Starting phenix.real_space_refine on Sun May 18 01:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdu_17621/05_2025/8pdu_17621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdu_17621/05_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_17621/05_2025/8pdu_17621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdu_17621/05_2025/8pdu_17621.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdu_17621/05_2025/8pdu_17621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdu_17621/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.26, per 1000 atoms: 0.57 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: 4.21 Conformation dependent library (CDL) restraints added in 2.0 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: 1.96 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: 5.74 Time building geometry restraints manager: 4.88 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: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- 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 : 1.649 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: 0.3066 time to fit residues: 204.7687 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 : 1.699 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143780 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: 0.3461 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 1.821 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: 0.8004 (mttm) cc_final: 0.7716 (mttm) REVERT: A 77 VAL cc_start: 0.8521 (p) cc_final: 0.8293 (t) REVERT: A 103 THR cc_start: 0.7979 (p) cc_final: 0.7695 (p) REVERT: A 125 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7758 (mm-30) REVERT: A 199 MET cc_start: 0.7975 (mmm) cc_final: 0.7771 (mmm) REVERT: A 205 MET cc_start: 0.8136 (tpp) cc_final: 0.7935 (tpp) REVERT: A 214 VAL cc_start: 0.8766 (p) cc_final: 0.8561 (m) REVERT: A 337 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 377 LEU cc_start: 0.8339 (mt) cc_final: 0.8011 (mt) REVERT: A 475 GLN cc_start: 0.7698 (tp40) cc_final: 0.7492 (tp40) REVERT: A 520 ASP cc_start: 0.7948 (p0) cc_final: 0.7262 (p0) REVERT: A 579 MET cc_start: 0.6460 (mtp) cc_final: 0.6083 (mtp) REVERT: A 580 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6951 (tp30) REVERT: A 588 LYS cc_start: 0.7506 (tmmt) cc_final: 0.7286 (ttmt) REVERT: A 591 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7914 (mtpp) REVERT: A 629 ASP cc_start: 0.7724 (m-30) cc_final: 0.7373 (m-30) REVERT: A 630 ASP cc_start: 0.7838 (m-30) cc_final: 0.7622 (m-30) REVERT: A 633 LYS cc_start: 0.8039 (mttt) cc_final: 0.7495 (mmtm) REVERT: A 634 SER cc_start: 0.7839 (t) cc_final: 0.7608 (p) REVERT: A 647 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8217 (mmtm) REVERT: A 650 ASP cc_start: 0.8014 (m-30) cc_final: 0.7801 (m-30) REVERT: A 678 MET cc_start: 0.6483 (mmm) cc_final: 0.6055 (mmm) REVERT: A 822 ILE cc_start: 0.8169 (mt) cc_final: 0.7923 (tp) REVERT: A 958 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7558 (ttpp) REVERT: A 967 MET cc_start: 0.7333 (mtp) cc_final: 0.6733 (mtp) REVERT: A 971 ASP cc_start: 0.7713 (m-30) cc_final: 0.7276 (m-30) REVERT: A 976 ARG cc_start: 0.8461 (mpt180) cc_final: 0.7965 (mmt-90) REVERT: A 982 PHE cc_start: 0.7662 (m-80) cc_final: 0.7167 (m-10) REVERT: A 986 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 1003 SER cc_start: 0.8734 (t) cc_final: 0.8500 (t) REVERT: A 1038 VAL cc_start: 0.8536 (t) cc_final: 0.8274 (p) REVERT: A 1058 THR cc_start: 0.8026 (t) cc_final: 0.7604 (p) REVERT: A 1060 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 125 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 199 MET cc_start: 0.8008 (mmm) cc_final: 0.7745 (mmm) REVERT: B 214 VAL cc_start: 0.8767 (p) cc_final: 0.8517 (m) REVERT: B 236 LEU cc_start: 0.8052 (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: 0.8385 (mtmm) cc_final: 0.7778 (mtmt) REVERT: B 475 GLN cc_start: 0.7708 (tp40) cc_final: 0.7500 (tp-100) REVERT: B 579 MET cc_start: 0.6573 (mtp) cc_final: 0.6046 (mtp) REVERT: B 580 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7166 (tp30) REVERT: B 588 LYS cc_start: 0.7577 (tmmt) cc_final: 0.7351 (ttmt) REVERT: B 591 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7888 (mtpp) REVERT: B 609 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7160 (mtp180) REVERT: B 632 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7904 (mtpp) REVERT: B 633 LYS cc_start: 0.8126 (mttt) cc_final: 0.7731 (mmtm) REVERT: B 678 MET cc_start: 0.6251 (mmm) cc_final: 0.5774 (mmm) REVERT: B 810 MET cc_start: 0.7047 (mmm) cc_final: 0.6703 (mmm) REVERT: B 823 LEU cc_start: 0.8350 (mt) cc_final: 0.8101 (mm) REVERT: B 832 GLN cc_start: 0.8053 (tp40) cc_final: 0.7710 (tp40) REVERT: B 926 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 955 ASN cc_start: 0.8051 (t0) cc_final: 0.7582 (t0) REVERT: B 958 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7592 (ttpp) REVERT: B 986 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7394 (mt-10) REVERT: B 1007 LYS cc_start: 0.8220 (tttt) cc_final: 0.7861 (tttp) REVERT: B 1104 MET cc_start: 0.6599 (mmm) cc_final: 0.6343 (tpt) REVERT: B 1125 TYR cc_start: 0.6968 (p90) cc_final: 0.6338 (p90) outliers start: 34 outliers final: 19 residues processed: 444 average time/residue: 0.2850 time to fit residues: 185.4057 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 : 1.682 ------------------------------------------------------------------------------- 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: 7.9990 