints weight = 23339.997| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.99 r_work: 0.3595 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16528 Z= 0.160 Angle : 0.578 9.836 22420 Z= 0.300 Chirality : 0.042 0.317 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.516 173.920 2244 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 18.54 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2020 helix: 1.56 (0.13), residues: 1476 sheet: 0.33 (0.57), residues: 62 loop : -0.26 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 420 TYR 0.021 0.001 TYR B 267 PHE 0.047 0.001 PHE B 201 TRP 0.016 0.002 TRP A 635 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16528) covalent geometry : angle 0.57839 / 0.30 (22420) hydrogen bonds : bond 0.04330 / 2.94 ( 1174) hydrogen bonds : angle 4.13180 / 3.08 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 386 time to evaluate : 0.553 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 125 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7464 (mp0) REVERT: A 128 ARG cc_start: 0.7436 (ptp90) cc_final: 0.7183 (ptp-110) REVERT: A 205 MET cc_start: 0.7333 (mpp) cc_final: 0.6903 (mpp) REVERT: A 218 LYS cc_start: 0.8249 (tttt) cc_final: 0.7870 (tttt) REVERT: A 347 VAL cc_start: 0.8931 (p) cc_final: 0.8670 (t) REVERT: A 377 LEU cc_start: 0.8334 (mt) cc_final: 0.7989 (mt) REVERT: A 390 ILE cc_start: 0.7451 (mm) cc_final: 0.7194 (mt) REVERT: A 678 MET cc_start: 0.6595 (mmm) cc_final: 0.6072 (mmm) REVERT: A 832 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7863 (tm-30) REVERT: A 841 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7870 (mmtt) REVERT: A 881 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7618 (mp0) REVERT: A 958 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7478 (ttpp) REVERT: A 967 MET cc_start: 0.7422 (mtp) cc_final: 0.6882 (mtp) REVERT: A 971 ASP cc_start: 0.7765 (m-30) cc_final: 0.7326 (m-30) REVERT: A 986 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7391 (mt-10) REVERT: A 1005 LEU cc_start: 0.7787 (tp) cc_final: 0.7518 (tt) REVERT: A 1060 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7733 (mp0) REVERT: A 1110 GLN cc_start: 0.6683 (mp10) cc_final: 0.6396 (mp10) REVERT: A 1126 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7001 (pt) REVERT: B 125 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7853 (mp0) REVERT: B 140 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7736 (mp10) REVERT: B 171 LEU cc_start: 0.8269 (tp) cc_final: 0.8023 (mp) REVERT: B 186 MET cc_start: 0.5911 (mpp) cc_final: 0.5505 (mmm) REVERT: B 236 LEU cc_start: 0.8037 (mm) cc_final: 0.7666 (mp) REVERT: B 280 TYR cc_start: 0.8294 (t80) cc_final: 0.8032 (t80) REVERT: B 579 MET cc_start: 0.6676 (mtp) cc_final: 0.6277 (mtp) REVERT: B 591 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7985 (mtpp) REVERT: B 596 LYS cc_start: 0.8320 (mmtp) cc_final: 0.8090 (mttm) REVERT: B 810 MET cc_start: 0.6844 (mmm) cc_final: 0.6525 (mmm) REVERT: B 832 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7986 (tm-30) REVERT: B 841 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7739 (mmmt) REVERT: B 887 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7843 (mmm-85) REVERT: B 957 LEU cc_start: 0.8610 (tp) cc_final: 0.8346 (tt) REVERT: B 967 MET cc_start: 0.7883 (mmm) cc_final: 0.7534 (mmm) REVERT: B 983 ASP cc_start: 0.7644 (t0) cc_final: 0.7290 (t0) REVERT: B 986 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 1078 ASP cc_start: 0.8218 (m-30) cc_final: 0.8009 (m-30) REVERT: B 1185 ARG cc_start: 0.6408 (mmt180) cc_final: 0.5676 (mmt180) outliers start: 53 outliers final: 48 residues processed: 417 average time/residue: 0.1096 time to fit residues: 68.7937 Evaluate side-chains 421 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 372 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.0010 chunk 187 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 157 optimal weight: 0.0000 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143522 restraints weight = 23315.034| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.99 r_work: 0.3619 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16528 Z= 0.124 Angle : 0.557 9.694 22420 Z= 0.286 Chirality : 0.041 0.336 2696 Planarity : 0.004 0.048 2748 Dihedral : 9.494 174.634 2244 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.50 % Allowed : 19.34 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 2020 helix: 1.73 (0.13), residues: 1466 sheet: 0.26 (0.57), residues: 62 loop : -0.24 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.023 0.001 TYR B 267 PHE 0.042 0.001 PHE B 201 TRP 0.017 0.001 TRP A 419 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16528) covalent geometry : angle 0.55719 / 0.29 (22420) hydrogen bonds : bond 0.03978 / 2.69 ( 1174) hydrogen bonds : angle 4.03207 / 3.01 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.06 seconds wall clock time: 69 minutes 16.91 seconds (4156.91 seconds total)