Starting phenix.real_space_refine on Sat Jun 14 17:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdu_17621/06_2025/8pdu_17621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdu_17621/06_2025/8pdu_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_17621/06_2025/8pdu_17621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdu_17621/06_2025/8pdu_17621.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdu_17621/06_2025/8pdu_17621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdu_17621/06_2025/8pdu_17621.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.39, per 1000 atoms: 0.58 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: 3.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.93 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: 5.44 Time building geometry restraints manager: 4.52 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: 0.08 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: 0.010 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (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 TRP 0.011 0.001 TRP B 278 HIS 0.007 0.001 HIS A1172 PHE 0.014 0.001 PHE B 457 TYR 0.007 0.001 TYR B 309 ARG 0.002 0.000 ARG B 499 Details of bonding type rmsd hydrogen bonds : bond 0.18975 ( 1174) hydrogen bonds : angle 6.80419 ( 3456) covalent geometry : bond 0.00318 (16528) covalent geometry : angle 0.59363 (22420) *********************** 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 : 1.797 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 76 LYS cc_start: 0.7895 (mttm) cc_final: 0.7610 (mttm) REVERT: A 113 LEU cc_start: 0.7529 (mt) cc_final: 0.7162 (mp) REVERT: A 120 VAL cc_start: 0.6948 (t) cc_final: 0.6017 (p) REVERT: A 124 GLU cc_start: 0.6127 (tt0) cc_final: 0.5841 (mt-10) REVERT: A 125 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7081 (mp0) 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: 0.6783 (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: 0.7395 (mm-30) REVERT: A 337 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 377 LEU cc_start: 0.7971 (mt) cc_final: 0.7770 (mt) REVERT: A 384 ASP cc_start: 0.7009 (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: 0.6961 (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: 0.6542 (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: 0.6936 (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: 0.7105 (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: 0.7573 (mttm) REVERT: B 125 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7306 (mp0) REVERT: B 128 ARG cc_start: 0.7117 (ttp-170) cc_final: 0.6812 (ptm160) REVERT: B 154 MET cc_start: 0.8053 (tpp) cc_final: 0.7448 (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: 0.6920 (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: 0.7293 (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: 0.7209 (mm-30) cc_final: 0.6957 (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: 0.7695 (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: 0.7306 (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: 0.5835 (t0) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.3078 time to fit residues: 207.7781 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 : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0020 chunk 154 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 597 GLN A 600 HIS A 636 GLN A 886 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.172993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143772 restraints weight = 23295.604| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.99 r_work: 0.3628 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16528 Z= 0.165 Angle : 0.571 7.906 22420 Z= 0.303 Chirality : 0.042 0.219 2696 Planarity : 0.004 0.045 2748 Dihedral : 10.154 179.459 2244 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.93 % Allowed : 11.32 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 2020 helix: 1.49 (0.13), residues: 1460 sheet: 0.02 (0.64), residues: 62 loop : -0.19 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 278 HIS 0.005 0.001 HIS A1120 PHE 0.014 0.001 PHE A 159 TYR 0.019 0.002 TYR B 984 ARG 0.006 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.05548 ( 1174) hydrogen bonds : angle 4.55694 ( 3456) covalent geometry : bond 0.00355 (16528) covalent geometry : angle 0.57144 (22420) *********************** 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 464 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 430 time to evaluate : 1.809 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: 0.8007 (mttm) cc_final: 0.7716 (mttm) REVERT: A 77 VAL cc_start: 0.8517 (p) cc_final: 0.8291 (t) REVERT: A 103 THR cc_start: 0.7981 (p) cc_final: 0.7698 (p) REVERT: A 125 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7753 (mm-30) REVERT: A 199 MET cc_start: 0.7973 (mmm) cc_final: 0.7768 (mmm) REVERT: A 205 MET cc_start: 0.8136 (tpp) cc_final: 0.7934 (tpp) REVERT: A 214 VAL cc_start: 0.8760 (p) cc_final: 0.8555 (m) REVERT: A 337 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 377 LEU cc_start: 0.8340 (mt) cc_final: 0.8012 (mt) REVERT: A 475 GLN cc_start: 0.7698 (tp40) cc_final: 0.7491 (tp40) REVERT: A 520 ASP cc_start: 0.7946 (p0) cc_final: 0.7261 (p0) REVERT: A 579 MET cc_start: 0.6463 (mtp) cc_final: 0.6088 (mtp) REVERT: A 580 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6956 (tp30) REVERT: A 588 LYS cc_start: 0.7503 (tmmt) cc_final: 0.7284 (ttmt) REVERT: A 591 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7911 (mtpp) REVERT: A 629 ASP cc_start: 0.7724 (m-30) cc_final: 0.7375 (m-30) REVERT: A 630 ASP cc_start: 0.7840 (m-30) cc_final: 0.7623 (m-30) REVERT: A 633 LYS cc_start: 0.8042 (mttt) cc_final: 0.7495 (mmtm) REVERT: A 634 SER cc_start: 0.7837 (t) cc_final: 0.7607 (p) REVERT: A 647 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8214 (mmtm) REVERT: A 650 ASP cc_start: 0.8017 (m-30) cc_final: 0.7803 (m-30) REVERT: A 678 MET cc_start: 0.6456 (mmm) cc_final: 0.6033 (mmm) REVERT: A 822 ILE cc_start: 0.8173 (mt) cc_final: 0.7927 (tp) REVERT: A 958 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7559 (ttpp) REVERT: A 967 MET cc_start: 0.7336 (mtp) cc_final: 0.6738 (mtp) REVERT: A 971 ASP cc_start: 0.7717 (m-30) cc_final: 0.7282 (m-30) REVERT: A 976 ARG cc_start: 0.8447 (mpt180) cc_final: 0.7951 (mmt-90) REVERT: A 982 PHE cc_start: 0.7664 (m-80) cc_final: 0.7168 (m-10) REVERT: A 986 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 1003 SER cc_start: 0.8734 (t) cc_final: 0.8501 (t) REVERT: A 1038 VAL cc_start: 0.8535 (t) cc_final: 0.8274 (p) REVERT: A 1058 THR cc_start: 0.8026 (t) cc_final: 0.7605 (p) REVERT: A 1060 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 125 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7886 (mp0) REVERT: B 199 MET cc_start: 0.8013 (mmm) cc_final: 0.7750 (mmm) REVERT: B 214 VAL cc_start: 0.8762 (p) cc_final: 0.8511 (m) REVERT: B 236 LEU cc_start: 0.8050 (mm) cc_final: 0.7698 (mp) REVERT: B 288 PHE cc_start: 0.8724 (t80) cc_final: 0.8463 (t80) REVERT: B 338 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7779 (mtmt) REVERT: B 475 GLN cc_start: 0.7708 (tp40) cc_final: 0.7500 (tp-100) REVERT: B 579 MET cc_start: 0.6578 (mtp) cc_final: 0.6053 (mtp) REVERT: B 580 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7174 (tp30) REVERT: B 588 LYS cc_start: 0.7574 (tmmt) cc_final: 0.7347 (ttmt) REVERT: B 591 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7889 (mtpp) REVERT: B 609 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7157 (mtp180) REVERT: B 632 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7905 (mtpp) REVERT: B 633 LYS cc_start: 0.8128 (mttt) cc_final: 0.7731 (mmtm) REVERT: B 678 MET cc_start: 0.6229 (mmm) cc_final: 0.5753 (mmm) REVERT: B 810 MET cc_start: 0.7050 (mmm) cc_final: 0.6707 (mmm) REVERT: B 823 LEU cc_start: 0.8352 (mt) cc_final: 0.8102 (mm) REVERT: B 832 GLN cc_start: 0.8060 (tp40) cc_final: 0.7718 (tp40) REVERT: B 926 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 955 ASN cc_start: 0.8051 (t0) cc_final: 0.7579 (t0) REVERT: B 958 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7590 (ttpp) REVERT: B 986 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7391 (mt-10) REVERT: B 1007 LYS cc_start: 0.8220 (tttt) cc_final: 0.7860 (tttp) REVERT: B 1104 MET cc_start: 0.6599 (mmm) cc_final: 0.6344 (tpt) REVERT: B 1125 TYR cc_start: 0.6967 (p90) cc_final: 0.6342 (p90) outliers start: 34 outliers final: 19 residues processed: 444 average time/residue: 0.2839 time to fit residues: 185.1823 Evaluate side-chains 419 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 400 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 1141 THR 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 1141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.172769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143795 restraints weight = 23205.453| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.92 r_work: 0.3595 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16528 Z= 0.149 Angle : 0.523 6.863 22420 Z= 0.281 Chirality : 0.041 0.214 2696 Planarity : 0.004 0.052 2748 Dihedral : 9.912 178.650 2244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 13.82 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 2020 helix: 1.56 (0.13), residues: 1460 sheet: 0.36 (0.63), residues: 62 loop : -0.32 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 PHE 0.017 0.001 PHE A 254 TYR 0.019 0.001 TYR B 984 ARG 0.005 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 1174) hydrogen bonds : angle 4.25283 ( 3456) covalent geometry : bond 0.00324 (16528) covalent geometry : angle 0.52338 (22420) *********************** 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 448 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 407 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.7956 (p) cc_final: 0.7733 (p) REVERT: A 154 MET cc_start: 0.8791 (tpp) cc_final: 0.8340 (tpp) REVERT: A 199 MET cc_start: 0.8034 (mmm) cc_final: 0.7785 (mmm) REVERT: A 214 VAL cc_start: 0.8874 (p) cc_final: 0.8659 (m) REVERT: A 269 LEU cc_start: 0.7560 (mt) cc_final: 0.7336 (mm) REVERT: A 305 LEU cc_start: 0.8711 (mt) cc_final: 0.8485 (mp) REVERT: A 337 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 347 VAL cc_start: 0.8859 (p) cc_final: 0.8601 (t) REVERT: A 377 LEU cc_start: 0.8370 (mt) cc_final: 0.8096 (mt) REVERT: A 494 MET cc_start: 0.7816 (mmm) cc_final: 0.7463 (tpt) REVERT: A 579 MET cc_start: 0.6568 (mtp) cc_final: 0.6267 (mtp) REVERT: A 580 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7010 (tp30) REVERT: A 591 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7931 (mtpp) REVERT: A 610 LEU cc_start: 0.8250 (mt) cc_final: 0.8047 (mt) REVERT: A 629 ASP cc_start: 0.7682 (m-30) cc_final: 0.7356 (m-30) REVERT: A 633 LYS cc_start: 0.7989 (mttt) cc_final: 0.7472 (mmtm) REVERT: A 634 SER cc_start: 0.7647 (t) cc_final: 0.7436 (p) REVERT: A 678 MET cc_start: 0.6470 (mmm) cc_final: 0.5973 (mmm) REVERT: A 822 ILE cc_start: 0.8326 (mt) cc_final: 0.8109 (tp) REVERT: A 835 LEU cc_start: 0.8782 (tt) cc_final: 0.8537 (tp) REVERT: A 841 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7932 (mmtt) REVERT: A 866 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7763 (tp30) REVERT: A 958 LYS cc_start: 0.7787 (ttpp) cc_final: 0.7567 (ttpp) REVERT: A 967 MET cc_start: 0.7354 (mtp) cc_final: 0.6762 (mtp) REVERT: A 971 ASP cc_start: 0.7778 (m-30) cc_final: 0.7363 (m-30) REVERT: A 986 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 1058 THR cc_start: 