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: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.172444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143443 restraints weight = 23197.874| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.92 r_work: 0.3592 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: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16528 Z= 0.151 Angle : 0.523 6.874 22420 Z= 0.281 Chirality : 0.041 0.211 2696 Planarity : 0.004 0.051 2748 Dihedral : 9.914 178.587 2244 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 14.05 % Favored : 83.62 % 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: 1.55 (0.19), residues: 2020 helix: 1.56 (0.13), residues: 1460 sheet: 0.35 (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 0.019 0.001 PHE B 517 TYR 0.019 0.001 TYR B 984 ARG 0.005 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1174) hydrogen bonds : angle 4.26198 ( 3456) covalent geometry : bond 0.00329 (16528) covalent geometry : angle 0.52300 (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 446 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 405 time to evaluate : 1.623 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: 0.8792 (tpp) cc_final: 0.8342 (tpp) REVERT: A 199 MET cc_start: 0.8037 (mmm) cc_final: 0.7789 (mmm) REVERT: A 214 VAL cc_start: 0.8879 (p) cc_final: 0.8664 (m) REVERT: A 269 LEU cc_start: 0.7559 (mt) cc_final: 0.7336 (mm) REVERT: A 337 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 347 VAL cc_start: 0.8858 (p) cc_final: 0.8595 (t) REVERT: A 377 LEU cc_start: 0.8375 (mt) cc_final: 0.8100 (mt) REVERT: A 494 MET cc_start: 0.7835 (mmm) cc_final: 0.7499 (tpt) REVERT: A 579 MET cc_start: 0.6484 (mtp) cc_final: 0.6199 (mtp) REVERT: A 580 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7050 (tp30) REVERT: A 591 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7943 (mtpp) REVERT: A 629 ASP cc_start: 0.7684 (m-30) cc_final: 0.7354 (m-30) REVERT: A 633 LYS cc_start: 0.7995 (mttt) cc_final: 0.7486 (mmtm) REVERT: A 678 MET cc_start: 0.6373 (mmm) cc_final: 0.5898 (mmm) REVERT: A 822 ILE cc_start: 0.8327 (mt) cc_final: 0.8111 (tp) REVERT: A 841 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7973 (mmtt) REVERT: A 866 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7765 (tp30) REVERT: A 958 LYS cc_start: 0.7781 (ttpp) cc_final: 0.7565 (ttpp) REVERT: A 967 MET cc_start: 0.7386 (mtp) cc_final: 0.6796 (mtp) REVERT: A 971 ASP cc_start: 0.7790 (m-30) cc_final: 0.7381 (m-30) REVERT: A 986 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 1058 THR cc_start: 0.8128 (t) cc_final: 0.7738 (p) REVERT: A 1126 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7198 (pt) REVERT: B 103 THR cc_start: 0.8021 (p) cc_final: 0.7784 (p) REVERT: B 125 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 171 LEU cc_start: 0.8312 (tp) cc_final: 0.7998 (mp) REVERT: B 236 LEU cc_start: 0.8069 (mm) cc_final: 0.7737 (mp) REVERT: B 269 LEU cc_start: 0.7666 (mt) cc_final: 0.7400 (mm) REVERT: B 288 PHE cc_start: 0.8695 (t80) cc_final: 0.8486 (t80) REVERT: B 347 VAL cc_start: 0.8863 (p) cc_final: 0.8650 (t) REVERT: B 579 MET cc_start: 0.6514 (mtp) cc_final: 0.6107 (mtp) REVERT: B 591 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7999 (mtpp) REVERT: B 609 ARG cc_start: 0.7608 (mtp-110) cc_final: 0.7250 (mtp180) REVERT: B 632 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7873 (mtpp) REVERT: B 633 LYS cc_start: 0.8083 (mttt) cc_final: 0.7760 (mmtm) REVERT: B 678 MET cc_start: 0.6059 (mmm) cc_final: 0.5621 (mmm) REVERT: B 810 MET cc_start: 0.7114 (mmm) cc_final: 0.6770 (mmm) REVERT: B 823 LEU cc_start: 0.8457 (mt) cc_final: 0.8249 (mm) REVERT: B 832 GLN cc_start: 0.8079 (tp40) cc_final: 0.7784 (tp40) REVERT: B 866 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7683 (tp30) REVERT: B 887 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7914 (mmm-85) REVERT: B 986 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 1007 LYS cc_start: 0.8182 (tttt) cc_final: 0.7970 (tttm) REVERT: B 1115 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7388 (tm-30) outliers start: 41 outliers final: 25 residues processed: 427 average time/residue: 0.2835 time to fit residues: 178.0197 Evaluate side-chains 404 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 378 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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: 0.0030 chunk 191 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 877 GLN A 886 GLN A1120 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B1064 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143994 restraints weight = 23258.918| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.92 r_work: 0.3598 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16528 Z= 0.134 Angle : 0.506 7.678 22420 Z= 0.269 Chirality : 0.040 0.224 2696 Planarity : 0.004 0.052 2748 Dihedral : 9.802 178.829 2244 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.67 % Allowed : 14.62 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2020 helix: 1.58 (0.13), residues: 1478 sheet: 0.54 (0.52), residues: 80 loop : -0.21 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.005 0.001 HIS A1120 PHE 0.014 0.001 PHE B 517 TYR 0.020 0.001 TYR B 984 ARG 0.008 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1174) hydrogen bonds : angle 4.10413 ( 3456) covalent geometry : bond 0.00287 (16528) covalent geometry : angle 0.50573 (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 : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.7806 (m-70) cc_final: 0.7480 (m90) REVERT: A 128 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7003 (ptp-110) REVERT: A 154 MET cc_start: 0.8759 (tpp) cc_final: 0.8229 (tpp) REVERT: A 197 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 199 MET cc_start: 0.8080 (mmm) cc_final: 0.7750 (mmm) REVERT: A 214 VAL cc_start: 0.8857 (p) cc_final: 0.8608 (m) REVERT: A 217 LEU cc_start: 0.8478 (mp) cc_final: 0.8244 (mm) REVERT: A 269 LEU cc_start: 0.7565 (mt) cc_final: 0.7315 (mm) REVERT: A 347 VAL cc_start: 0.8876 (p) cc_final: 0.8635 (t) REVERT: A 377 LEU cc_start: 0.8336 (mt) cc_final: 0.7972 (mt) REVERT: A 520 ASP cc_start: 0.7960 (p0) cc_final: 0.7731 (p0) REVERT: A 591 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7949 (mtpp) REVERT: A 633 LYS cc_start: 0.8019 (mttt) cc_final: 0.7580 (mmtm) REVERT: A 678 MET cc_start: 0.6429 (mmm) cc_final: 0.5918 (mmm) REVERT: A 841 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8017 (mmtt) REVERT: A 863 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.6034 (tt) REVERT: A 877 GLN cc_start: 0.7777 (mt0) cc_final: 0.7264 (mt0) REVERT: A 881 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7531 (mp0) REVERT: A 958 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7641 (ttpp) REVERT: A 967 MET cc_start: 0.7395 (mtp) cc_final: 0.6804 (mtp) REVERT: A 971 ASP cc_start: 0.7827 (m-30) cc_final: 0.7415 (m-30) REVERT: A 986 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 1058 THR cc_start: 0.8069 (t) cc_final: 0.7781 (p) REVERT: A 1060 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 1122 GLU cc_start: 0.7396 (tp30) cc_final: 0.7164 (tp30) REVERT: A 1126 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7120 (pt) REVERT: B 103 THR cc_start: 0.7994 (p) cc_final: 0.7788 (p) REVERT: B 125 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7899 (mp0) REVERT: B 171 LEU cc_start: 0.8338 (tp) cc_final: 0.8043 (mp) REVERT: B 236 LEU cc_start: 0.8078 (mm) cc_final: 0.7713 (mp) REVERT: B 269 LEU cc_start: 0.7652 (mt) cc_final: 0.7382 (mm) REVERT: B 280 TYR cc_start: 0.8295 (t80) cc_final: 0.8008 (t80) REVERT: B 338 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8129 (mtmm) REVERT: B 347 VAL cc_start: 0.8885 (p) cc_final: 0.8659 (t) REVERT: B 579 MET cc_start: 0.6567 (mtp) cc_final: 0.6270 (mtp) REVERT: B 591 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8015 (mtpp) REVERT: B 609 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7281 (mtp-110) REVERT: B 632 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7889 (mtpp) REVERT: B 633 LYS cc_start: 0.8071 (mttt) cc_final: 0.7787 (mmtt) REVERT: B 678 MET cc_start: 0.5988 (mmm) cc_final: 0.5559 (mmm) REVERT: B 695 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 810 MET cc_start: 0.7075 (mmm) cc_final: 0.6741 (mmm) REVERT: B 863 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6151 (tt) REVERT: B 866 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 986 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 1007 LYS cc_start: 0.8168 (tttt) cc_final: 0.7954 (tttm) REVERT: B 1068 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7640 (mm) REVERT: B 1185 ARG cc_start: 0.6371 (mmt180) cc_final: 0.5139 (mmt180) outliers start: 47 outliers final: 34 residues processed: 423 average time/residue: 0.2839 time to fit residues: 176.9710 Evaluate side-chains 416 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG 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 487 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 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 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 695 ILE Chi-restraints excluded: chain B residue 780 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 1068 ILE 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: 1.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 128 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 ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 832 GLN B 889 HIS ** B1156 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 = 0.4138 r_free = 0.4138 target = 0.171956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142741 restraints weight = 23547.678| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.93 r_work: 0.3585 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16528 Z= 0.162 Angle : 0.535 10.012 22420 Z= 0.281 Chirality : 0.041 0.253 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.669 174.788 2244 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.01 % Allowed : 15.47 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2020 helix: 1.56 (0.13), residues: 1474 sheet: 0.56 (0.59), residues: 62 loop : -0.25 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 635 HIS 0.003 0.001 HIS B 889 PHE 0.016 0.001 PHE A 517 TYR 0.018 0.001 TYR B 984 ARG 0.013 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 1174) hydrogen bonds : angle 4.13807 ( 3456) covalent geometry : bond 0.00364 (16528) covalent geometry : angle 0.53514 (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 442 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 389 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7144 (ptp-110) REVERT: A 154 MET cc_start: 0.8712 (tpp) cc_final: 0.8280 (ttm) REVERT: A 197 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6729 (mp0) REVERT: A 199 MET cc_start: 0.8047 (mmm) cc_final: 0.7667 (mmm) REVERT: A 217 LEU cc_start: 0.8499 (mp) cc_final: 0.8266 (mm) REVERT: A 377 LEU cc_start: 0.8342 (mt) cc_final: 0.7979 (mt) REVERT: A 591 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7997 (mtpp) REVERT: A 609 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7309 (mtp-110) REVERT: A 633 LYS cc_start: 0.8008 (mttt) cc_final: 0.7570 (mmtm) REVERT: A 678 MET cc_start: 0.6346 (mmm) cc_final: 0.5865 (mmm) REVERT: A 822 ILE cc_start: 0.8390 (tp) cc_final: 0.8071 (pt) REVERT: A 832 GLN cc_start: 0.8171 (tp40) cc_final: 0.7896 (tp40) REVERT: A 841 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7584 (mmmt) REVERT: A 863 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.6171 (tt) REVERT: A 866 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7714 (tp30) REVERT: A 877 GLN cc_start: 0.7826 (mt0) cc_final: 0.7297 (mt0) REVERT: A 881 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7557 (mp0) REVERT: A 958 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7691 (ttpp) REVERT: A 967 MET cc_start: 0.7437 (mtp) cc_final: 0.6869 (mtp) REVERT: A 971 ASP cc_start: 0.7842 (m-30) cc_final: 0.7431 (m-30) REVERT: A 972 PHE cc_start: 0.7866 (t80) cc_final: 0.7558 (t80) REVERT: A 986 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 1058 THR cc_start: 0.8150 (t) cc_final: 0.7831 (p) REVERT: A 1060 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7574 (mp0) REVERT: A 1122 GLU cc_start: 0.7404 (tp30) cc_final: 0.7075 (tp30) REVERT: A 1126 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7101 (pt) REVERT: B 125 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7860 (mp0) REVERT: B 140 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7828 (mp10) REVERT: B 171 LEU cc_start: 0.8332 (tp) cc_final: 0.8033 (mp) REVERT: B 214 VAL cc_start: 0.8926 (p) cc_final: 0.8617 (m) REVERT: B 236 LEU cc_start: 0.8106 (mm) cc_final: 0.7743 (mp) REVERT: B 280 TYR cc_start: 0.8320 (t80) cc_final: 0.8039 (t80) REVERT: B 347 VAL cc_start: 0.8905 (p) cc_final: 0.8685 (t) REVERT: B 517 PHE cc_start: 0.6960 (m-10) cc_final: 0.6553 (m-10) REVERT: B 579 MET cc_start: 0.6536 (mtp) cc_final: 0.6257 (mtp) REVERT: B 588 LYS cc_start: 0.7697 (tmmt) cc_final: 0.7496 (ttmt) REVERT: B 591 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7989 (mtpp) REVERT: B 632 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7924 (mtpt) REVERT: B 633 LYS cc_start: 0.8148 (mttt) cc_final: 0.7857 (mmtt) REVERT: B 678 MET cc_start: 0.5877 (mmm) cc_final: 0.5415 (mmm) REVERT: B 810 MET cc_start: 0.7068 (mmm) cc_final: 0.6738 (mmm) REVERT: B 832 GLN cc_start: 0.8231 (tp40) cc_final: 0.7929 (tm-30) REVERT: B 986 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 1007 LYS cc_start: 0.8141 (tttt) cc_final: 0.7925 (tttm) REVERT: B 1185 ARG cc_start: 0.6418 (mmt180) cc_final: 0.5285 (mmt180) outliers start: 53 outliers final: 39 residues processed: 418 average time/residue: 0.2879 time to fit residues: 175.8444 Evaluate side-chains 424 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 382 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG 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 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 837 TYR 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 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 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 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: 0.3980 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 600 HIS A 886 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.172066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142891 restraints weight = 23373.384| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.91 r_work: 0.3590 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16528 Z= 0.147 Angle : 0.524 8.892 22420 Z= 0.277 Chirality : 0.041 0.253 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.594 173.999 2244 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.41 % Allowed : 15.98 % 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: 1.64 (0.19), residues: 2020 helix: 1.59 (0.13), residues: 1476 sheet: 0.46 (0.57), residues: 62 loop : -0.25 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.004 0.001 HIS B 889 PHE 0.013 0.001 PHE B 201 TYR 0.019 0.001 TYR B 984 ARG 0.008 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 1174) hydrogen bonds : angle 4.08451 ( 3456) covalent geometry : bond 0.00327 (16528) covalent geometry : angle 0.52394 (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 440 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7217 (ptp-110) REVERT: A 154 MET cc_start: 0.8613 (tpp) cc_final: 0.8302 (ttm) REVERT: A 197 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6679 (mp0) REVERT: A 199 MET cc_start: 0.8059 (mmm) cc_final: 0.7668 (mmm) REVERT: A 217 LEU cc_start: 0.8495 (mp) cc_final: 0.8276 (mm) REVERT: A 377 LEU cc_start: 0.8337 (mt) cc_final: 0.7993 (mt) REVERT: A 390 ILE cc_start: 0.7476 (mm) cc_final: 0.7240 (mt) REVERT: A 600 HIS cc_start: 0.7585 (m-70) cc_final: 0.7355 (m-70) REVERT: A 633 LYS cc_start: 0.7988 (mttt) cc_final: 0.7566 (mmtm) REVERT: A 678 MET cc_start: 0.6594 (mmm) cc_final: 0.6043 (mmm) REVERT: A 822 ILE cc_start: 0.8442 (tp) cc_final: 0.8060 (pt) REVERT: A 841 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7546 (mmmt) REVERT: A 848 GLU cc_start: 0.7799 (tp30) cc_final: 0.7586 (tp30) REVERT: A 863 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6067 (tt) REVERT: A 877 GLN cc_start: 0.7843 (mt0) cc_final: 0.7286 (mt0) REVERT: A 881 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7556 (mp0) REVERT: A 958 LYS cc_start: 0.7943 (ttpp) cc_final: 0.7733 (ttpp) REVERT: A 967 MET cc_start: 0.7464 (mtp) cc_final: 0.6912 (mtp) REVERT: A 971 ASP