0.8118 (t) cc_final: 0.7727 (p) REVERT: A 1126 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7191 (pt) REVERT: B 103 THR cc_start: 0.8020 (p) cc_final: 0.7791 (p) REVERT: B 125 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7960 (mp0) REVERT: B 171 LEU cc_start: 0.8318 (tp) cc_final: 0.8004 (mp) REVERT: B 236 LEU cc_start: 0.8060 (mm) cc_final: 0.7728 (mp) REVERT: B 269 LEU cc_start: 0.7663 (mt) cc_final: 0.7396 (mm) REVERT: B 288 PHE cc_start: 0.8699 (t80) cc_final: 0.8489 (t80) REVERT: B 347 VAL cc_start: 0.8866 (p) cc_final: 0.8650 (t) REVERT: B 579 MET cc_start: 0.6514 (mtp) cc_final: 0.6101 (mtp) REVERT: B 580 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7156 (tp30) REVERT: B 591 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7991 (mtpp) REVERT: B 609 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7212 (mtp180) REVERT: B 632 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7868 (mtpp) REVERT: B 633 LYS cc_start: 0.8085 (mttt) cc_final: 0.7757 (mmtm) REVERT: B 678 MET cc_start: 0.6172 (mmm) cc_final: 0.5732 (mmm) REVERT: B 810 MET cc_start: 0.7073 (mmm) cc_final: 0.6736 (mmm) REVERT: B 823 LEU cc_start: 0.8460 (mt) cc_final: 0.8251 (mm) REVERT: B 832 GLN cc_start: 0.8093 (tp40) cc_final: 0.7798 (tp40) REVERT: B 866 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7679 (tp30) REVERT: B 887 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: B 986 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 1007 LYS cc_start: 0.8175 (tttt) cc_final: 0.7958 (tttm) REVERT: B 1115 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 41 outliers final: 25 residues processed: 429 average time/residue: 0.2867 time to fit residues: 183.0077 Evaluate side-chains 406 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 450 VAL 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 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 164 SER Chi-restraints excluded: chain B residue 450 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 155 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 877 GLN A 886 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142478 restraints weight = 23260.239| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.99 r_work: 0.3575 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16528 Z= 0.163 Angle : 0.526 8.375 22420 Z= 0.280 Chirality : 0.041 0.236 2696 Planarity : 0.004 0.050 2748 Dihedral : 9.820 178.550 2244 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.67 % Allowed : 14.90 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2020 helix: 1.46 (0.13), residues: 1478 sheet: 0.54 (0.52), residues: 80 loop : -0.31 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 278 HIS 0.006 0.001 HIS B1120 PHE 0.015 0.001 PHE B 517 TYR 0.019 0.001 TYR B 984 ARG 0.009 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 1174) hydrogen bonds : angle 4.20462 ( 3456) covalent geometry : bond 0.00362 (16528) covalent geometry : angle 0.52602 (22420) *********************** 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 442 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 395 time to evaluate : 1.589 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 125 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 128 ARG cc_start: 0.7292 (ptp-110) cc_final: 0.7092 (ptp-110) REVERT: A 199 MET cc_start: 0.8040 (mmm) cc_final: 0.7692 (mmm) REVERT: A 205 MET cc_start: 0.8140 (tpp) cc_final: 0.7920 (mpp) REVERT: A 217 LEU cc_start: 0.8419 (mp) cc_final: 0.8179 (mm) REVERT: A 269 LEU cc_start: 0.7575 (mt) cc_final: 0.7319 (mm) REVERT: A 346 GLU cc_start: 0.7588 (tt0) cc_final: 0.7340 (tt0) REVERT: A 347 VAL cc_start: 0.8874 (p) cc_final: 0.8637 (t) REVERT: A 377 LEU cc_start: 0.8351 (mt) cc_final: 0.7943 (mt) REVERT: A 580 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6996 (tp30) REVERT: A 591 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7962 (mtpp) REVERT: A 633 LYS cc_start: 0.8095 (mttt) cc_final: 0.7624 (mmtm) REVERT: A 647 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8469 (mtmt) REVERT: A 678 MET cc_start: 0.6544 (mmm) cc_final: 0.6005 (mmm) REVERT: A 822 ILE cc_start: 0.8313 (mt) cc_final: 0.8077 (tp) REVERT: A 841 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7914 (mmtt) REVERT: A 863 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6023 (tt) REVERT: A 877 GLN cc_start: 0.7876 (mt0) cc_final: 0.7389 (mt0) REVERT: A 881 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7576 (mp0) REVERT: A 958 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7638 (ttpp) REVERT: A 967 MET cc_start: 0.7389 (mtp) cc_final: 0.6776 (mtp) REVERT: A 971 ASP cc_start: 0.7767 (m-30) cc_final: 0.7346 (m-30) REVERT: A 986 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 1058 THR cc_start: 0.8061 (t) cc_final: 0.7720 (p) REVERT: A 1060 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 1126 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7132 (pt) REVERT: B 103 THR cc_start: 0.8045 (p) cc_final: 0.7817 (p) REVERT: B 125 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7810 (mp0) REVERT: B 171 LEU cc_start: 0.8288 (tp) cc_final: 0.7991 (mp) REVERT: B 214 VAL cc_start: 0.8793 (p) cc_final: 0.8495 (m) REVERT: B 236 LEU cc_start: 0.8059 (mm) cc_final: 0.7704 (mp) REVERT: B 269 LEU cc_start: 0.7665 (mt) cc_final: 0.7393 (mm) REVERT: B 338 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7764 (mtmm) REVERT: B 346 GLU cc_start: 0.7678 (tt0) cc_final: 0.7417 (tt0) REVERT: B 347 VAL cc_start: 0.8916 (p) cc_final: 0.8684 (t) REVERT: B 579 MET cc_start: 0.6497 (mtp) cc_final: 0.6181 (mtp) REVERT: B 580 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7172 (tp30) REVERT: B 591 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8019 (mtpp) REVERT: B 609 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7355 (mtp-110) REVERT: B 632 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7862 (mtpp) REVERT: B 633 LYS cc_start: 0.8114 (mttt) cc_final: 0.7709 (mmtm) REVERT: B 678 MET cc_start: 0.6114 (mmm) cc_final: 0.5664 (mmm) REVERT: B 810 MET cc_start: 0.7092 (mmm) cc_final: 0.6753 (mmm) REVERT: B 863 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6001 (tt) REVERT: B 866 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 967 MET cc_start: 0.7509 (mtp) cc_final: 0.7278 (mmm) REVERT: B 986 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 1007 LYS cc_start: 0.8187 (tttt) cc_final: 0.7949 (tttm) REVERT: B 1115 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 1185 ARG cc_start: 0.6458 (mmt180) cc_final: 0.5213 (mmt180) outliers start: 47 outliers final: 35 residues processed: 422 average time/residue: 0.2810 time to fit residues: 176.1431 Evaluate side-chains 418 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 380 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL 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 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 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 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 450 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 126 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN A 600 HIS A 886 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 B1120 HIS ** 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 = 0.4143 r_free = 0.4143 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143123 restraints weight = 23570.739| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.93 r_work: 0.3591 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16528 Z= 0.141 Angle : 0.518 10.241 22420 Z= 0.271 Chirality : 0.041 0.246 2696 Planarity : 0.004 0.052 2748 Dihedral : 9.645 174.425 2244 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.79 % Allowed : 15.42 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2020 helix: 1.59 (0.13), residues: 1478 sheet: 0.48 (0.59), residues: 62 loop : -0.34 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.004 0.001 HIS B1120 PHE 0.018 0.001 PHE A 254 TYR 0.019 0.001 TYR B 984 ARG 0.012 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1174) hydrogen bonds : angle 4.09499 ( 3456) covalent geometry : bond 0.00312 (16528) covalent geometry : angle 0.51765 (22420) *********************** 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 454 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 405 time to evaluate : 1.816 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 126 HIS cc_start: 0.7797 (m-70) cc_final: 0.7592 (m90) REVERT: A 197 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6660 (mp0) REVERT: A 199 MET cc_start: 0.8046 (mmm) cc_final: 0.7665 (mmm) REVERT: A 217 LEU cc_start: 0.8504 (mp) cc_final: 0.8273 (mm) REVERT: A 269 LEU cc_start: 0.7582 (mt) cc_final: 0.7338 (mm) REVERT: A 347 VAL cc_start: 0.8908 (p) cc_final: 0.8658 (t) REVERT: A 377 LEU cc_start: 0.8349 (mt) cc_final: 0.7996 (mt) REVERT: A 609 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7303 (mtp-110) REVERT: A 633 LYS cc_start: 0.8037 (mttt) cc_final: 0.7801 (mttt) REVERT: A 678 MET cc_start: 0.6362 (mmm) cc_final: 0.5885 (mmm) REVERT: A 822 ILE cc_start: 0.8370 (mt) cc_final: 0.8160 (tp) REVERT: A 841 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7848 (mmmt) REVERT: A 863 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.6163 (tt) REVERT: A 866 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7655 (tp30) REVERT: A 877 GLN cc_start: 0.7797 (mt0) cc_final: 0.7246 (mt0) REVERT: A 881 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7533 (mp0) REVERT: A 967 MET cc_start: 0.7398 (mtp) cc_final: 0.6848 (mtp) REVERT: A 971 ASP cc_start: 0.7826 (m-30) cc_final: 0.7414 (m-30) REVERT: A 972 PHE cc_start: 0.7876 (t80) cc_final: 0.7570 (t80) REVERT: A 986 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 1033 GLU cc_start: 0.6959 (mp0) cc_final: 0.6755 (mp0) REVERT: A 1058 THR cc_start: 0.8152 (t) cc_final: 0.7834 (p) REVERT: A 1060 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7551 (mp0) REVERT: A 1126 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7127 (pt) REVERT: B 125 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7860 (mp0) REVERT: B 171 LEU cc_start: 0.8312 (tp) cc_final: 0.8003 (mp) REVERT: B 214 VAL cc_start: 0.8922 (p) cc_final: 0.8611 (m) REVERT: B 236 LEU cc_start: 0.8072 (mm) cc_final: 0.7705 (mp) REVERT: B 280 TYR cc_start: 0.8323 (t80) cc_final: 0.8032 (t80) REVERT: B 579 MET cc_start: 0.6554 (mtp) cc_final: 0.6277 (mtp) REVERT: B 591 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7997 (mtpp) REVERT: B 632 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7869 (mtpp) REVERT: B 633 LYS cc_start: 0.8127 (mttt) cc_final: 0.7789 (mmtm) REVERT: B 678 MET cc_start: 0.5980 (mmm) cc_final: 0.5534 (mmm) REVERT: B 810 MET cc_start: 0.7115 (mmm) cc_final: 0.6794 (mmm) REVERT: B 832 GLN cc_start: 0.8218 (tp40) cc_final: 0.7737 (tp-100) REVERT: B 986 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 1007 LYS cc_start: 0.8171 (tttt) cc_final: 0.7966 (tttm) REVERT: B 1185 ARG cc_start: 0.6384 (mmt180) cc_final: 0.5278 (mmt180) outliers start: 49 outliers final: 35 residues processed: 431 average time/residue: 0.2983 time to fit residues: 187.9754 Evaluate side-chains 417 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 380 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 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 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 886 GLN 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 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 363 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 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 99 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 HIS ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.172463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143119 restraints weight = 23337.822| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.98 r_work: 0.3589 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16528 Z= 0.136 Angle : 0.523 10.228 22420 Z= 0.273 Chirality : 0.040 0.251 2696 Planarity : 0.004 0.048 2748 Dihedral : 9.620 175.024 2244 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.07 % Allowed : 16.