cc_start: 0.7810 (m-30) cc_final: 0.7388 (m-30) REVERT: A 972 PHE cc_start: 0.7798 (t80) cc_final: 0.7538 (t80) REVERT: A 986 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 1058 THR cc_start: 0.8185 (t) cc_final: 0.7863 (p) REVERT: A 1060 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7473 (mp0) REVERT: A 1122 GLU cc_start: 0.7395 (tp30) cc_final: 0.6975 (tp30) REVERT: A 1126 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7092 (pt) REVERT: B 125 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7788 (mp0) REVERT: B 140 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7772 (mp10) REVERT: B 154 MET cc_start: 0.8513 (tpp) cc_final: 0.8185 (mtp) REVERT: B 171 LEU cc_start: 0.8297 (tp) cc_final: 0.7979 (mp) REVERT: B 236 LEU cc_start: 0.8066 (mm) cc_final: 0.7694 (mp) REVERT: B 280 TYR cc_start: 0.8313 (t80) cc_final: 0.8012 (t80) REVERT: B 347 VAL cc_start: 0.8971 (p) cc_final: 0.8698 (t) REVERT: B 517 PHE cc_start: 0.6906 (m-10) cc_final: 0.6455 (m-10) REVERT: B 579 MET cc_start: 0.6739 (mtp) cc_final: 0.6352 (mtp) REVERT: B 591 LYS cc_start: 0.8289 (mtpp) cc_final: 0.8010 (mtpp) REVERT: B 632 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7926 (mtpt) REVERT: B 633 LYS cc_start: 0.8166 (mttt) cc_final: 0.7783 (mmtm) REVERT: B 678 MET cc_start: 0.6074 (mmm) cc_final: 0.5544 (mmm) REVERT: B 810 MET cc_start: 0.7012 (mmm) cc_final: 0.6675 (mmm) REVERT: B 832 GLN cc_start: 0.8235 (tp40) cc_final: 0.7936 (tm-30) REVERT: B 841 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7837 (mmmt) REVERT: B 866 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 887 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7843 (mmm-85) REVERT: B 967 MET cc_start: 0.7864 (mmm) cc_final: 0.7539 (mmm) REVERT: B 986 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 1007 LYS cc_start: 0.8121 (tttt) cc_final: 0.7828 (tttp) REVERT: B 1051 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7811 (pttp) REVERT: B 1185 ARG cc_start: 0.6423 (mmt180) cc_final: 0.5383 (mmt180) outliers start: 60 outliers final: 46 residues processed: 415 average time/residue: 0.2872 time to fit residues: 175.0653 Evaluate side-chains 422 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 372 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 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 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR 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 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 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 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: 0.8980 chunk 68 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 636 GLN A 886 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142707 restraints weight = 23357.763| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.93 r_work: 0.3601 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16528 Z= 0.154 Angle : 0.541 11.248 22420 Z= 0.281 Chirality : 0.041 0.263 2696 Planarity : 0.004 0.058 2748 Dihedral : 9.582 173.809 2244 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.30 % Allowed : 16.67 % Favored : 80.03 % 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: 1.60 (0.13), residues: 1476 sheet: 0.48 (0.49), residues: 80 loop : -0.11 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.005 0.001 HIS B 889 PHE 0.016 0.001 PHE B 201 TYR 0.011 0.001 TYR B 309 ARG 0.014 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 1174) hydrogen bonds : angle 4.12658 ( 3456) covalent geometry : bond 0.00343 (16528) covalent geometry : angle 0.54131 (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 444 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 386 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7120 (ptp-110) REVERT: A 154 MET cc_start: 0.8595 (tpp) cc_final: 0.8370 (ttm) REVERT: A 197 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6633 (mp0) REVERT: A 199 MET cc_start: 0.8073 (mmm) cc_final: 0.7669 (mmm) REVERT: A 217 LEU cc_start: 0.8464 (mp) cc_final: 0.8242 (mm) REVERT: A 377 LEU cc_start: 0.8342 (mt) cc_final: 0.7994 (mt) REVERT: A 390 ILE cc_start: 0.7468 (mm) cc_final: 0.7224 (mt) REVERT: A 600 HIS cc_start: 0.7612 (m-70) cc_final: 0.7396 (m-70) REVERT: A 678 MET cc_start: 0.6492 (mmm) cc_final: 0.5942 (mmm) REVERT: A 684 ILE cc_start: 0.8232 (mp) cc_final: 0.7982 (pt) REVERT: A 822 ILE cc_start: 0.8467 (tp) cc_final: 0.8060 (pt) REVERT: A 841 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7789 (mmmt) REVERT: A 866 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7549 (tp30) REVERT: A 967 MET cc_start: 0.7507 (mtp) cc_final: 0.6942 (mtp) REVERT: A 971 ASP cc_start: 0.7818 (m-30) cc_final: 0.7391 (m-30) REVERT: A 972 PHE cc_start: 0.7837 (t80) cc_final: 0.7571 (t80) REVERT: A 986 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 1060 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7538 (mp0) REVERT: A 1122 GLU cc_start: 0.7435 (tp30) cc_final: 0.6980 (tp30) REVERT: A 1126 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7083 (pt) REVERT: B 125 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7922 (mp0) REVERT: B 140 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7780 (mp10) REVERT: B 171 LEU cc_start: 0.8300 (tp) cc_final: 0.7986 (mp) REVERT: B 205 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7747 (mpp) REVERT: B 236 LEU cc_start: 0.8089 (mm) cc_final: 0.7719 (mp) REVERT: B 280 TYR cc_start: 0.8319 (t80) cc_final: 0.8059 (t80) REVERT: B 347 VAL cc_start: 0.8952 (p) cc_final: 0.8692 (t) REVERT: B 579 MET cc_start: 0.6752 (mtp) cc_final: 0.6354 (mtp) REVERT: B 591 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7989 (mtpp) REVERT: B 632 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7947 (mtpt) REVERT: B 633 LYS cc_start: 0.8171 (mttt) cc_final: 0.7860 (mmtt) REVERT: B 678 MET cc_start: 0.6042 (mmm) cc_final: 0.5520 (mmm) REVERT: B 810 MET cc_start: 0.6860 (mmm) cc_final: 0.6554 (mmm) REVERT: B 832 GLN cc_start: 0.8240 (tp40) cc_final: 0.7905 (tm-30) REVERT: B 841 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7804 (mmmm) REVERT: B 866 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 887 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: B 986 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 1007 LYS cc_start: 0.8118 (tttt) cc_final: 0.7832 (tttp) REVERT: B 1110 GLN cc_start: 0.6849 (mp10) cc_final: 0.6587 (mp10) REVERT: B 1185 ARG cc_start: 0.6429 (mmt180) cc_final: 0.5628 (mmt180) outliers start: 58 outliers final: 44 residues processed: 419 average time/residue: 0.2882 time to fit residues: 176.9095 Evaluate side-chains 424 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG 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 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 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 205 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 405 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 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: 3.9990 chunk 148 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 877 GLN A 886 GLN A1114 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.171373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141743 restraints weight = 23108.134| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.95 r_work: 0.3605 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.145 Angle : 0.554 12.105 22420 Z= 0.285 Chirality : 0.041 0.274 2696 Planarity : 0.004 0.050 2748 Dihedral : 9.554 173.182 2244 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.70 % Allowed : 17.06 % Favored : 79.24 % 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: 1.77 (0.19), residues: 2020 helix: 1.66 (0.13), residues: 1476 sheet: 0.33 (0.48), residues: 80 loop : -0.10 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.006 0.001 HIS B 889 PHE 0.016 0.001 PHE A 201 TYR 0.013 0.001 TYR B 984 ARG 0.006 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1174) hydrogen bonds : angle 4.10081 ( 3456) covalent geometry : bond 0.00323 (16528) covalent geometry : angle 0.55408 (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 459 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 394 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7160 (ptp-110) REVERT: A 197 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6597 (mp0) REVERT: A 217 LEU cc_start: 0.8460 (mp) cc_final: 0.8240 (mm) REVERT: A 233 GLU cc_start: 0.8047 (tt0) cc_final: 0.7569 (tm-30) REVERT: A 300 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 346 GLU cc_start: 0.7251 (tp30) cc_final: 0.6728 (tp30) REVERT: A 377 LEU cc_start: 0.8334 (mt) cc_final: 0.7996 (mt) REVERT: A 390 ILE cc_start: 0.7465 (mm) cc_final: 0.7221 (mt) REVERT: A 600 HIS cc_start: 0.7595 (m-70) cc_final: 0.7376 (m-70) REVERT: A 678 MET cc_start: 0.6501 (mmm) cc_final: 0.5966 (mmm) REVERT: A 684 ILE cc_start: 0.8215 (mp) cc_final: 0.7962 (pt) REVERT: A 822 ILE cc_start: 0.8451 (tp) cc_final: 0.8047 (pt) REVERT: A 841 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7849 (mmtt) REVERT: A 958 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7806 (ttpp) REVERT: A 967 MET cc_start: 0.7492 (mtp) cc_final: 0.6938 (mtp) REVERT: A 971 ASP cc_start: 0.7810 (m-30) cc_final: 0.7381 (m-30) REVERT: A 972 PHE cc_start: 0.7842 (t80) cc_final: 0.7570 (t80) REVERT: A 1122 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 1126 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7072 (pt) REVERT: B 140 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7740 (mp10) REVERT: B 171 LEU cc_start: 0.8281 (tp) cc_final: 0.7988 (mp) REVERT: B 186 MET cc_start: 0.5859 (mpp) cc_final: 0.5469 (mmm) REVERT: B 236 LEU cc_start: 0.8070 (mm) cc_final: 0.7711 (mp) REVERT: B 251 MET cc_start: 0.7700 (mtm) cc_final: 0.7474 (ptp) REVERT: B 280 TYR cc_start: 0.8309 (t80) cc_final: 0.8044 (t80) REVERT: B 338 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7677 (mtmm) REVERT: B 347 VAL cc_start: 0.8939 (p) cc_final: 0.8712 (t) REVERT: B 579 MET cc_start: 0.6732 (mtp) cc_final: 0.6326 (mtp) REVERT: B 591 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7969 (mtpp) REVERT: B 605 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7195 (ttm-80) REVERT: B 632 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7923 (mtpt) REVERT: B 633 LYS cc_start: 0.8171 (mttt) cc_final: 0.7870 (mmtt) REVERT: B 678 MET cc_start: 0.5996 (mmm) cc_final: 0.5477 (mmm) REVERT: B 810 MET cc_start: 0.7054 (mmm) cc_final: 0.6697 (mmm) REVERT: B 832 GLN cc_start: 0.8228 (tp40) cc_final: 0.7902 (tm-30) REVERT: B 841 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7745 (mmmt) REVERT: B 849 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 866 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 887 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7798 (mmm-85) REVERT: B 967 MET cc_start: 0.7906 (mmm) cc_final: 0.7628 (mmm) REVERT: B 983 ASP cc_start: 0.7593 (t0) cc_final: 0.7220 (t0) REVERT: B 986 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 1007 LYS cc_start: 0.8088 (tttt) cc_final: 0.7819 (tttp) REVERT: B 1051 