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2020 helix: 1.65 (0.13), residues: 1476 sheet: 0.49 (0.48), residues: 80 loop : -0.22 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.000 HIS A 908 PHE 0.018 0.001 PHE A 254 TYR 0.019 0.001 TYR B 984 ARG 0.009 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 1174) hydrogen bonds : angle 4.04872 ( 3456) covalent geometry : bond 0.00299 (16528) covalent geometry : angle 0.52299 (22420) *********************** 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 443 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 1.794 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 126 HIS cc_start: 0.7695 (m-70) cc_final: 0.7488 (m90) REVERT: A 154 MET cc_start: 0.8735 (ttp) cc_final: 0.8441 (mtp) REVERT: A 197 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6653 (mp0) REVERT: A 199 MET cc_start: 0.7998 (mmm) cc_final: 0.7594 (mmm) REVERT: A 217 LEU cc_start: 0.8405 (mp) cc_final: 0.8194 (mm) REVERT: A 377 LEU cc_start: 0.8311 (mt) cc_final: 0.7928 (mt) REVERT: A 390 ILE cc_start: 0.7436 (mm) cc_final: 0.7186 (mt) REVERT: A 600 HIS cc_start: 0.7577 (m-70) cc_final: 0.7355 (m-70) REVERT: A 633 LYS cc_start: 0.8067 (mttt) cc_final: 0.7828 (mttt) REVERT: A 678 MET cc_start: 0.6461 (mmm) cc_final: 0.5946 (mmm) REVERT: A 822 ILE cc_start: 0.8327 (mt) cc_final: 0.8043 (tp) REVERT: A 841 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7879 (mmtt) REVERT: A 863 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6105 (tt) REVERT: A 866 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7534 (tp30) REVERT: A 877 GLN cc_start: 0.7896 (mt0) cc_final: 0.7309 (mt0) REVERT: A 881 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7582 (mp0) REVERT: A 967 MET cc_start: 0.7396 (mtp) cc_final: 0.6855 (mtp) REVERT: A 971 ASP cc_start: 0.7793 (m-30) cc_final: 0.7352 (m-30) REVERT: A 972 PHE cc_start: 0.7829 (t80) cc_final: 0.7518 (t80) REVERT: A 986 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 1058 THR cc_start: 0.8157 (t) cc_final: 0.7803 (p) REVERT: A 1060 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7393 (mp0) REVERT: A 1126 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7115 (pt) REVERT: B 125 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7729 (mp0) REVERT: B 140 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7807 (mp10) REVERT: B 154 MET cc_start: 0.8537 (tpp) cc_final: 0.8205 (mtp) REVERT: B 171 LEU cc_start: 0.8270 (tp) cc_final: 0.7956 (mp) REVERT: B 236 LEU cc_start: 0.8040 (mm) cc_final: 0.7677 (mp) REVERT: B 280 TYR cc_start: 0.8315 (t80) cc_final: 0.8066 (t80) REVERT: B 579 MET cc_start: 0.6729 (mtp) cc_final: 0.6323 (mtp) REVERT: B 591 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7982 (mtpp) REVERT: B 633 LYS cc_start: 0.8206 (mttt) cc_final: 0.7773 (mmtm) REVERT: B 643 TRP cc_start: 0.8165 (t60) cc_final: 0.7872 (t60) REVERT: B 678 MET cc_start: 0.6059 (mmm) cc_final: 0.5543 (mmm) REVERT: B 810 MET cc_start: 0.7062 (mmm) cc_final: 0.6723 (mmm) REVERT: B 832 GLN cc_start: 0.8278 (tp40) cc_final: 0.7930 (tm-30) REVERT: B 866 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 967 MET cc_start: 0.7695 (mmm) cc_final: 0.7464 (mmm) REVERT: B 986 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 1007 LYS cc_start: 0.8164 (tttt) cc_final: 0.7838 (tttm) REVERT: B 1051 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7836 (pttm) REVERT: B 1185 ARG cc_start: 0.6466 (mmt180) cc_final: 0.5398 (mmt180) outliers start: 54 outliers final: 43 residues processed: 421 average time/residue: 0.2998 time to fit residues: 184.3723 Evaluate side-chains 423 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 377 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL 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 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 863 ILE Chi-restraints excluded: chain A residue 873 THR 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 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 164 SER Chi-restraints excluded: chain B residue 217 LEU 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 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 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 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 100 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN A 886 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142987 restraints weight = 23322.265| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.93 r_work: 0.3599 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16528 Z= 0.154 Angle : 0.548 10.716 22420 Z= 0.284 Chirality : 0.041 0.270 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.564 172.830 2244 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.24 % Allowed : 16.89 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2020 helix: 1.61 (0.13), residues: 1474 sheet: 0.47 (0.48), residues: 80 loop : -0.16 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.003 0.001 HIS A 908 PHE 0.020 0.001 PHE A 254 TYR 0.012 0.001 TYR A 313 ARG 0.009 