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7766 (pttp) REVERT: B 1185 ARG cc_start: 0.6434 (mmt180) cc_final: 0.5539 (mmt180) outliers start: 65 outliers final: 48 residues processed: 430 average time/residue: 0.2776 time to fit residues: 176.5767 Evaluate side-chains 440 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 347 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 837 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR 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 1122 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 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 838 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.172089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143000 restraints weight = 23196.916| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.90 r_work: 0.3612 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16528 Z= 0.146 Angle : 0.566 10.931 22420 Z= 0.291 Chirality : 0.042 0.281 2696 Planarity : 0.004 0.050 2748 Dihedral : 9.550 173.607 2244 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.36 % Allowed : 18.09 % Favored : 78.56 % 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: 1480 sheet: 0.15 (0.49), residues: 80 loop : -0.19 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 635 HIS 0.006 0.001 HIS B 889 PHE 0.043 0.001 PHE B 201 TYR 0.011 0.001 TYR B 191 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 1174) hydrogen bonds : angle 4.10278 ( 3456) covalent geometry : bond 0.00324 (16528) covalent geometry : angle 0.56600 (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 457 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 398 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: A 125 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 128 ARG cc_start: 0.7333 (ptp-110) cc_final: 0.7130 (ptp-110) REVERT: A 197 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6576 (mp0) REVERT: A 217 LEU cc_start: 0.8477 (mp) cc_final: 0.8260 (mm) REVERT: A 218 LYS cc_start: 0.8296 (tttt) cc_final: 0.7928 (tttt) REVERT: A 233 GLU cc_start: 0.8031 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 300 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 377 LEU cc_start: 0.8315 (mt) cc_final: 0.8002 (mt) REVERT: A 390 ILE cc_start: 0.7457 (mm) cc_final: 0.7205 (mt) REVERT: A 600 HIS cc_start: 0.7543 (m-70) cc_final: 0.7330 (m-70) REVERT: A 678 MET cc_start: 0.6727 (mmm) cc_final: 0.6151 (mmm) REVERT: A 822 ILE cc_start: 0.8475 (tp) cc_final: 0.8083 (pt) REVERT: A 841 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7880 (mmtt) REVERT: A 872 GLU cc_start: 0.7134 (tp30) cc_final: 0.6610 (tp30) REVERT: A 958 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7815 (ttpp) REVERT: A 967 MET cc_start: 0.7471 (mtp) cc_final: 0.6928 (mtp) REVERT: A 971 ASP cc_start: 0.7824 (m-30) cc_final: 0.7390 (m-30) REVERT: A 972 PHE cc_start: 0.7836 (t80) cc_final: 0.7569 (t80) REVERT: A 986 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 1122 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6932 (tp30) REVERT: A 1126 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7059 (pt) REVERT: B 125 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7351 (mp0) REVERT: B 140 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7664 (mp10) REVERT: B 171 LEU cc_start: 0.8257 (tp) cc_final: 0.8009 (mp) REVERT: B 186 MET cc_start: 0.5876 (mpp) cc_final: 0.5500 (mmm) REVERT: B 205 MET cc_start: 0.7665 (mpp) cc_final: 0.7386 (mpp) REVERT: B 236 LEU cc_start: 0.8048 (mm) cc_final: 0.7701 (mp) REVERT: B 280 TYR cc_start: 0.8295 (t80) cc_final: 0.8022 (t80) REVERT: B 579 MET cc_start: 0.6697 (mtp) cc_final: 0.6295 (mtp) REVERT: B 591 LYS cc_start: 0.8282 (mtpp) cc_final: 0.8010 (mtpp) REVERT: B 632 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7930 (mtpt) REVERT: B 633 LYS cc_start: 0.8175 (mttt) cc_final: 0.7868 (mmtt) REVERT: B 678 MET cc_start: 0.6009 (mmm) cc_final: 0.5561 (mmm) REVERT: B 810 MET cc_start: 0.6783 (mmm) cc_final: 0.6481 (mmm) REVERT: B 832 GLN cc_start: 0.8224 (tp40) cc_final: 0.7901 (tm-30) REVERT: B 841 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7751 (mmmt) REVERT: B 887 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: B 983 ASP cc_start: 0.7624 (t0) cc_final: 0.7354 (t0) REVERT: B 986 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 1007 LYS cc_start: 0.8068 (tttt) cc_final: 0.7777 (tttp) REVERT: B 1051 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7649 (pttp) REVERT: B 1078 ASP cc_start: 0.8177 (m-30) cc_final: 0.7962 (m-30) REVERT: B 1185 ARG cc_start: 0.6429 (mmt180) cc_final: 0.5603 (mmt180) outliers start: 59 outliers final: 48 residues processed: 432 average time/residue: 0.2781 time to fit residues: 177.7961 Evaluate side-chains 440 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 389 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 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 837 TYR 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 917 GLN 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 1122 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 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 838 ASP 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: 3.