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 1174) hydrogen bonds : angle 4.11602 ( 3456) covalent geometry : bond 0.00344 (16528) covalent geometry : angle 0.54820 (22420) *********************** 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 443 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8713 (ttp) cc_final: 0.8429 (mtp) REVERT: A 197 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6618 (mp0) REVERT: A 217 LEU cc_start: 0.8467 (mp) cc_final: 0.8249 (mm) REVERT: A 377 LEU cc_start: 0.8330 (mt) cc_final: 0.7995 (mt) REVERT: A 390 ILE cc_start: 0.7475 (mm) cc_final: 0.7229 (mt) REVERT: A 633 LYS cc_start: 0.8064 (mttt) cc_final: 0.7575 (mmtm) REVERT: A 678 MET cc_start: 0.6519 (mmm) cc_final: 0.5991 (mmm) REVERT: A 822 ILE cc_start: 0.8381 (mt) cc_final: 0.8113 (tp) REVERT: A 841 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7560 (mmmt) REVERT: A 958 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7521 (ttpp) REVERT: A 967 MET cc_start: 0.7448 (mtp) cc_final: 0.6907 (mtp) REVERT: A 971 ASP cc_start: 0.7750 (m-30) cc_final: 0.7333 (m-30) REVERT: A 986 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 1060 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7540 (mp0) REVERT: A 1126 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7133 (pt) REVERT: B 171 LEU cc_start: 0.8290 (tp) cc_final: 0.7971 (mp) REVERT: B 214 VAL cc_start: 0.8859 (p) cc_final: 0.8605 (m) REVERT: B 236 LEU cc_start: 0.8080 (mm) cc_final: 0.7701 (mp) REVERT: B 280 TYR cc_start: 0.8333 (t80) cc_final: 0.8076 (t80) REVERT: B 346 GLU cc_start: 0.7631 (tt0) cc_final: 0.7426 (tt0) REVERT: B 506 ASN cc_start: 0.8219 (m-40) cc_final: 0.7864 (t0) REVERT: B 517 PHE cc_start: 0.6908 (m-80) cc_final: 0.6484 (m-10) REVERT: B 579 MET cc_start: 0.6778 (mtp) cc_final: 0.6373 (mtp) REVERT: B 591 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7995 (mtpp) REVERT: B 632 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7897 (mtpp) REVERT: B 633 LYS cc_start: 0.8180 (mttt) cc_final: 0.7879 (mmtt) REVERT: B 678 MET cc_start: 0.6054 (mmm) cc_final: 0.5529 (mmm) REVERT: B 810 MET cc_start: 0.6876 (mmm) cc_final: 0.6566 (mmm) REVERT: B 866 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 887 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: B 986 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7311 (mt-10) REVERT: B 1007 LYS cc_start: 0.8151 (tttt) cc_final: 0.7841 (tttm) REVERT: B 1051 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7750 (pttp) REVERT: B 1185 ARG cc_start: 0.6465 (mmt180) cc_final: 0.5561 (mmt180) outliers start: 57 outliers final: 45 residues processed: 419 average time/residue: 0.2794 time to fit residues: 173.6382 Evaluate side-chains 420 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ARG 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 867 LEU Chi-restraints excluded: chain A residue 873 THR 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 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 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 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 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 56 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 114 optimal weight: 0.3980 chunk 113 optimal weight: 0.2980 chunk 136 optimal weight: 0.4980 chunk 174 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A 877 GLN A 886 GLN A1114 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.172561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143462 restraints weight = 23190.859| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.93 r_work: 0.3613 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3500 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= 0.129 Angle : 0.552 10.955 22420 Z= 0.285 Chirality : 0.041 0.268 2696 Planarity : 0.004 0.048 2748 Dihedral : 9.567 173.970 2244 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.96 % Allowed : 17.63 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 2020 helix: 1.74 (0.13), residues: 1474 sheet: 0.30 (0.49), residues: 80 loop : -0.13 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.003 0.001 HIS B 126 PHE 0.043 0.001 PHE B 201 TYR 0.015 0.001 TYR A 313 ARG 0.007 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1174) hydrogen bonds : angle 4.04396 ( 3456) covalent geometry : bond 0.00279 (16528) covalent geometry : angle 0.55195 (22420) *********************** 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 436 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 384 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6589 (mp0) REVERT: A 205 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7648 (mpp) REVERT: A 217 LEU cc_start: 0.8453 (mp) cc_final: 0.8240 (mm) REVERT: A 377 LEU cc_start: 0.8302 (mt) cc_final: 0.7995 (mt) REVERT: A 390 ILE cc_start: 0.7419 (mm) cc_final: 0.7165 (mt) REVERT: A 633 LYS cc_start: 0.8057 (mttt) cc_final: 0.7578 (mmtm) REVERT: A 678 MET cc_start: 0.6461 (mmm) cc_final: 0.5941 (mmm) REVERT: A 841 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7865 (mmtt) REVERT: A 877 GLN cc_start: 0.7768 (mt0) cc_final: 0.7534 (mt0) REVERT: A 958 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7498 (ttpp) REVERT: A 967 MET cc_start: 0.7433 (mtp) cc_final: 0.6924 (mtp) REVERT: A 971 ASP cc_start: 0.7777 (m-30) cc_final: 0.7364 (m-30) REVERT: A 986 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 1060 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7500 (mp0) REVERT: A 1126 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7116 (pt) REVERT: B 125 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7314 (mp0) REVERT: B 140 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7737 (mp10) REVERT: B 171 LEU cc_start: 0.8286 (tp) cc_final: 0.8008 (mp) REVERT: B 205 MET cc_start: 0.7625 (mpp) cc_final: 0.7390 (mpp) REVERT: B 214 VAL cc_start: 0.8850 (p) cc_final: 0.8593 (m) REVERT: B 236 LEU cc_start: 0.8029 (mm) cc_final: 0.7684 (mp) REVERT: B 280 TYR cc_start: 0.8292 (t80) cc_final: 0.8032 (t80) REVERT: B 346 GLU cc_start: 0.7641 (tt0) cc_final: 0.7434 (tt0) REVERT: B 579 MET cc_start: 0.6753 (mtp) cc_final: 0.6348 (mtp) REVERT: B 591 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7986 (mtpp) REVERT: B 633 LYS cc_start: 0.8190 (mttt) cc_final: 0.7908 (mmtt) REVERT: B 678 MET cc_start: 0.5992 (mmm) cc_final: 0.5476 (mmm) REVERT: B 810 MET cc_start: 0.7043 (mmm) cc_final: 0.6689 (mmm) REVERT: B 832 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7957 (tm-30) REVERT: B 867 LEU cc_start: 0.7996 (mm) cc_final: 0.7731 (mt) REVERT: B 887 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7824 (mmm-85) REVERT: B 967 MET cc_start: 0.7872 (mmm) cc_final: 0.7610 (mmm) REVERT: B 986 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 1007 LYS cc_start: 0.8165 (tttt) cc_final: 0.7846 (tttm) REVERT: B 1051 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7738 (pttp) REVERT: B 1185 ARG cc_start: 0.6419 (mmt180) cc_final: 0.5519 (mmt180) outliers start: 52 outliers final: 43 residues processed: 416 average time/residue: 0.2914 time to fit residues: 179.5965 Evaluate side-chains 412 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 405 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 705 MET 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 886 GLN Chi-restraints excluded: chain A residue 917 GLN 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 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 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 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 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 168 optimal weight: 10.0000 chunk 148 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A 886 GLN A1114 GLN ** A1172 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 = 0.4147 r_free = 0.4147 target = 0.172309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142825 restraints weight = 23376.194| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.94 r_work: 0.3606 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16528 Z= 0.145 Angle : 0.570 9.251 22420 Z= 0.296 Chirality : 0.042 0.287 2696 Planarity : 0.004 0.057 2748 Dihedral : 9.563 174.128 2244 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.24 % Allowed : 18.15 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2020 helix: 1.71 (0.13), residues: 1476 sheet: 0.15 (0.48), residues: 80 loop : -0.17 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 635 HIS 0.003 0.001 HIS B 600 PHE 0.036 0.001 PHE B 201 TYR 0.015 0.001 TYR A 358 ARG 0.013 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1174) hydrogen bonds : angle 4.06626 ( 3456) covalent geometry : bond 0.00321 (16528) covalent geometry : angle 0.57005 (22420) *********************** 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 443 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 2.643 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 217 LEU cc_start: 0.8432 (mp) cc_final: 0.8220 (mm) REVERT: A 218 LYS cc_start: 0.8251 (tttt) cc_final: 0.7873 (tttt) REVERT: A 377 LEU cc_start: 0.8316 (mt) cc_final: 0.8006 (mt) REVERT: A 390 ILE cc_start: 0.7451 (mm) cc_final: 0.7206 (mt) REVERT: A 633 LYS cc_start: 0.8159 (mttt) cc_final: 0.7686 (mmtm) REVERT: A 678 MET cc_start: 0.6781 (mmm) cc_final: 0.6185 (mmm) REVERT: A 841 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7880 (mmtt) REVERT: A 847 GLU cc_start: 0.7249 (tp30) cc_final: 0.6879 (tm-30) REVERT: A 958 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7493 (ttpp) REVERT: A 967 MET cc_start: 0.7416 (mtp) cc_final: 0.6893 (mtp) REVERT: A 971 ASP cc_start: 0.7787 (m-30) cc_final: 0.7368 (m-30) REVERT: A 986 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 1060 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7506 (mp0) REVERT: A 1126 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7068 (pt) REVERT: B 125 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7391 (mp0) REVERT: B 140 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7717 (mp10) REVERT: B 171 LEU cc_start: 0.8261 (tp) cc_final: 0.8006 (mp) REVERT: B 214 VAL cc_start: 0.8883 (p) cc_final: 0.8619 (m) REVERT: B 236 LEU cc_start: 0.8052 (mm) cc_final: 0.7699 (mp) REVERT: B 280 TYR cc_start: 0.8310 (t80) cc_final: 0.8034 (t80) REVERT: B 579 MET cc_start: 0.6768 (mtp) cc_final: 0.6369 (mtp) REVERT: B 591 LYS cc_start: 0.8279 (mtpp) cc_final: 0.8001 (mtpp) REVERT: B 596 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8066 (mttm) REVERT: B 633 LYS cc_start: 0.8234 (mttt) cc_final: 0.8027 (mttt) REVERT: B 643 TRP cc_start: 0.7835 (t60) cc_final: 0.7441 (t60) REVERT: B 810 MET cc_start: 0.6818 (mmm) cc_final: 0.6514 (mmm) REVERT: B 832 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7973 (tm-30) REVERT: B 841 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7785 (mmmt) REVERT: B 887 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7845 (mmm-85) REVERT: B 986 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 1078 ASP cc_start: 0.8199 (m-30) cc_final: 0.7987 (m-30) REVERT: B 1185 ARG cc_start: 0.6468 (mmt180) cc_final: 0.5599 (mmt180) outliers start: 57 outliers final: 52 residues processed: 419 average time/residue: 0.3466 time to fit residues: 214.4819 Evaluate side-chains 433 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LEU 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 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 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 863 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 917 GLN 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 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 251 MET 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 456 LEU 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 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 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 184 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 193 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 199 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 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 = 0.4144 r_free = 0.4144 target = 0.172272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142996 restraints weight = 23413.400| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.92 r_work: 0.3611 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16528 Z= 0.146 Angle : 0.586 9.539 22420 Z= 0.304 Chirality : 0.042 0.301 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.569 174.437 2244 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.24 % Allowed : 18.49 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 2020 helix: 1.70 (0.13), residues: 1472 sheet: 0.09 (0.48), residues: 80 loop : -0.11 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 643 HIS 0.003 0.001 HIS B 600 PHE 0.047 0.001 PHE B 201 TYR 0.025 0.001 TYR B 267 ARG 0.006 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 1174) hydrogen bonds : angle 4.08722 ( 3456) covalent geometry : bond 0.00325 (16528) covalent geometry : angle 0.58626 (22420) ********************** 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: 57 poor density : 382 time to evaluate : 1.933 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: 0.7335 (ptp-170) cc_final: 0.7123 (ptp-110) REVERT: A 205 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7444 (mpp) REVERT: A 218 LYS cc_start: 0.8257 (tttt) cc_final: 0.7894 (tttt) REVERT: A 377 LEU cc_start: 0.8311 (mt) cc_final: 0.7988 (mt) REVERT: A 390 ILE cc_start: 0.7445 (mm) cc_final: 0.7198 (mt) REVERT: A 633 LYS cc_start: 0.8147 (mttt) cc_final: 0.7698 (mmtm) REVERT: A 678 MET cc_start: 0.6796 (mmm) cc_final: 0.6267 (mmm) REVERT: A 841 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7888 (mmtt) REVERT: A 958 LYS cc_start: 0.7943 (ttpp) cc_final: 0.7550 (ttpp) REVERT: A 967 MET cc_start: 0.7392 (mtp) cc_final: 0.7017 (mmm) REVERT: A 971 ASP cc_start: 0.7790 (m-30) cc_final: 0.7286 (m-30) REVERT: A 986 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 1060 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7485 (mp0) REVERT: A 1126 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7002 (pt) REVERT: B 140 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7705 (mp10) REVERT: B 171 LEU cc_start: 0.8257 (tp) cc_final: 0.8002 (mp) REVERT: B 214 VAL cc_start: 0.8902 (p) cc_final: 0.8642 (m) REVERT: B 236 LEU cc_start: 0.8068 (mm) cc_final: 0.7719 (mp) REVERT: B 280 TYR cc_start: 0.8258 (t80) cc_final: 0.8004 (t80) REVERT: B 579 MET cc_start: 0.6784 (mtp) cc_final: 0.6390 (mtp) REVERT: B 591 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8011 (mtpp) REVERT: B 596 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8067 (mttm) REVERT: B 643 TRP cc_start: 0.7783 (t60) cc_final: 0.7392 (t60) REVERT: B 810 MET cc_start: 0.6953 (mmm) cc_final: 0.6634 (mmm) REVERT: B 832 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7969 (tm-30) REVERT: B 841 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7785 (mmmt) REVERT: B 957 LEU cc_start: 0.8633 (tp) cc_final: 0.8386 (tt) REVERT: B 967 MET cc_start: 0.7880 (mmm) cc_final: 0.7543 (mmm) REVERT: B 986 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 1045 MET cc_start: 0.6864 (pmm) cc_final: 0.6516 (tmm) REVERT: B 1078 ASP cc_start: 0.8185 (m-30) cc_final: 0.7976 (m-30) REVERT: B 1185 ARG cc_start: 0.6438 (mmt180) cc_final: 0.5613 (mmt180) outliers start: 57 outliers final: 51 residues processed: 412 average time/residue: 0.3133 time to fit residues: 191.2591 Evaluate side-chains 430 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 205 MET 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 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 863 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 917 GLN 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 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 251 MET 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 456 LEU 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 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 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 136 optimal weight: 0.1980 chunk 191 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.172938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143648 restraints weight = 23232.360| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.92 r_work: 0.3611 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16528 Z= 0.145 Angle : 0.592 11.039 22420 Z= 0.305 Chirality : 0.042 0.308 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.552 173.887 2244 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.19 % Allowed : 18.94 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.19), residues: 2020 helix: 1.68 (0.13), residues: 1476 sheet: 0.08 (0.49), residues: 80 loop : -0.24 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.004 0.001 HIS B 600 PHE 0.044 0.001 PHE B 201 TYR 0.023 0.001 TYR B 267 ARG 0.010 0.000 ARG B 887 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1174) hydrogen bonds : angle 4.07952 ( 3456) covalent geometry : bond 0.00324 (16528) covalent geometry : angle 0.59181 (22420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10550.11 seconds wall clock time: 183 minutes 18.17 seconds (10998.17 seconds total)