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 120 optimal weight: 0.0000 chunk 199 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.172069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142508 restraints weight = 23382.976| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.96 r_work: 0.3613 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3674 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= 0.137 Angle : 0.581 9.453 22420 Z= 0.296 Chirality : 0.042 0.301 2696 Planarity : 0.004 0.050 2748 Dihedral : 9.533 173.933 2244 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.79 % Allowed : 18.89 % Favored : 78.33 % 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: 1.76 (0.19), residues: 2020 helix: 1.70 (0.13), residues: 1476 sheet: -0.15 (0.48), residues: 84 loop : -0.17 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 635 HIS 0.005 0.001 HIS B 889 PHE 0.049 0.001 PHE A 201 TYR 0.020 0.001 TYR B 267 ARG 0.007 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1174) hydrogen bonds : angle 4.09330 ( 3456) covalent geometry : bond 0.00303 (16528) covalent geometry : angle 0.58058 (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 448 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 128 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.7090 (ptp-170) REVERT: A 217 LEU cc_start: 0.8451 (mp) cc_final: 0.8236 (mm) REVERT: A 218 LYS cc_start: 0.8279 (tttt) cc_final: 0.7902 (tttt) REVERT: A 233 GLU cc_start: 0.8044 (tt0) cc_final: 0.7581 (tm-30) REVERT: A 300 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 338 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7945 (mtmm) REVERT: A 377 LEU cc_start: 0.8309 (mt) cc_final: 0.7988 (mt) REVERT: A 390 ILE cc_start: 0.7434 (mm) cc_final: 0.7179 (mt) REVERT: A 600 HIS cc_start: 0.7422 (m-70) cc_final: 0.7204 (m-70) REVERT: A 678 MET cc_start: 0.6554 (mmm) cc_final: 0.6066 (mmm) REVERT: A 822 ILE cc_start: 0.8456 (tp) cc_final: 0.8041 (pt) REVERT: A 832 GLN cc_start: 0.8121 (tp40) cc_final: 0.7897 (tp40) REVERT: A 841 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7790 (mmmt) REVERT: A 967 MET cc_start: 0.7470 (mtp) cc_final: 0.7038 (mmm) REVERT: A 971 ASP cc_start: 0.7801 (m-30) cc_final: 0.7295 (m-30) REVERT: A 972 PHE cc_start: 0.7838 (t80) cc_final: 0.7569 (t80) REVERT: A 986 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 1122 GLU cc_start: 0.7390 (tp30) cc_final: 0.6942 (tp30) REVERT: A 1126 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7038 (pt) REVERT: B 125 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7461 (mp0) REVERT: B 140 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7744 (mp10) REVERT: B 171 LEU cc_start: 0.8256 (tp) cc_final: 0.8014 (mp) REVERT: B 186 MET cc_start: 0.5889 (mpp) cc_final: 0.5556 (mmm) REVERT: B 236 LEU cc_start: 0.8047 (mm) cc_final: 0.7700 (mp) REVERT: B 280 TYR cc_start: 0.8296 (t80) cc_final: 0.8033 (t80) REVERT: B 346 GLU cc_start: 0.7925 (tp30) cc_final: 0.7686 (tp30) REVERT: B 579 MET cc_start: 0.6734 (mtp) cc_final: 0.6336 (mtp) REVERT: B 591 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7967 (mtpp) REVERT: B 633 LYS cc_start: 0.8161 (mttt) cc_final: 0.7861 (mmtt) REVERT: B 643 TRP cc_start: 0.8180 (t60) cc_final: 0.7834 (t60) REVERT: B 678 MET cc_start: 0.6021 (mmm) cc_final: 0.5559 (mmm) REVERT: B 810 MET cc_start: 0.6983 (mmm) cc_final: 0.6634 (mmm) REVERT: B 832 GLN cc_start: 0.8235 (tp40) cc_final: 0.7936 (tm-30) REVERT: B 841 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7744 (mmmt) REVERT: B 957 LEU cc_start: 0.8643 (tp) cc_final: 0.8388 (tt) REVERT: B 967 MET cc_start: 0.7941 (mmm) cc_final: 0.7609 (mmm) REVERT: B 983 ASP cc_start: 0.7662 (t0) cc_final: 0.7333 (t0) REVERT: B 986 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 1007 LYS cc_start: 0.8121 (tttt) cc_final: 0.7835 (tttp) REVERT: B 1045 MET cc_start: 0.6885 (pmm) cc_final: 0.6492 (tmm) REVERT: B 1051 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7629 (pttp) REVERT: B 1078 ASP cc_start: 0.8196 (m-30) cc_final: 0.7986 (m-30) REVERT: B 1185 ARG cc_start: 0.6429 (mmt180) cc_final: 0.5607 (mmt180) outliers start: 49 outliers final: 46 residues processed: 429 average time/residue: 0.2852 time to fit residues: 179.2466 Evaluate side-chains 433 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 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 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 876 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 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 838 ASP 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: 0.0000 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 102 optimal weight: 0.0060 chunk 8 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 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 = 0.4164 r_free = 0.4164 target = 0.174038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145045 restraints weight = 23316.067| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.93 r_work: 0.3624 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16528 Z= 0.125 Angle : 0.574 10.367 22420 Z= 0.294 Chirality : 0.041 0.331 2696 Planarity : 0.004 0.049 2748 Dihedral : 9.526 174.376 2244 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.79 % Allowed : 19.28 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.13), residues: 1470 sheet: -0.02 (0.49), residues: 80 loop : -0.18 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.004 0.001 HIS B 600 PHE 0.050 0.001 PHE A 201 TYR 0.022 0.001 TYR B 267 ARG 0.007 0.000 ARG B 887 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1174) hydrogen bonds : angle 4.05142 ( 3456) covalent geometry : bond 0.00270 (16528) covalent geometry : angle 0.57369 (22420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9722.45 seconds wall clock time: 168 minutes 13.98 seconds (10093.98 seconds total)